Bump auf Abgabeversion
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img
.directory
anhang
einleitung
ergebnisse
inc
abkuerzungen.texabstract.texanhang.texdiskussion.texeinleitung.texergebnisse.texmaterial.texzusammenfassung.tex
library.bibmasterarbeit.kileprmasterarbeit.pdfmasterarbeit.texmisc
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id="tspan1578">-135</tspan></text>
|
||||
|
||||
|
||||
<path
|
||||
inkscape:connector-curvature="0"
|
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id="path1580"
|
||||
|
|
@ -3143,12 +3157,13 @@
|
|||
id="text1584"
|
||||
x="69.752296"
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y="-407"><tspan
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
|
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x="69.752296 74.747299 82.247299"
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sodipodi:role="line"
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id="tspan1586">-90</tspan></text>
|
||||
|
||||
|
||||
<path
|
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inkscape:connector-curvature="0"
|
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id="path1588"
|
||||
|
|
@ -3158,12 +3173,13 @@
|
|||
id="text1592"
|
||||
x="69.752296"
|
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y="-456.5"><tspan
|
||||
style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
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x="69.752296 74.747299 82.247299"
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y="-456.5"
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sodipodi:role="line"
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id="tspan1594">-45</tspan></text>
|
||||
|
||||
|
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<path
|
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inkscape:connector-curvature="0"
|
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id="path1596"
|
||||
|
|
@ -3173,11 +3189,12 @@
|
|||
id="text1600"
|
||||
x="79.75"
|
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y="-506"><tspan
|
||||
style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
|
||||
x="79.75"
|
||||
y="-506"
|
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id="tspan1602">0</tspan></text>
|
||||
|
||||
|
||||
<path
|
||||
inkscape:connector-curvature="0"
|
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id="path1604"
|
||||
|
|
@ -3187,12 +3204,13 @@
|
|||
id="text1608"
|
||||
x="74.125"
|
||||
y="-555.5"><tspan
|
||||
style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
|
||||
x="74.125 81.625"
|
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y="-555.5"
|
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sodipodi:role="line"
|
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id="tspan1610">45</tspan></text>
|
||||
|
||||
|
||||
<path
|
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inkscape:connector-curvature="0"
|
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id="path1612"
|
||||
|
|
@ -3202,12 +3220,13 @@
|
|||
id="text1616"
|
||||
x="74.125"
|
||||
y="-605"><tspan
|
||||
style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
|
||||
x="74.125 81.625"
|
||||
y="-605"
|
||||
sodipodi:role="line"
|
||||
id="tspan1618">90</tspan></text>
|
||||
|
||||
|
||||
<path
|
||||
inkscape:connector-curvature="0"
|
||||
id="path1620"
|
||||
|
|
@ -3217,12 +3236,13 @@
|
|||
id="text1624"
|
||||
x="68.5"
|
||||
y="-654.5"><tspan
|
||||
style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
|
||||
x="68.5 76 83.5"
|
||||
y="-654.5"
|
||||
sodipodi:role="line"
|
||||
id="tspan1626">135</tspan></text>
|
||||
|
||||
|
||||
<path
|
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inkscape:connector-curvature="0"
|
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id="path1628"
|
||||
|
|
@ -3232,12 +3252,13 @@
|
|||
id="text1632"
|
||||
x="68.5"
|
||||
y="-704"><tspan
|
||||
style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
|
||||
x="68.5 76 83.5"
|
||||
y="-704"
|
||||
sodipodi:role="line"
|
||||
id="tspan1634">180</tspan></text>
|
||||
|
||||
|
||||
<path
|
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inkscape:connector-curvature="0"
|
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id="path1636"
|
||||
|
|
@ -3255,23 +3276,25 @@
|
|||
id="text1652"
|
||||
x="260.22089"
|
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y="-277.99979"><tspan
|
||||
style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
|
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x="260.22089 268.56091 276.06091 280.2309 283.9809 288.97589 296.47589 303.13589 310.63589 315.63089 322.29089 328.9509 334.78589"
|
||||
y="-277.99979"
|
||||
sodipodi:role="line"
|
||||
id="tspan1654">Phi (degrees)</tspan></text>
|
||||
|
||||
|
||||
<text
|
||||
transform="matrix(0,1,1,0,0,0)"
|
||||
id="text1656"
|
||||
x="472.05399"
|
||||
y="55"><tspan
|
||||
style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
|
||||
x="472.05399 480.39401 486.229 490.39899 494.14899 499.14401 506.64401 513.30402 520.80402 525.79901 532.45898 539.11902 544.95398"
|
||||
y="55"
|
||||
sodipodi:role="line"
|
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id="tspan1658">Psi (degrees)</tspan></text>
|
||||
|
||||
|
||||
<path
|
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inkscape:connector-curvature="0"
|
||||
id="path1660"
|
||||
|
|
@ -3357,12 +3380,13 @@
|
|||
id="text1702"
|
||||
x="88.735199"
|
||||
y="-348.237"><tspan
|
||||
style="font-size:10px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#ff0000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
style="font-size:10px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#ff0000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
|
||||
x="88.735199 94.8452 102.0652 107.6252 110.1252 115.1252 120.1252"
|
||||
y="-348.237"
|
||||
sodipodi:role="line"
|
||||
id="tspan1704">LYS 11 </tspan></text>
|
||||
|
||||
|
||||
<path
|
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inkscape:connector-curvature="0"
|
||||
id="path1706"
|
||||
|
|
@ -5440,12 +5464,13 @@
|
|||
id="text2744"
|
||||
x="430.89499"
|
||||
y="-689.427"><tspan
|
||||
style="font-size:10px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#ff0000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
style="font-size:10px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#ff0000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
|
||||
x="430.89499 437.005 444.22501 449.785 452.285 457.285 462.285 467.285"
|
||||
y="-689.427"
|
||||
sodipodi:role="line"
|
||||
id="tspan2746">LYS 270 </tspan></text>
|
||||
|
||||
|
||||
<path
|
||||
inkscape:connector-curvature="0"
|
||||
id="path2748"
|
||||
|
|
@ -7467,12 +7492,13 @@
|
|||
id="text3758"
|
||||
x="370.57001"
|
||||
y="-483.827"><tspan
|
||||
style="font-size:10px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#ff0000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
style="font-size:10px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#ff0000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
|
||||
x="370.57001 377.79001 383.35001 390.57001 393.07001 398.07001 403.07001 408.07001"
|
||||
y="-483.827"
|
||||
sodipodi:role="line"
|
||||
id="tspan3760">ASN 522 </tspan></text>
|
||||
|
||||
|
||||
<path
|
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inkscape:connector-curvature="0"
|
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id="path3762"
|
||||
|
|
@ -7878,12 +7904,13 @@
|
|||
id="text3964"
|
||||
x="330.07001"
|
||||
y="-328.29599"><tspan
|
||||
style="font-size:10px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#ff0000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
style="font-size:10px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#ff0000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
|
||||
x="330.07001 335.63 341.73999 348.41 350.91 355.91 360.91 365.91"
|
||||
y="-328.29599"
|
||||
sodipodi:role="line"
|
||||
id="tspan3966">SER 572 </tspan></text>
|
||||
|
||||
|
||||
<path
|
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inkscape:connector-curvature="0"
|
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id="path3968"
|
||||
|
|
@ -10308,146 +10335,137 @@
|
|||
inkscape:connector-curvature="0"
|
||||
id="path5178"
|
||||
style="fill:none;stroke:#000000;stroke-width:0.2;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:10;stroke-opacity:1;stroke-dasharray:none"
|
||||
d="m 227.16,460.38 4.03984,0 0,3.95977 -4.03984,0 0,-3.95977 z" /><text
|
||||
transform="scale(1,-1)"
|
||||
id="text5182"
|
||||
x="268.159"
|
||||
y="-257"><tspan
|
||||
style="font-size:12px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="268.159 274.83099 278.16699 284.16699 287.50299 290.50299 295.17099 298.50699 303.83499 307.17099 310.50699 315.17499 318.51099 321.84698 327.17499"
|
||||
y="-257"
|
||||
sodipodi:role="line"
|
||||
id="tspan5184">Plot statistics</tspan></text>
|
||||
d="m 227.16,460.38 4.03984,0 0,3.95977 -4.03984,0 0,-3.95977 z" />
|
||||
|
||||
<text
|
||||
transform="scale(1,-1)"
|
||||
id="text5186"
|
||||
x="148"
|
||||
y="-238.75"><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.00301 157.99899 161.5 164.002 168.502 173.002 176.998 180.49899 182.74899 185.25101 189.75101 192.00101 199.00299 203.50299 207.004 209.506 211.756 214.75299 218.74899 223.24899 227.74899 232.24899 235.246 239.242 243.742 245.992 248.989 252.985 257.48499 259.987 264.487 268.987 272.48801 276.98801 279.98499 286.483 288.733 294.73599 296.98599 302.48499 305.48199"
|
||||
y="-238.75"
|
||||
x="109.59352"
|
||||
y="-253.23492"
|
||||
style="font-size:14.86953926px"><tspan
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="109.59352 117.03197 121.98351 126.32168 129.42198 134.99806 140.57414 145.5257 149.86388 152.65192 155.75223 161.32831 164.11635 172.79271 178.36879 182.70699 185.80728 188.59532 192.30898 197.26053 202.83661 208.41269 213.98877 217.70245 222.65399 228.23007 231.01811 234.73177 239.68332 245.25937 248.35966 253.93575 259.51181 263.85001 269.42609 273.13971 281.19159 283.97964 291.41812 294.20615 301.02011 304.7338"
|
||||
y="-253.23492"
|
||||
sodipodi:role="line"
|
||||
id="tspan5188">Residues in most favoured regions [A,B,L] </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="394.625 399.125 403.625 425.25156 427.50156 432.00156 436.50156 438.75156 443.25156"
|
||||
y="-238"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="415.19339 420.76947 426.34555 453.14365 455.93167 461.50775 467.08383 469.87186 475.44797"
|
||||
y="-252.30559"
|
||||
sodipodi:role="line"
|
||||
id="tspan5190">712 94.7%</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.00301 157.99899 161.5 164.002 168.502 173.002 176.998 180.49899 182.74899 185.25101 189.75101 192.00101 195.99701 200.49701 204.99701 207.49899 210.00101 212.50299 217.00299 221.50299 225.49899 228.00101 230.25101 234.24701 236.74899 239.25101 243.75101 250.24899 254.245 258.745 260.995 263.992 267.98801 272.48801 274.98999 279.48999 283.98999 287.491 291.991 294.98801 298.98401 301.23401 305.73401 307.98401 310.48599 312.73599 317.23599 320.233"
|
||||
y="-228.75"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="109.59352 117.03197 121.98351 126.32168 129.42198 134.99806 140.57414 145.5257 149.86388 152.65192 155.75223 161.32831 164.11635 169.0679 174.64398 180.22006 183.32034 186.42065 189.52094 195.09702 200.6731 205.62465 208.72496 211.513 216.46457 219.56485 222.66516 228.24124 236.29305 241.2446 246.82068 249.60872 253.32237 258.27393 263.85001 266.95029 272.52637 278.10245 282.44064 288.01672 291.73038 296.68195 299.47 305.04605 307.83411 310.93439 313.72241 319.29849 323.01218"
|
||||
y="-240.84364"
|
||||
sodipodi:role="line"
|
||||
id="tspan5192">Residues in additional allowed regions [a,b,l,p] </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="398 402.5 426.37656 430.87656 435.37656 437.62656 442.12656"
|
||||
y="-228"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="419.37546 424.95154 454.53766 460.11374 465.68982 468.47784 474.05396"
|
||||
y="-239.91431"
|
||||
sodipodi:role="line"
|
||||
id="tspan5194">36 4.8%</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.00301 157.99899 161.5 164.002 168.502 173.002 176.998 180.49899 182.74899 185.25101 189.75101 192.00101 196.50101 200.49701 204.99701 208.993 211.99001 216.48999 220.98999 224.491 226.993 231.493 233.743 237.739 240.241 242.743 247.243 253.741 257.737 262.237 264.487 267.48401 271.48001 275.98001 278.48199 282.98199 287.48199 290.983 295.483 298.47998 303.349 307.345 309.595 314.46399 318.96399 321.21399 326.08301 328.58502 330.83502 335.70398 340.20398"
|
||||
y="-218.75"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="109.59352 117.03197 121.98351 126.32168 129.42198 134.99806 140.57414 145.5257 149.86388 152.65192 155.75223 161.32831 164.11635 169.69243 174.64398 180.22006 185.1716 188.88528 194.46133 200.03741 204.37561 207.47591 213.05199 215.84003 220.7916 223.89188 226.99219 232.56825 240.62009 245.57166 251.14772 253.93575 257.64941 262.60098 268.17703 271.27731 276.85339 282.42947 286.76767 292.34375 296.0574 302.09073 307.0423 309.83032 315.86362 321.4397 324.22775 330.26108 333.36139 336.14944 342.18271 347.75879"
|
||||
y="-228.45236"
|
||||
sodipodi:role="line"
|
||||
id="tspan5196">Residues in generously allowed regions [~a,~b,~l,~p]</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="390.125 401.375 426.37656 430.87656 435.37656 437.62656 442.12656"
|
||||
y="-218"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="409.61734 423.55753 454.53766 460.11374 465.68982 468.47784 474.05396"
|
||||
y="-227.52301"
|
||||
sodipodi:role="line"
|
||||
id="tspan5198"> 4 0.5%</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.00301 157.99899 161.5 164.002 168.502 173.002 176.998 180.49899 182.74899 185.25101 189.75101 192.00101 196.50101 199.00299 202.504 206.5 209.002 211.504 216.004 222.502 226.498 230.998 233.248 236.245 240.241 244.741 247.243 251.743 256.24298 259.74402"
|
||||
y="-208.75"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="109.59352 117.03197 121.98351 126.32168 129.42198 134.99806 140.57414 145.5257 149.86388 152.65192 155.75223 161.32831 164.11635 169.69243 172.79271 177.13091 182.08246 185.18275 188.28305 193.85913 201.911 206.86255 212.43863 215.22667 218.94034 223.89188 229.46794 232.56825 238.14433 243.72037 248.05858"
|
||||
y="-216.06108"
|
||||
sodipodi:role="line"
|
||||
id="tspan5200">Residues in disallowed regions </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="401.375 426.37656 430.87656 435.37656 437.62656 442.12656"
|
||||
y="-208"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="423.55753 454.53766 460.11374 465.68982 468.47784 474.05396"
|
||||
y="-215.13173"
|
||||
sodipodi:role="line"
|
||||
id="tspan5202">0 0.0%</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148"
|
||||
y="-198.75"
|
||||
id="tspan5204"> </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="394.25598 397.25299 400.25 403.24701 429.00912 432.00613 435.00314 438.00015 440.99713 443.99414"
|
||||
y="-198"
|
||||
id="tspan5202">0 0.0% </tspan><tspan
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="414.73615 418.44983 422.16351 425.87717 457.79974 461.51343 465.22711 468.9408 472.65442 476.36813"
|
||||
y="-202.74045"
|
||||
sodipodi:role="line"
|
||||
id="tspan5206">----------</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.498 158.998 166 170.5 174.496 177.493 179.743 184.243 187.24001 189.49001 193.99001 198.49001 202.99001 205.987 210.487 212.989 217.489 221.485 223.987 228.487 232.483 234.733 238.729 243.229 247.729 249.979 254.479 258.979 263.479 266.47601 270.97601 273.97299 278.47302 280.97501 283.47699 287.97699 291.97302 294.22302 297.22 301.216 304.71698 307.21899 311.71899 316.21899 320.215 323.716"
|
||||
y="-188.75"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="109.59352 117.64532 123.22139 131.89778 137.47385 142.4254 146.13907 148.92711 154.50317 158.21686 161.0049 166.58098 172.15704 177.73312 181.44679 187.02286 190.12317 195.69923 200.6508 203.7511 209.32718 214.27873 217.06677 222.01834 227.59442 233.17046 235.95851 241.53458 247.11066 252.68672 256.40036 261.97644 265.69009 271.2662 274.36649 277.46677 283.04285 287.99445 290.78247 294.49612 299.44766 303.78583 306.88614 312.46222 318.0383 322.98987 327.32806"
|
||||
y="-191.27852"
|
||||
sodipodi:role="line"
|
||||
id="tspan5208">Number of non-glycine and non-proline residues </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="394.625 399.125 403.625 424.12656 428.62656 433.12656 437.62656 439.87656 444.37656"
|
||||
y="-188"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="415.19339 420.76947 426.34555 451.7496 457.32568 462.90176 468.47784 471.2659 476.84204"
|
||||
y="-190.34917"
|
||||
sodipodi:role="line"
|
||||
id="tspan5210">752100.0%</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.498 158.998 166 170.5 174.496 177.493 179.743 184.243 187.24001 189.49001 193.48599 197.98599 202.48599 205.483 208.48 212.476 215.97699 218.479 222.979 227.479 231.47501 234.976 237.226 240.22299 244.21899 248.71899 252.715 255.21701 257.46701 259.71701 266.215 268.71701 273.21701 275.46701 279.46301 283.96301 288.46301 290.71301 295.71698 298.71399 303.21399 306.211"
|
||||
y="-173.75"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="109.59352 117.64532 123.22139 131.89778 137.47385 142.4254 146.13907 148.92711 154.50317 158.21686 161.0049 165.95644 171.53252 177.1086 180.82227 184.53593 189.48749 193.82567 196.92598 202.50206 208.07814 213.02969 217.36787 220.15591 223.86957 228.82112 234.3972 239.34872 242.44907 245.23709 248.02513 256.07693 259.17725 264.75333 267.54138 272.49292 278.069 283.64508 286.43314 292.63367 296.34735 301.92343 305.63712"
|
||||
y="-172.69159"
|
||||
sodipodi:role="line"
|
||||
id="tspan5212">Number of end-residues (excl. Gly and Pro) </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="401.375 431.24997"
|
||||
y="-173"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="423.55753 460.57645"
|
||||
y="-171.76225"
|
||||
sodipodi:role="line"
|
||||
id="tspan5214">2 </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.498 158.998 166 170.5 174.496 177.493 179.743 184.243 187.24001 189.49001 193.99001 196.492 200.992 204.98801 207.49001 211.99001 215.98599 218.23599 221.233 225.229 228.73001 231.23199 235.73199 240.23199 244.228 247.729 249.979 252.976 256.47699 260.97699 265.47699 271.97501 276.47501 278.72501 282.72101 286.22198 288.47198 290.974 293.97101 296.47302 300.46899 304.96899 309.46899 311.97101 315.96698 319.46802 322.465"
|
||||
y="-158.75"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="109.59352 117.64532 123.22139 131.89778 137.47385 142.4254 146.13907 148.92711 154.50317 158.21686 161.0049 166.58098 169.68127 175.25735 180.20891 183.3092 188.88528 193.83682 196.62486 200.33855 205.2901 209.6283 212.72858 218.30466 223.88074 228.83226 233.17046 235.95851 239.67215 244.01035 249.58638 255.16246 263.21432 268.79041 271.57846 276.53 280.86816 283.65619 286.75653 290.47018 293.57053 298.52203 304.09811 309.67419 312.77451 317.72604 322.06427 325.77789"
|
||||
y="-154.10468"
|
||||
sodipodi:role="line"
|
||||
id="tspan5216">Number of glycine residues (shown as triangles) </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="398 402.5 431.24997"
|
||||
y="-158"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="419.37546 424.95154 460.57645"
|
||||
y="-153.17532"
|
||||
sodipodi:role="line"
|
||||
id="tspan5218">83 </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.498 158.998 166 170.5 174.496 177.493 179.743 184.243 187.24001 189.49001 193.99001 196.987 201.487 203.989 206.491 210.991 214.987 217.237 220.23401 224.23001 227.731 230.233 234.733 239.233 243.229 246.73001"
|
||||
y="-148.75"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="109.59352 117.64532 123.22139 131.89778 137.47385 142.4254 146.13907 148.92711 154.50317 158.21686 161.0049 166.58098 170.29463 175.87071 178.97101 182.0713 187.64738 192.59894 195.38698 199.10066 204.05222 208.3904 211.49069 217.06677 222.64285 227.59442 231.9326"
|
||||
y="-141.71338"
|
||||
sodipodi:role="line"
|
||||
id="tspan5220">Number of proline residues </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="398 402.5 431.24997"
|
||||
y="-148"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="419.37546 424.95154 460.57645"
|
||||
y="-140.78403"
|
||||
sodipodi:role="line"
|
||||
id="tspan5222">39 </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="394.25598 397.25299 400.25 403.24701 431.24979"
|
||||
y="-138"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="414.73615 418.44983 422.16351 425.87717 460.5762"
|
||||
y="-128.39268"
|
||||
sodipodi:role="line"
|
||||
id="tspan5224">---- </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 153.49899 157.99899 160.50101 164.49699 166.99899 169.24899 173.74899 178.24899 185.25101 189.75101 193.74701 196.744 198.994 203.494 206.491 208.741 211.73801 215.73401 219.235 221.737 226.237 230.737 234.733 238.23401"
|
||||
y="-128.75"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="109.59352 116.40742 121.98351 125.08383 130.03535 133.13565 135.92369 141.49976 147.07584 155.75223 161.32831 166.27988 169.99353 172.78157 178.35765 182.0713 184.85934 188.57303 193.52458 197.86276 200.96306 206.53914 212.11522 217.06677 221.40497"
|
||||
y="-116.93076"
|
||||
sodipodi:role="line"
|
||||
id="tspan5226">Total number of residues </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="394.625 399.125 403.625 431.24997"
|
||||
y="-128"
|
||||
style="font-size:11.15215397px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="415.19339 420.76947 426.34555 460.57645"
|
||||
y="-116.00143"
|
||||
sodipodi:role="line"
|
||||
id="tspan5228">876 </tspan></text>
|
||||
|
||||
|
||||
<text
|
||||
transform="scale(1,-1)"
|
||||
id="text5230"
|
||||
x="176.24001"
|
||||
y="-98.333199"><tspan
|
||||
style="font-size:8px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="176.24001 181.576 185.12801 188.24001 191.79201 195.79201 197.79201 201.79201 205.79201 207.79201 211.34399 215.34399 217.34399 220.896 224.896 228.448 230.672 234.672 237.784 240.008 243.12 245.12 249.12 251.784 253.784 257.784 261.784 265.784 267.784 270.896 273.12 275.784 279.784 283.336 285.56 289.56 292.224 295.776 298.888 300.888 304.888 307.552 309.552 312.216 315.76801 318.88 322.88 325.104 329.104 331.328 333.552 337.552 341.552 343.552 347.552 350.216 352.216 355.76801 357.992 359.992 362.216 365.76801 369.32001 372.43201 374.65601 376.65601 380.65601 382.65601 386.65601 388.65601 394.43201 398.43201 402.43201 405.54401 407.76801 410.43201 414.43201 420.65601"
|
||||
y="-98.333199"
|
||||
x="144.58644"
|
||||
y="-79.24044"
|
||||
style="font-size:14.86953926px"><tspan
|
||||
style="font-size:9.91302586px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="144.58644 151.19844 155.59982 159.45599 163.85738 168.81389 171.29214 176.24866 181.20517 183.68343 188.08479 193.04131 195.51956 199.92094 204.87746 209.27884 212.03467 216.99118 220.84735 223.60318 227.45932 229.93758 234.89409 238.19511 240.67337 245.62988 250.58638 255.54289 258.02112 261.87729 264.63312 267.93417 272.89069 277.29205 280.04788 285.00439 288.30542 292.70682 296.56299 299.04123 303.99774 307.2988 309.77704 313.07809 317.47946 321.33563 326.29214 329.04797 334.00449 336.76031 339.51611 344.47263 349.42914 351.90741 356.86392 360.16495 362.64322 367.04462 369.80042 372.27869 375.03452 379.43588 383.83728 387.69345 390.44925 392.92752 397.88403 400.36227 405.31879 407.79706 414.95425 419.91077 424.86728 428.72345 431.47928 434.7803 439.73682 447.44916"
|
||||
y="-79.24044"
|
||||
sodipodi:role="line"
|
||||
id="tspan5232">Based on an analysis of 118 structures of resolution of at least 2.0 Angstroms</tspan><tspan
|
||||
style="font-size:8px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="178.69469 182.24669 186.24669 190.24669 192.24669 197.58269 200.24669 202.91069 206.46269 210.01469 212.23869 216.23869 218.90269 220.90269 224.90269 228.90269 230.90269 234.90269 237.5667 241.1187 244.67068 246.8947 250.44669 253.11069 255.11069 257.33469 261.33469 264.88669 268.88669 270.88669 274.88669 278.88669 285.55069 287.55069 289.55069 293.10269 295.10269 299.10269 303.10269 307.10269 311.10269 313.10269 317.10269 321.10269 324.65469 326.87869 329.10269 331.32669 335.32669 337.32669 343.55069 347.55069 351.55069 355.10269 357.32669 359.32669 365.10269 369.10269 373.10269 375.32669 379.32669 381.32669 385.32669 388.87869 390.87869 394.43069 398.43069 402.43069 405.9827 409.5347 411.7587 415.3107 419.3107"
|
||||
y="-88.333199"
|
||||
style="font-size:9.91302586px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
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x="440.25 447.75 455.25"
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y="-297"
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sodipodi:role="line"
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id="tspan1562">135</tspan></text>
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<path
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id="text1568"
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x="490.75"
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y="-297"><tspan
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x="490.75 498.25 505.75"
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id="tspan1570">180</tspan></text>
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x="64.127296"
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y="-357.5"><tspan
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sodipodi:role="line"
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<path
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id="text1584"
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x="69.752296"
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y="-407"><tspan
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x="69.752296 74.747299 82.247299"
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sodipodi:role="line"
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id="text1592"
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x="69.752296"
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y="-456.5"><tspan
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x="69.752296 74.747299 82.247299"
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<path
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id="path1596"
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id="text1600"
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x="79.75"
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y="-506"><tspan
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
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x="79.75"
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y="-506"
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id="tspan1602">0</tspan></text>
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<path
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inkscape:connector-curvature="0"
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id="path1604"
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|
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@ -3204,13 +3221,14 @@
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id="text1608"
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x="74.125"
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y="-555.5"><tspan
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
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x="74.125 81.625"
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y="-555.5"
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sodipodi:role="line"
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id="tspan1610">45</tspan></text>
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<path
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inkscape:connector-curvature="0"
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id="path1612"
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|
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@ -3220,13 +3238,14 @@
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id="text1616"
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x="74.125"
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y="-605"><tspan
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
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x="74.125 81.625"
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y="-605"
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sodipodi:role="line"
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id="tspan1618">90</tspan></text>
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|
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<path
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inkscape:connector-curvature="0"
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id="path1620"
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|
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@ -3236,13 +3255,14 @@
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id="text1624"
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x="68.5"
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y="-654.5"><tspan
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
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x="68.5 76 83.5"
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y="-654.5"
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sodipodi:role="line"
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id="tspan1626">135</tspan></text>
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<path
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inkscape:connector-curvature="0"
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id="path1628"
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|
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@ -3252,13 +3272,14 @@
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id="text1632"
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x="68.5"
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y="-704"><tspan
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
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x="68.5 76 83.5"
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y="-704"
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sodipodi:role="line"
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id="tspan1634">180</tspan></text>
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|
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|
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|
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<path
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inkscape:connector-curvature="0"
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id="path1636"
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|
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@ -3278,25 +3299,27 @@
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id="text1652"
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x="260.22092"
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y="-277.99979"><tspan
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
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x="260.22092 268.56091 276.06091 280.23093 283.98093 288.97592 296.47592 303.13593 310.63593 315.63092 322.29092 328.95093 334.78592"
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y="-277.99979"
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sodipodi:role="line"
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id="tspan1654">Phi (degrees)</tspan></text>
|
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|
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|
||||
|
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<text
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transform="matrix(0,1,1,0,0,0)"
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id="text1656"
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x="472.05399"
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y="55"><tspan
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
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style="font-size:15px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
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x="472.05399 480.39401 486.229 490.39899 494.14899 499.14401 506.64401 513.30402 520.80402 525.79901 532.45898 539.11902 544.95398"
|
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y="55"
|
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sodipodi:role="line"
|
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id="tspan1658">Psi (degrees)</tspan></text>
|
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|
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|
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|
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<path
|
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inkscape:connector-curvature="0"
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id="path1660"
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|
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@ -4662,13 +4685,14 @@
|
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id="text2342"
|
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x="480.5"
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y="-476.987"><tspan
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style="font-size:10px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#ff0000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
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style="font-size:10px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#ff0000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
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x="480.5 486.60999 493.82999 500.5 503 508 513 518"
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y="-476.987"
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sodipodi:role="line"
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id="tspan2344">THR 171 </tspan></text>
|
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|
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|
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<path
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inkscape:connector-curvature="0"
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id="path2346"
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|
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@ -5522,13 +5546,14 @@
|
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id="text2772"
|
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x="84.4953"
|
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y="-329.996"><tspan
|
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style="font-size:10px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#ff0000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
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style="font-size:10px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#ff0000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Times-Roman"
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x="84.4953 91.715302 97.825302 105.0453 107.5453 112.5453 117.5453 122.5453"
|
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y="-329.996"
|
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sodipodi:role="line"
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id="tspan2774">ALA 277 </tspan></text>
|
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|
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|
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|
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<path
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inkscape:connector-curvature="0"
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id="path2776"
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|
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@ -10297,149 +10322,140 @@
|
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inkscape:connector-curvature="0"
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id="path5158"
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style="fill:none;stroke:#000000;stroke-width:0.2;stroke-linecap:round;stroke-linejoin:round;stroke-miterlimit:10;stroke-opacity:1;stroke-dasharray:none"
|
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d="m 219.62,466.37 4.04023,0 0,3.96016 -4.04023,0 0,-3.96016 z" /><text
|
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transform="scale(1,-1)"
|
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id="text5162"
|
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x="268.159"
|
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y="-257"><tspan
|
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style="font-size:12px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
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x="268.159 274.83099 278.16699 284.16699 287.50299 290.50299 295.17099 298.50699 303.83499 307.17099 310.50699 315.17499 318.51099 321.84698 327.17499"
|
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y="-257"
|
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sodipodi:role="line"
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id="tspan5164">Plot statistics</tspan></text>
|
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d="m 219.62,466.37 4.04023,0 0,3.96016 -4.04023,0 0,-3.96016 z" />
|
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|
||||
|
||||
<text
|
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transform="scale(1,-1)"
|
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id="text5166"
|
||||
x="148"
|
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y="-238.75"><tspan
|
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style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
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x="148 154.00301 157.99899 161.5 164.002 168.502 173.002 176.998 180.49899 182.74899 185.25101 189.75101 192.00101 199.00299 203.50299 207.004 209.506 211.756 214.75299 218.74899 223.24899 227.74899 232.24899 235.246 239.242 243.742 245.992 248.989 252.985 257.48499 259.987 264.487 268.987 272.48801 276.98801 279.98499 286.483 288.733 294.73599 296.98599 302.48499 305.48199"
|
||||
y="-238.75"
|
||||
x="110.58215"
|
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y="-255.66"
|
||||
style="font-size:15.02438831px"><tspan
|
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style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
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x="110.58215 118.09808 123.10117 127.48455 130.61714 136.25131 141.88547 146.8886 151.27194 154.08902 157.22162 162.85577 165.67284 174.43956 180.07372 184.45708 187.58966 190.40674 194.15907 199.1622 204.79633 210.43048 216.06464 219.81697 224.8201 230.45424 233.27132 237.02364 242.02676 247.66087 250.79347 256.42758 262.06174 266.4451 272.07925 275.83157 283.96729 286.78436 294.30029 297.11737 304.00229 307.75467"
|
||||
y="-255.66"
|
||||
sodipodi:role="line"
|
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id="tspan5168">Residues in most favoured regions [A,B,L] </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="394.625 399.125 403.625 425.25156 427.50156 432.00156 436.50156 438.75156 443.25156"
|
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y="-238"
|
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style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="419.36459 424.99872 430.63287 457.71002 460.5271 466.16125 471.79541 474.61249 480.24661"
|
||||
y="-254.72098"
|
||||
sodipodi:role="line"
|
||||
id="tspan5170">709 94.5%</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.00301 157.99899 161.5 164.002 168.502 173.002 176.998 180.49899 182.74899 185.25101 189.75101 192.00101 195.99701 200.49701 204.99701 207.49899 210.00101 212.50299 217.00299 221.50299 225.49899 228.00101 230.25101 234.24701 236.74899 239.25101 243.75101 250.24899 254.245 258.745 260.995 263.992 267.98801 272.48801 274.98999 279.48999 283.98999 287.491 291.991 294.98801 298.98401 301.23401 305.73401 307.98401 310.48599 312.73599 317.23599 320.233"
|
||||
y="-228.75"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="110.58215 118.09808 123.10117 127.48455 130.61714 136.25131 141.88547 146.8886 151.27194 154.08902 157.22162 162.85577 165.67284 170.67598 176.3101 181.94426 185.07683 188.20943 191.342 196.97614 202.61029 207.6134 210.746 213.56308 218.56621 221.69878 224.83136 230.46552 238.60121 243.60431 249.23845 252.0555 255.80785 260.81097 266.4451 269.57767 275.21182 280.84598 285.22934 290.86349 294.61584 299.61899 302.43607 308.07019 310.88727 314.01984 316.83691 322.47104 326.22339"
|
||||
y="-243.13971"
|
||||
sodipodi:role="line"
|
||||
id="tspan5172">Residues in additional allowed regions [a,b,l,p] </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="398 402.5 426.37656 430.87656 435.37656 437.62656 442.12656"
|
||||
y="-228"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="423.59021 429.22437 459.11856 464.75272 470.38687 473.20392 478.83807"
|
||||
y="-242.20068"
|
||||
sodipodi:role="line"
|
||||
id="tspan5174">39 5.2%</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.00301 157.99899 161.5 164.002 168.502 173.002 176.998 180.49899 182.74899 185.25101 189.75101 192.00101 196.50101 200.49701 204.99701 208.993 211.99001 216.48999 220.98999 224.491 226.993 231.493 233.743 237.739 240.241 242.743 247.243 253.741 257.737 262.237 264.487 267.48401 271.48001 275.98001 278.48199 282.98199 287.48199 290.983 295.483 298.47998 303.349 307.345 309.595 314.46399 318.96399 321.21399 326.08301 328.58502 330.83502 335.70398 340.20398"
|
||||
y="-218.75"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="110.58215 118.09808 123.10117 127.48455 130.61714 136.25131 141.88547 146.8886 151.27194 154.08902 157.22162 162.85577 165.67284 171.30699 176.3101 181.94426 186.94737 190.69972 196.33383 201.96799 206.35136 209.48395 215.1181 217.93517 222.93829 226.07089 229.20348 234.8376 242.9733 247.97641 253.61053 256.42758 260.17993 265.18304 270.8172 273.9498 279.58392 285.21805 289.60144 295.2356 298.98788 305.08408 310.08719 312.90427 319.00043 324.63455 327.4516 333.54779 336.68039 339.49747 345.59357 351.22772"
|
||||
y="-230.61937"
|
||||
sodipodi:role="line"
|
||||
id="tspan5176">Residues in generously allowed regions [~a,~b,~l,~p]</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="390.125 401.375 426.37656 430.87656 435.37656 437.62656 442.12656"
|
||||
y="-218"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="413.73044 427.8158 459.11856 464.75272 470.38687 473.20392 478.83807"
|
||||
y="-229.68034"
|
||||
sodipodi:role="line"
|
||||
id="tspan5178"> 2 0.3%</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.00301 157.99899 161.5 164.002 168.502 173.002 176.998 180.49899 182.74899 185.25101 189.75101 192.00101 196.50101 199.00299 202.504 206.5 209.002 211.504 216.004 222.502 226.498 230.998 233.248 236.245 240.241 244.741 247.243 251.743 256.24298 259.74402"
|
||||
y="-208.75"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="110.58215 118.09808 123.10117 127.48455 130.61714 136.25131 141.88547 146.8886 151.27194 154.08902 157.22162 162.85577 165.67284 171.30699 174.43956 178.82292 183.82607 186.95865 190.09123 195.72537 203.86107 208.86421 214.49835 217.31541 221.06776 226.07089 231.70502 234.8376 240.47173 246.10587 250.48926"
|
||||
y="-218.09904"
|
||||
sodipodi:role="line"
|
||||
id="tspan5180">Residues in disallowed regions </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="401.375 426.37656 430.87656 435.37656 437.62656 442.12656"
|
||||
y="-208"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="427.8158 459.11856 464.75272 470.38687 473.20392 478.83807"
|
||||
y="-217.16002"
|
||||
sodipodi:role="line"
|
||||
id="tspan5182">0 0.0%</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148"
|
||||
y="-198.75"
|
||||
id="tspan5184"> </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="394.25598 397.25299 400.25 403.24701 429.00912 432.00613 435.00314 438.00015 440.99713 443.99414"
|
||||
y="-198"
|
||||
id="tspan5182">0 0.0% </tspan><tspan
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="418.90256 422.65491 426.40729 430.15961 462.41464 466.16696 469.91934 473.67166 477.42401 481.17636"
|
||||
y="-204.63969"
|
||||
sodipodi:role="line"
|
||||
id="tspan5186">----------</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.498 158.998 166 170.5 174.496 177.493 179.743 184.243 187.24001 189.49001 193.99001 198.49001 202.99001 205.987 210.487 212.989 217.489 221.485 223.987 228.487 232.483 234.733 238.729 243.229 247.729 249.979 254.479 258.979 263.479 266.47601 270.97601 273.97299 278.47302 280.97501 283.47699 287.97699 291.97302 294.22302 297.22 301.216 304.71698 307.21899 311.71899 316.21899 320.215 323.716"
|
||||
y="-188.75"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="110.58215 118.71782 124.35197 133.11873 138.75288 143.75601 147.50835 150.32542 155.95956 159.71191 162.52899 168.16315 173.79727 179.43143 183.18376 188.8179 191.95049 197.58464 202.58775 205.72035 211.35449 216.35762 219.1747 224.17781 229.81195 235.44611 238.26317 243.89729 249.53145 255.16557 258.91788 264.55203 268.30438 273.93857 277.07111 280.20367 285.8378 290.84097 293.65805 297.41037 302.41348 306.79684 309.92944 315.5636 321.19772 326.20084 330.58423"
|
||||
y="-193.05841"
|
||||
sodipodi:role="line"
|
||||
id="tspan5188">Number of non-glycine and non-proline residues </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="394.625 399.125 403.625 424.12656 428.62656 433.12656 437.62656 439.87656 444.37656"
|
||||
y="-188"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="419.36459 424.99872 430.63287 456.30148 461.93564 467.56979 473.20392 476.021 481.65515"
|
||||
y="-192.11938"
|
||||
sodipodi:role="line"
|
||||
id="tspan5190">750100.0%</tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.498 158.998 166 170.5 174.496 177.493 179.743 184.243 187.24001 189.49001 193.48599 197.98599 202.48599 205.483 208.48 212.476 215.97699 218.479 222.979 227.479 231.47501 234.976 237.226 240.22299 244.21899 248.71899 252.715 255.21701 257.46701 259.71701 266.215 268.71701 273.21701 275.46701 279.46301 283.96301 288.46301 290.71301 295.71698 298.71399 303.21399 306.211"
|
||||
y="-173.75"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="110.58215 118.71782 124.35197 133.11873 138.75288 143.75601 147.50835 150.32542 155.95956 159.71191 162.52899 167.53209 173.16624 178.80038 182.55273 186.30507 191.3082 195.69156 198.82416 204.4583 210.09245 215.09557 219.47893 222.29601 226.04832 231.05145 236.68561 241.68872 244.82129 247.63837 250.45541 258.59109 261.72369 267.35785 270.17493 275.17807 280.81219 286.44632 289.2634 295.52853 299.28091 304.91504 308.66739"
|
||||
y="-174.27791"
|
||||
sodipodi:role="line"
|
||||
id="tspan5192">Number of end-residues (excl. Gly and Pro) </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="401.375 431.24997"
|
||||
y="-173"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="427.8158 465.22021"
|
||||
y="-173.33888"
|
||||
sodipodi:role="line"
|
||||
id="tspan5194">5 </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.498 158.998 166 170.5 174.496 177.493 179.743 184.243 187.24001 189.49001 193.99001 196.492 200.992 204.98801 207.49001 211.99001 215.98599 218.23599 221.233 225.229 228.73001 231.23199 235.73199 240.23199 244.228 247.729 249.979 252.976 256.47699 260.97699 265.47699 271.97501 276.47501 278.72501 282.72101 286.22198 288.47198 290.974 293.97101 296.47302 300.46899 304.96899 309.46899 311.97101 315.96698 319.46802 322.465"
|
||||
y="-158.75"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="110.58215 118.71782 124.35197 133.11873 138.75288 143.75601 147.50835 150.32542 155.95956 159.71191 162.52899 168.16315 171.29573 176.92986 181.93298 185.06557 190.69972 195.70282 198.5199 202.27225 207.27538 211.65874 214.79131 220.42546 226.05959 231.06273 235.44611 238.26317 242.0155 246.39883 252.03296 257.66708 265.8028 271.43695 274.25403 279.25717 283.64047 286.45755 289.59018 293.34253 296.47513 301.47821 307.11237 312.74652 315.87912 320.8822 325.26562 329.01791"
|
||||
y="-155.49744"
|
||||
sodipodi:role="line"
|
||||
id="tspan5196">Number of glycine residues (shown as triangles) </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="398 402.5 431.24997"
|
||||
y="-158"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="423.59021 429.22437 465.22021"
|
||||
y="-154.55841"
|
||||
sodipodi:role="line"
|
||||
id="tspan5198">83 </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 154.498 158.998 166 170.5 174.496 177.493 179.743 184.243 187.24001 189.49001 193.99001 196.987 201.487 203.989 206.491 210.991 214.987 217.237 220.23401 224.23001 227.731 230.233 234.733 239.233 243.229 246.73001"
|
||||
y="-148.75"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="110.58215 118.71782 124.35197 133.11873 138.75288 143.75601 147.50835 150.32542 155.95956 159.71191 162.52899 168.16315 171.91548 177.54962 180.68221 183.81479 189.44893 194.45206 197.26913 201.02148 206.02461 210.40796 213.54054 219.1747 224.80882 229.81195 234.19534"
|
||||
y="-142.97711"
|
||||
sodipodi:role="line"
|
||||
id="tspan5200">Number of proline residues </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="398 402.5 431.24997"
|
||||
y="-148"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="423.59021 429.22437 465.22021"
|
||||
y="-142.03809"
|
||||
sodipodi:role="line"
|
||||
id="tspan5202">39 </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="394.25598 397.25299 400.25 403.24701 431.24979"
|
||||
y="-138"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="418.90256 422.65491 426.40729 430.15961 465.22"
|
||||
y="-129.51776"
|
||||
sodipodi:role="line"
|
||||
id="tspan5204">---- </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="148 153.49899 157.99899 160.50101 164.49699 166.99899 169.24899 173.74899 178.24899 185.25101 189.75101 193.74701 196.744 198.994 203.494 206.491 208.741 211.73801 215.73401 219.235 221.737 226.237 230.737 234.733 238.23401"
|
||||
y="-128.75"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="110.58215 117.46705 123.10117 126.23379 131.23691 134.36949 137.18658 142.82074 148.45486 157.22162 162.85577 167.8589 171.61124 174.42831 180.06245 183.81479 186.63185 190.38422 195.38733 199.77069 202.90327 208.53741 214.17155 219.1747 223.55806"
|
||||
y="-117.93651"
|
||||
sodipodi:role="line"
|
||||
id="tspan5206">Total number of residues </tspan><tspan
|
||||
style="font-size:9px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="394.625 399.125 403.625 431.24997"
|
||||
y="-128"
|
||||
style="font-size:11.26829147px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="419.36459 424.99872 430.63287 465.22021"
|
||||
y="-116.99747"
|
||||
sodipodi:role="line"
|
||||
id="tspan5208">877 </tspan></text>
|
||||
|
||||
|
||||
|
||||
<text
|
||||
transform="scale(1,-1)"
|
||||
id="text5210"
|
||||
x="176.24001"
|
||||
y="-98.333199"><tspan
|
||||
style="font-size:8px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="176.24001 181.576 185.12801 188.24001 191.79201 195.79201 197.79201 201.79201 205.79201 207.79201 211.34399 215.34399 217.34399 220.896 224.896 228.448 230.672 234.672 237.784 240.008 243.12 245.12 249.12 251.784 253.784 257.784 261.784 265.784 267.784 270.896 273.12 275.784 279.784 283.336 285.56 289.56 292.224 295.776 298.888 300.888 304.888 307.552 309.552 312.216 315.76801 318.88 322.88 325.104 329.104 331.328 333.552 337.552 341.552 343.552 347.552 350.216 352.216 355.76801 357.992 359.992 362.216 365.76801 369.32001 372.43201 374.65601 376.65601 380.65601 382.65601 386.65601 388.65601 394.43201 398.43201 402.43201 405.54401 407.76801 410.43201 414.43201 420.65601"
|
||||
y="-98.333199"
|
||||
x="145.93956"
|
||||
y="-79.853737"
|
||||
style="font-size:15.02438831px"><tspan
|
||||
style="font-size:10.01625919px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
x="145.93956 152.62041 157.06763 160.96394 165.41116 170.4193 172.92337 177.9315 182.93962 185.4437 189.89088 194.89902 197.40309 201.85031 206.85844 211.30566 214.09018 219.09831 222.99463 225.77916 229.67546 232.17955 237.18765 240.52306 243.02715 248.03523 253.04337 258.05145 260.55554 264.45187 267.23639 270.57181 275.57996 280.02713 282.81168 287.81979 291.15521 295.60242 299.49875 302.00281 307.01096 310.34637 312.85043 316.18588 320.63306 324.52939 329.53754 332.32205 337.3302 340.11472 342.89923 347.90732 352.91547 355.41953 360.42767 363.76309 366.26715 370.71436 373.49887 376.00296 378.78748 383.23471 387.68195 391.57822 394.36276 396.86682 401.87494 404.37903 409.38715 411.89124 419.12296 424.13107 429.13922 433.03555 435.82007 439.15549 444.16357 451.95624"
|
||||
y="-79.853737"
|
||||
sodipodi:role="line"
|
||||
id="tspan5212">Based on an analysis of 118 structures of resolution of at least 2.0 Angstroms</tspan><tspan
|
||||
style="font-size:8px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Times New Roman;-inkscape-font-specification:Times-Roman"
|
||||
x="178.69469 182.24669 186.24669 190.24669 192.24669 197.58269 200.24669 202.91069 206.46269 210.01469 212.23869 216.23869 218.90269 220.90269 224.90269 228.90269 230.90269 234.90269 237.5667 241.1187 244.67068 246.8947 250.44669 253.11069 255.11069 257.33469 261.33469 264.88669 268.88669 270.88669 274.88669 278.88669 285.55069 287.55069 289.55069 293.10269 295.10269 299.10269 303.10269 307.10269 311.10269 313.10269 317.10269 321.10269 324.65469 326.87869 329.10269 331.32669 335.32669 337.32669 343.55069 347.55069 351.55069 355.10269 357.32669 359.32669 365.10269 369.10269 373.10269 375.32669 379.32669 381.32669 385.32669 388.87869 390.87869 394.43069 398.43069 402.43069 405.9827 409.5347 411.7587 415.3107 419.3107"
|
||||
y="-88.333199"
|
||||
style="font-size:10.01625919px;font-variant:normal;font-weight:normal;writing-mode:lr-tb;fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Linux Libertine O;-inkscape-font-specification:Linux Libertine O"
|
||||
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y="-54.813095"
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sodipodi:role="line"
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id="tspan5216">to have over 90% in the most favoured regions.</tspan></text>
|
||||
|
||||
|
||||
|
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|
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|
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id="tspan38">PPDK</tspan></text>
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id="tspan42">2 PPi2 Pi</tspan><tspan
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id="tspan44">2 Pyr</tspan><tspan
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y="-249.667"
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sodipodi:role="line"
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id="tspan46">2 ATP2 AMP</tspan><tspan
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id="text50"><tspan
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x="0 11.4483354"
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<text
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id="text54"><tspan
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y="0"
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id="tspan56">4 ADP</tspan><tspan
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sodipodi:role="line"
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sodipodi:role="line"
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id="tspan62">Konven</tspan></text>
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x="0"
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y="0"
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width="1"
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height="1"
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id="text74"><tspan
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style="fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Calibri;font-variant:normal;font-weight:bold;font-size:16.9479;writing-mode:lr;-inkscape-font-specification:Calibri-Bold"
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x="0 9.1179702 18.2189925 26.7437862 30.9129696 35.082153 43.6069467 47.4880158 58.2838281 62.4530115 70.4863161 78.18047627 87.29844647 91.46762987 99.41616904 106.17838114"
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y="0"
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sodipodi:role="line"
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id="tspan76">onelle Glykolyse</tspan></text>
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<text
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transform="matrix(1,0,0,-1,11.6875,96.0314)"
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id="text78"><tspan
|
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style="fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Calibri;font-variant:normal;font-weight:normal;font-size:16.9479;writing-mode:lr;-inkscape-font-specification:Calibri"
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x="0 5.1860574 9.0162828 17.6088681 21.4390935 29.92994056 38.18356786 46.94563216 50.77585756 59.67350506 68.11355926 74.02837636 77.85860176 85.84106266 89.72213176 98.61977926 105.67028429 114.60182759 121.22845649 129.66851069 133.49873609 141.93879029 150.66677236 156.34431886 162.36073489"
|
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y="0"
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sodipodi:role="line"
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id="tspan80">- 2 ATP per glucose entry</tspan><tspan
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style="fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Calibri;font-variant:normal;font-weight:normal;font-size:16.9479;writing-mode:lr;-inkscape-font-specification:Calibri"
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x="-4.24648 4.1935742 8.0237996 16.6163849 20.4466103 28.92039421 37.17402151 45.93608581 49.76631121 53.81685931 62.25691351 66.08713891 74.73070671 83.49277101 94.18689591 103.99973001"
|
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y="20.0691"
|
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sodipodi:role="line"
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id="tspan82">+ 2 ATP je 3PGAK</tspan><tspan
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x="-4.24648 4.1935742 8.0237996 16.6163849 20.4466103 28.92039421 37.17402151 45.93608581 49.76631121 53.81685931 62.25691351 66.08713891 74.89991116 83.66197546 94.08493396"
|
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y="40.5199"
|
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sodipodi:role="line"
|
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id="tspan84">+ 2 ATP je PPDK</tspan></text>
|
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</g><path
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|
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style="fill:none;stroke:#000000;stroke-opacity:1;stroke-width:6.63107;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none"
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id="path86" /><g
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id="g88"
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transform="scale(10,10)"><text
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transform="matrix(1,0,0,-1,7.45039,19.9852)"
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id="text90"><tspan
|
||||
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|
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x="0 8.4400542 12.2702796 20.8628649 24.6930903 33.16687421 41.42050151"
|
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y="0"
|
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sodipodi:role="line"
|
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id="tspan92">= 2 ATP</tspan></text>
|
||||
<text
|
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transform="matrix(1,0,0,-1,244.42039,125.5092)"
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id="text94"><tspan
|
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x="0 10.7958123 14.9649957 22.9983003 30.69247234 39.81044254 43.97962594 51.92816511 58.69037721 67.21517091 71.04539631 84.82403901 88.99322241 94.92498741 98.75521281 107.77149561 116.83865719 127.51583419 136.78633549 140.61656089 152.56483039 156.39505579 165.46231499 173.24140109"
|
||||
y="0"
|
||||
sodipodi:role="line"
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id="tspan96">Glykolyse mit PPDK & PFK</tspan></text>
|
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<text
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transform="matrix(1,0,0,-1,257.27469,96.976)"
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id="text98"><tspan
|
||||
style="fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Calibri;font-variant:normal;font-weight:normal;font-size:16.9479;writing-mode:lr;-inkscape-font-specification:Calibri"
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x="0 5.1860574 9.0162828 17.6088681 21.4390935 29.92993378 38.18356108 46.94562538 50.77585078 54.82639888 63.26645308 67.09667848 77.79080338 81.72289769 90.62054519 97.77241663 106.70395993 113.33058883"
|
||||
y="0"
|
||||
sodipodi:role="line"
|
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id="tspan100">- 1 ATP je Glukose</tspan><tspan
|
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|
||||
y="20.0695"
|
||||
sodipodi:role="line"
|
||||
id="tspan102">+ 2 ATP je 3PGAK</tspan><tspan
|
||||
style="fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Calibri;font-variant:normal;font-weight:normal;font-size:16.9479;writing-mode:lr;-inkscape-font-specification:Calibri"
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|
||||
y="40.5203"
|
||||
sodipodi:role="line"
|
||||
id="tspan104">+ 2 ATP je AK</tspan></text>
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</g><path
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d="m 2458.48,216.5 1912.14,0"
|
||||
style="fill:none;stroke:#000000;stroke-opacity:1;stroke-width:6.63107;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none"
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id="path106" /><g
|
||||
id="g108"
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||||
transform="scale(10,10)"><text
|
||||
transform="matrix(1,0,0,-1,253.037,1.15742)"
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id="text110"><tspan
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style="fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Calibri;font-variant:normal;font-weight:normal;font-size:16.9479;writing-mode:lr;-inkscape-font-specification:Calibri"
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y="0"
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sodipodi:role="line"
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id="tspan112">= 5 ATP</tspan><tspan
|
||||
style="fill:#000000;fill-opacity:1;fill-rule:nonzero;stroke:none;font-family:Calibri;font-variant:normal;font-weight:normal;font-size:16.9479;writing-mode:lr;-inkscape-font-specification:Calibri"
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|
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y="-35.5367"
|
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sodipodi:role="line"
|
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id="tspan114">+ 2 ATP je PPDK</tspan></text>
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|
||||
|
Before 
(image error) Size: 16 KiB |
|
|
@ -1,338 +0,0 @@
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xmlns:xlink="http://www.w3.org/1999/xlink"
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|
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|
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<path id='gpPt2' stroke-width='0.222' stroke='currentColor' d='M-1,0 L1,0 M0,-1 L0,1 M-1,-1 L1,1 M-1,1 L1,-1'/>
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<rect id='gpPt3' stroke-width='0.222' stroke='currentColor' x='-1' y='-1' width='2' height='2'/>
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<text><tspan> 6</tspan></text>
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<text><tspan> 8</tspan></text>
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<text><tspan> 10</tspan></text>
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<text><tspan> 12</tspan></text>
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<text><tspan> 14</tspan></text>
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<path d='M63.6,422.4 L63.6,413.4 M63.6,16.7 L63.6,25.7 h0.01'/> <g transform="translate(63.6,444.9)" style="stroke:none; fill:black; font-family:Linux Biolinum O; font-size:12.00pt; text-anchor:middle">
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<text><tspan> 1</tspan></text>
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<text><tspan>Absorption [mAu]</tspan></text>
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<text><tspan>-10</tspan></text>
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<text><tspan> 10</tspan></text>
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<text><tspan> 190</tspan></text>
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<text><tspan> 240</tspan></text>
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<text><tspan> 250</tspan></text>
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<text><tspan> 260</tspan></text>
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<g style="fill:none; color:black; stroke:currentColor; stroke-width:1.00; stroke-linecap:butt; stroke-linejoin:miter">
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<path d='M63.6,16.7 L63.6,422.4 L575.0,422.4 L575.0,16.7 L63.6,16.7 Z h0.01'/> <g transform="translate(17.6,219.6) rotate(270)" style="stroke:none; fill:black; font-family:Linux Biolinum O; font-size:12.00pt; text-anchor:middle">
|
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<text><tspan>Δε [mdeg M</tspan><tspan font-size="9.6pt" dy="-6.00pt">-1</tspan><tspan font-size="12.0pt" dy="6.00pt">cm</tspan><tspan font-size="9.6pt" dy="-6.00pt">-1</tspan><tspan font-size="12.0pt" dy="6.00pt">]</tspan></text>
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<text><tspan>λ [nm]</tspan></text>
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<g id="gnuplot_plot_1" ><title>gnuplot_plot_1</title>
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<text><tspan>PPDK (experimentell)</tspan></text>
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<text><tspan>v</tspan><tspan font-size="9.6pt" dy="3.60pt">0</tspan><tspan font-size="12.0pt" dy="-3.60pt"> [mM min</tspan><tspan font-size="9.6pt" dy="-6.00pt">-1</tspan><tspan font-size="12.0pt" dy="6.00pt">]</tspan></text>
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<text><tspan>R</tspan><tspan font-size="9.6pt" dy="-6.00pt">2</tspan><tspan font-size="12.0pt" dy="6.00pt"> = 0,906</tspan></text>
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<text><tspan>K</tspan><tspan font-size="9.6pt" dy="3.60pt">M</tspan><tspan font-size="12.0pt" dy="-3.60pt"> = (0,050 ± 0,009) mM</tspan></text>
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\addchap{Abkürzungsverzeichnis}
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||||
\begin{acronym}[C. symbiosum]
|
||||
\setlength{\itemsep}{-\parsep}
|
||||
\acro{2YT}{\textit{2x Yeast extract and Tryptone} (engl.)}
|
||||
\acro{2YT}{\textit{2\texttimes Yeast extract and Tryptone} (engl.)}
|
||||
\acro{3PGAK}{3-Phosphoglycerat Kinase}
|
||||
\acro{AA/BAA}{Acrylamid/Bisacrylamid}
|
||||
\acro{ADP}{Adenosindiphosphat}
|
||||
|
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@ -18,6 +18,7 @@
|
|||
\acro{ddH2O}[\ce{ddH2O}]{Doppelt destilliertes Wasser}
|
||||
\acro{DNA}{Desocyribonukleinsäure}
|
||||
\acro{dNTP}{Desoxyribonukleinsäuretriphosphat}
|
||||
\acro{DOPE}{\textit{Discrete Optimized Protein Energy}~(engl.)}
|
||||
\acro{DTT}{Dithiothreitol}
|
||||
\acro{EDTA}{Ethylendiamintetraessigsäure}
|
||||
\acro{E. coli}[\textit{E. coli}]{\textit{Escherichia coli}}
|
||||
|
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@ -50,6 +51,8 @@
|
|||
\acro{PMSF}{Phenylmethylsulfonylfluorid}
|
||||
\acro{PPDK}{Pyruvat-Phosphat Dikinase}
|
||||
\acro{rcf}{\textit{relative centrifugal force}~(engl.)}
|
||||
\acro{RMSD}{\textit{root mean square deviation}~(engl.)}
|
||||
\acro{RNA}{Ribonukleinsäure}
|
||||
\acro{RuBisCO}{Ribulose"=1,5"=bisphosphat"=carboxylase/"=oxygenase}
|
||||
\acro{SDS}{Natriumdodecylsulfat}
|
||||
\acro{SLIC}{Sequenz und Ligase unabhängige Klonierung}
|
||||
|
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@ -60,5 +63,6 @@
|
|||
\acro{TEMED}{Tetramethylethylendiamin}
|
||||
\acro{TEV}{\textit{Tobacco etch virus}~(engl.)}
|
||||
\acro{Tris}{Tris(hydroxymethyl)-aminomethan}
|
||||
\acro{tRNA}{Transfer-\acs{RNA}}
|
||||
\acro{UV}{Ultraviolett}
|
||||
\end{acronym}
|
||||
|
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@ -1,4 +1,13 @@
|
|||
\selectlanguage{english}
|
||||
\addchap{Abstract}
|
||||
\acresetall
|
||||
The objective of this work was the heterologous expression and purification of the pyruvate, phosphate dikinase (PPDK) from \ac{F. trinervia} and to provide evidence for its functional folding by conducting an activity assay.
|
||||
|
||||
Codon-optimized \acs{DNA} was cloned in an expression vector derived from pET-16b. Cells of the \ac{E. coli} strain BL21 (DE3) were subsequently transformed using this vector and used for the expression of the \ac{PPDK}. The expressed protein was purified using its His-tag for an affinity chromatography. Yields of up to \SI{118}{\milli\gram\per\liter} culture could be achieved in high purity.
|
||||
|
||||
The functional folding of the expressed \ac{PPDK} was tested measuring \acs{CD} spectra in combination with a coupled enzyme assay in which pyruvate, \acs{ATP} and inorganic phosphate react to phosphoenolpyruvate (PEP), \acs{AMP} and pyrophosphate. Using this assay, the kinetic parameters of the heterologous expressed \acs{PPDK} from \acs{F. trinervia} could be obtained: the \ce{K_m} were measured as \SI[seperr]{50(9)}{\micro\Molar} (\acs{ATP}) and \SI[seperr]{270(44)}{\micro\Molar} (pyruvate), the specific activity was \SI[seperr]{0,99(9)}{\Unit\per\milli\gram}.
|
||||
|
||||
As a result of a size exclusion chromatography it could be shown that certain fractions of the purified \acs{PPDK} were monodisperse and hence suitable for crystallization experiments.
|
||||
|
||||
In conclusion, the \ac{PPDK} from \ac{F. trinervia} could be successfully expressed and purified to a high degree. Furthermore the purified protein was active and hence folded natively.
|
||||
\selectlanguage{ngerman}
|
||||
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@ -20,6 +20,7 @@
|
|||
\showcaption{Sequenzalignment der \acs{PPDK}-kodierenden Sequenz im Vektor pETEV-16b-ppdk und der
|
||||
Referenzsequenz}
|
||||
\shortcaption{Sequenzalignment pETEV-16b-ppdk}
|
||||
\label{abb:pair_align}
|
||||
\end{texshade}
|
||||
|
||||
\clearpage
|
||||
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@ -28,6 +29,10 @@
|
|||
\shadingmode{similar}
|
||||
\threshold[80]{50}
|
||||
|
||||
\feature{top}{1}{1..380}{box[Green,Green]:Nukleotid-Bindedomäne[Black]}{}
|
||||
\feature{top}{1}{381..516}{box[Yellow,Yellow]:Phosphohistidin-Domäne[Black]}{}
|
||||
\feature{top}{1}{517..871}{box[Blue,Blue]:PEP/Pyruvat-Bindedomäne[White]}{}
|
||||
|
||||
\nameseq{1}{F. trinervia}
|
||||
\nameseq{2}{F. brownii}
|
||||
\nameseq{3}{Zea mays}
|
||||
|
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@ -45,7 +50,7 @@
|
|||
\hidenumbering
|
||||
\defconsensus{{$\bullet$}}{{$\bullet$}}{{$\bullet$}}
|
||||
\showconsensus[ColdHot]{bottom}
|
||||
\nameconsensus{conservation}
|
||||
\nameconsensus{Konservierung}
|
||||
% \showlegend
|
||||
\showcaption{Multiples Alignment der Aminosäuresequenzen der \acs{PPDK}s aus \acs{F. trinervia}, \acs{F. brownii}, \textit{Zea mays} und
|
||||
\acs{C. symbiosum}. Sequenzidentitäten sind farbkodiert dargestellt: \SI{100}{\percent} Identität (violett), \SI{75}{\percent} (blau) und
|
||||
|
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@ -60,19 +65,29 @@
|
|||
\section{Evalutation der Homologiemodelle}
|
||||
\begin{figure}[htb]
|
||||
\centering
|
||||
\includegraphics[height=0.5\textheight,keepaspectratio=true]{./img/anhang/FtPPDK_Zm.eps}
|
||||
\includegraphics[height=0.65\textheight,keepaspectratio=true]{./img/anhang/FtPPDK_Zm.eps}
|
||||
% FtPPDK_Zm.eps: 0x0 pixel, 300dpi, 0.00x0.00 cm, bb=0 -1 474 638
|
||||
\caption{Ramachandran-Plot des von \textit{Zea mays} abgeleiteten Homologiemodells}
|
||||
\label{abb:ramachandran_Zm}
|
||||
\end{figure}
|
||||
\begin{figure}[htb]
|
||||
\centering
|
||||
\includegraphics[height=0.5\textheight,keepaspectratio=true]{./img/anhang/FtPPDK_Cs.eps}
|
||||
\includegraphics[height=0.65\textheight,keepaspectratio=true]{./img/anhang/FtPPDK_Cs.eps}
|
||||
% FtPPDK_Cs.svg: 765x990 pixel, 72dpi, 26.99x34.92 cm, bb=0 0 765 990
|
||||
\caption{Ramachandran-Plot des von \acs{C. symbiosum} abgeleiteten Homologiemodells}
|
||||
\label{abb:ramachandran_Cs}
|
||||
\end{figure}
|
||||
|
||||
\chapter{Danksagung}
|
||||
Ich bedanke mich bei Herrn Prof. Dr. Georg Groth für das mir entgegengebrachte Vertrauen, die interessante und fordernde Fragestellung, sowie die Denkanstöße zur richtigen Zeit. Herrn Prof. Dr. Holger Gohlke gilt mein Dank für die Übernahme des Zweitgutachtens und die Betreuung meines Forschungspraktikums. Ohne die Fertigkeiten, die mir während dieses Praktikums vermittelt wurden, wäre die Erstellung der Homologiemodelle weitaus schwieriger gewesen.
|
||||
|
||||
Darüberhinaus danke ich der gesamten Arbeitsgruppe für jegliche erbrachte Unterstützung, den freundlichen Umgang miteinander und insbesondere Mareike dafür, dass wir wieder einmal eine Abschlussarbeit "`im Tandem"' absolvieren konnten.
|
||||
|
||||
Ich danke Benni, Mel und Daniel dafür, dass sie mir jederzeit mit Rat und Tat zur Seite gestanden haben. Es gibt wirklich keine Frage, die nicht einer von Euch beantworten kann. Danke! Mel gilt mein besonderer Dank, da sie einmal mehr -- in Ermangelung einer eigenen S2"=Einweisung -- die CD-Spektren für mich aufgenommen hat.
|
||||
|
||||
Ohne Christian und Judith wäre der Aktivitätstest in dieser Form nicht möglich gewesen. Danke Christian, dass ich Deine Vorräte an PEPCase plündern durfte.
|
||||
|
||||
Zu guter letzt möchte ich auch Patricia danken, ohne die sicherlich unsere Chemikalienbestände dauerhaft leer wären. Danke auch, dass ich mir immer mal wieder etwas von Dir ausborgen durfte, von der Pipette bis zum Puffer. Danke Euch allen!
|
||||
|
||||
\chapter{Erklärung}
|
||||
Hiermit versichere ich, dass ich die vorliegende Masterarbeit selbstständig verfasst und keine anderen, als die angegebenen Quellen und
|
||||
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|
|||
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@ -1,37 +1,30 @@
|
|||
\chapter{Diskussion}
|
||||
\section{Expression und Reinigung der \acs{PPDK}}
|
||||
Die \acs{PPDK} aus \acs{F. trinervia} konnte erfolgreich in \acs{E. coli} BL21 (DE3) exprimiert werden. Sowohl in einer vierstündigen Expression,
|
||||
als auch in einer Expression über Nacht zeigten sich in der differentiellen Zentrifugation nur geringe unlösliche Anteile, gemessen an der
|
||||
Gesamtmenge Protein (vgl. \ref{sec:ergebnisse_dz}). Dies spricht dafür, dass nur in geringem Maße \textit{Inclusion Bodies} gebildet wurden und legt die
|
||||
Vermutung nahe, das der lösliche Proteinanteil nativ gefaltet ist.
|
||||
Die \acs{PPDK} aus \acs{F. trinervia} konnte erfolgreich in \acs{E. coli} BL21 (DE3) exprimiert werden. Sowohl in einer vierstündigen Expression, als auch in einer Expression über Nacht zeigten sich in der differentiellen Zentrifugation nur geringe unlösliche Anteile, gemessen an der Gesamtmenge Protein (vgl. \ref{sec:ergebnisse_dz}). Dies spricht dafür, dass nur in geringem Maße \textit{Inclusion Bodies} gebildet wurden und legt die Vermutung nahe, das der lösliche Proteinanteil nativ gefaltet ist.
|
||||
|
||||
Dies konnte durch die \acs{CD}-Spektroskopie gestützt werden. Es konnten Sekundärstrukturanteile nachgewiesen werden, welche sich mit
|
||||
Sequenz basierten \textit{ab initio} Vorhersagen, sowie bekannten Strukturdaten decken (vgl. Tabelle \ref{tab:cd}). In einem letzten Schritt konnte die tatsächlich funktionelle
|
||||
Faltung der rekombinanten \acs{PPDK} in einem Aktivitätsassay gezeigt werden.
|
||||
Dies konnte durch die \acs{CD}-Spektroskopie gestützt werden. Es konnten Sekundärstrukturanteile nachgewiesen werden, welche sich mit Sequenz basierten \textit{ab initio} Vorhersagen, sowie bekannten Strukturdaten decken (vgl. Tabelle \ref{tab:cd}). In einem letzten Schritt konnte die tatsächlich funktionelle Faltung der rekombinanten \acs{PPDK} in einem Aktivitätstest gezeigt werden.
|
||||
|
||||
Im Rahmen der Reinigung konnten mit steigender Imidazolkonzentration insgesamt drei Fraktionen \acs{PPDK} gewonnen werden, die eine jeweils hohe Reinheit aufweisen (vgl. \ref{abb:reinigung_sds} und sich
|
||||
durch ihre Dispersität unterscheiden (siehe Abbildung \ref{abb:chromatogramm_gefi}). Der Oligomerisierungsgrad beeinflusst offenbar die Bindungsaffinität der \acs{PPDK} an die Säule,
|
||||
was zu einem unterschiedlichen Elutionsverhalten führt. Ursächlich könnte eine zunehmende Maskierung des Hexa-Histidin-Tags in den Oligomeren sein. Eine zuverlässige Größenzuordnung
|
||||
konnte in der Größenausschluschromatographie aufgrund der sehr eng zusammen liegenden Elutionsvolumina nicht vorgenommen werden. Es konnte aber gezeigt werden, dass
|
||||
die bei \SI{250}{\milli\Molar} gewonnene Fraktion monodispers vorliegt und sich somit gut für zukünftige Kristallisationsexperimente eignet.
|
||||
Im Rahmen der Reinigung konnten mit steigender Imidazolkonzentration insgesamt drei Fraktionen \acs{PPDK} gewonnen werden, die eine jeweils hohe Reinheit aufweisen (vgl. \ref{abb:reinigung_sds}) und sich durch ihre Dispersität unterscheiden (siehe Abbildung \ref{abb:chromatogramm_gefi}). Der Oligomerisierungsgrad beeinflusst offenbar die Bindungsaffinität der \acs{PPDK} an die Säule,
|
||||
was zu einem unterschiedlichen Elutionsverhalten führt. Ursächlich könnte eine zunehmende Maskierung des Hexa-Histidin-Tags in den Oligomeren sein. Eine zuverlässige Größenzuordnung konnte in der Größenausschluschromatographie aufgrund der sehr eng zusammen liegenden Elutionsvolumina nicht vorgenommen werden. Es konnte aber gezeigt werden, dass die bei \SI{250}{\milli\Molar} gewonnene Fraktion monodispers vorliegt und sich somit gut für zukünftige Kristallisationsexperimente eignet.
|
||||
|
||||
Die Proteinausbeute liegt -- betrachtet man nur die monodispers gereinigte Fraktion -- bei etwa \SI{47}{\milli\gram\per\liter} Kulturmedium und ist somit als
|
||||
hoch einzuschätzen. Der in der Literatur beschriebene Effekt der ausgeprägten Kältelabilität der \acs{PPDK} aus \acs{F. trinervia} \citep{Burnell1990},
|
||||
welcher zum Zerfall der funktionellen Tetramere in Monomere führt, ließe sich unter Umständen zur Erhöhung der effektiv nutzbaren Ausbeute einsetzen. Durch eine
|
||||
Vereinigung aller gereinigter PPDK-Fraktionen und anschließender Kältebehandlung sollte zu einer einheitlichen Population der PPDK-Monomere führen. Die Ausbeute
|
||||
beträgt dann etwa \SI{118}{\milli\gram\per\liter} Kultur.
|
||||
In Bezug auf den Oligomerisierungsgrad der \acs{PPDK} können auf Grund der Instabilität der eingesetzten Eichproteine im verwendeten Reinigungspuffer keine gesicherten Aussagen getroffen werden. Die mit \SI{200}{\milli\Molar} Imidazol eluierte Fraktion 2 weist jedoch eine recht geringe spezifische Aktivität im Vergleich zur mit \SI{250}{\milli\Molar} eluierten Fraktion 3 auf (Tabelle \ref{tab:aktivitaet}). Aus dem Chromatogramm (Abbildung \ref{abb:chromatogramm_gefi}) wird ersichtlich, dass bei Fraktion 2 der \textit{Peak} bei einem Elutionsvolumen von etwa \SI{1,7}{\milli\liter} im Vergleich zu Fraktion 3 deutlich niedriger und ein zusätzlicher \textit{Peak} bei etwa \SI{1,97}{\milli\liter} zu erkennen ist. Bei letzterem könnte es sich demnach um die inaktive monomere Form handeln, der \textit{Peak} bei \SI{1,68}{\milli\liter} könnte somit die aktive tetramere Form darstellen. Das Ausschlussvolumen der Säule wurde mit \SI{1,2}{\milli\liter} bestimmt, so dass es sich bei dem in Fraktion 1 sichtbaren \textit{Peak} bei \SI{1,28}{\milli\liter} um Aggregate handeln könnte.
|
||||
|
||||
Die Proteinausbeute liegt -- betrachtet man nur die monodispers gereinigte Fraktion -- bei etwa \SI{47}{\milli\gram\per\liter} Kulturmedium. Aus der Literatur ist für die heterologe Expression der \acs{PPDK} aus \textit{Zea mays} in \acs{E. coli} eine Ausbeute von \SI{5}{\milli\gram\per\liter} Kultur bekannt \citep{Chastain1997}. Die im Rahmen dieser Arbeit erzielte Ausbeute ist mit \SI{47}{\milli\gram\per\liter} für die monodisperse Fraktion bzw. \SI{118}{\milli\gram\per\liter} für die Summe aller \acs{PPDK}"=Fraktionen um den Faktor 10 bis 20 höher. Dies kann durch die Verwendung Codon optimierter \acs{DNA} erklärt werden, welche zu einer höheren Translationsrate und somit Expressionsrate führt. Zu beachten ist hierbei allerdings die erhöhte Gefahr einer Fehlfaltung des Proteins durch die höhere Translationsgeschwindigkeit \citep{Komar1999,Cortazzo2002}. Die damit einhergehende Bildung von \textit{Inclusion bodies} konnte aber nicht beobachtet werden (vgl. Abbildung \ref{abb:dz}). Ebenfalls gegen eine Fehlfaltung spricht die Ausbildung von Sekundärstrukturen (vgl. \ref{sec:ergebnisse_cd}) und die beobachtete Aktivität (vgl.~\ref{sec:ergebnisse_aktivitaetsassay}) der heterolog exprimierten \acs{PPDK} aus \acs{F. trinervia}.\pagebreak
|
||||
|
||||
Der in der Literatur beschriebene Effekt der ausgeprägten Kältelabilität der \acs{PPDK} aus \acs{F. trinervia} \citep{Burnell1990}, welcher zum Zerfall der funktionellen Tetramere in Monomere führt, ließe sich unter Umständen zur Erhöhung der effektiv nutzbaren Ausbeute einsetzen. Die Vereinigung aller gereinigter PPDK-Fraktionen und eine anschließende Kältebehandlung sollte zu einer einheitlichen Population von PPDK-Monomeren führen.
|
||||
|
||||
\section{Aktivität der gereinigten PPDK}
|
||||
Die spezifische Aktivität der \acs{PPDK} aus \acs{F. trinervia} liegt mit \SI[seperr]{0,99(9)}{\Unit\per\milli\gram} in der \acs{PEP}-bildenden Richtung in der Größenordnung
|
||||
von Literaturwerten für \textit{Zea mays} \citep{Hatch1975}. In ähnlicher Weise stimmen auch die bestimmten \ce{K_m}-Werte für ATP \SI[seperr]{50(9)}{\micro\Molar} und
|
||||
Pyruvat \SI[seperr]{270(44)}{\micro\Molar} mit bekannten Literaturwerten von \textit{Zea mays} und \textit{F. brownii} überein \citep{Hatch1975,Ohta1997}, die ebenfalls
|
||||
im zwei- bis dreistelligen mikromolaren Bereich liegen. Ein Vergleich der experimentellen Daten mit Literaturwerten ist in Tabelle \ref{tab:literatur} aufgeführt.
|
||||
Die spezifische Aktivität der \acs{PPDK} aus \acs{F. trinervia} liegt mit \SI[seperr]{0,99(9)}{\Unit\per\milli\gram} in der \acs{PEP}-bildenden Richtung in der Größenordnung von Literaturwerten für \textit{Zea mays} \citep{Hatch1975}. In ähnlicher Weise stimmen auch die bestimmten \ce{K_m}-Werte für ATP \SI[seperr]{50(9)}{\micro\Molar} und Pyruvat \SI[seperr]{270(44)}{\micro\Molar} mit Literaturwerten von \textit{Zea mays} und \textit{F. brownii} überein \citep{Hatch1975,Ohta1997}, die ebenfalls im zwei- bis dreistelligen mikromolaren Bereich liegen. Ein Vergleich der experimentellen Daten mit Literaturwerten ist in Tabelle \ref{tab:literatur} aufgeführt. Auffällig ist hierbei, dass die \ce{K_m}"=Werte der heterolog exprimierten \acs{PPDK}s jeweils deutlich unterhalb der nativ isolierten liegen. Dies ist vermutlich auf fehlende Regulationsmechanismen -- beispielsweise die lichtinduzierte Phosphorylierung durch das \ac{PDRP} (siehe \ref{sec:c4_ppdk}) -- bei der heterolog exprimierten \acs{PPDK} zurückzuführen.
|
||||
|
||||
\ce{V_{max}} wurde im Rahmen der nichtlinearen Regression für \acs{ATP} und Pyruvat bestimmt. Unter Berücksichtigung der Standardabweichung sind die beiden Werte
|
||||
-- \SI[seperr]{0,095(5)}{\milli\Molar\per\minute} (ATP) und \SI[seperr]{0,093(5)}{\milli\Molar\per\minute} (Pyruvat) -- als identisch anzusehen. Dies entspricht der
|
||||
Erwartung, da die maximale Reaktionsgeschwindigkeit bei Substratsättigung in beiden Fällen identisch sein sollte.
|
||||
%
|
||||
\begin{table}[htb]
|
||||
\begin{table}[H]
|
||||
\centering
|
||||
\begin{threeparttable}
|
||||
\caption[Vergleich der kinetischen Parameter mit Literaturwerten]{Vergleich der kinetischen Parameter mit Literaturwerten der PPDK aus \textit{F. bidentis}, \textit{F. brownii} und \textit{Zea mays}.
|
||||
Die Literaturwerte beziehen sich jeweils auf die \acs{PEP}-bildende Reaktion.}
|
||||
Die Literaturwerte beziehen sich jeweils auf die \acs{PEP}-bildende Reaktion. Ohne Klammern sind die \ce{K_m}"=Werte der heterolog in \acs{E. coli} exprimierten \acs{PPDK} angegeben, in Klammern die der nativ isolierten.}
|
||||
\label{tab:literatur}
|
||||
|
||||
\begin{tabular}{llll}
|
||||
|
|
@ -41,43 +34,39 @@ im zwei- bis dreistelligen mikromolaren Bereich liegen. Ein Vergleich der experi
|
|||
\midrule
|
||||
\acs{F. trinervia} & \num[seperr]{50(9)} & \num[seperr]{270(44)} & \num[seperr]{ 0,99(9)} \\
|
||||
\midrule
|
||||
\textit{F. bidentis} & 25\tnote{2} & 73\tnote{2} & \\
|
||||
\textit{F. brownii} & 88\tnote{2} & 67\tnote{2} & \\
|
||||
\textit{Zea mays} & 95\tnote{2} & 158\tnote{2} & 1,2\tnote{1} \\
|
||||
\textit{F. bidentis} & 49 (25)\tnote{2} & 59 (73)\tnote{2} & \\
|
||||
\textit{F. brownii} & 50 (88)\tnote{2} & 32 (67)\tnote{2} & \\
|
||||
\textit{Zea mays} & 47 (95)\tnote{2} & 65 (158)\tnote{2} & 1,2\tnote{1} \\
|
||||
& & (178)\tnote{3} & \\
|
||||
\bottomrule
|
||||
\end{tabular}
|
||||
\begin{tablenotes}
|
||||
\item[1] \citet{Hatch1975}
|
||||
\item[2] \citet{Ohta1997}
|
||||
\item[3] \citet{Chastain2011}
|
||||
\end{tablenotes}
|
||||
|
||||
\end{threeparttable}
|
||||
\end{table}
|
||||
|
||||
\ce{V_{max}} wurde im Rahmen der nichtlinearen Regression für \acs{ATP} und Pyruvat bestimmt. Unter Berücksichtigung der Standardabweichung sind die beiden Werte
|
||||
-- \SI[seperr]{0,095(5)}{\milli\Molar\per\minute} (ATP) und \SI[seperr]{0,093(5)}{\milli\Molar\per\minute} (Pyruvat) -- als identisch anzusehen. Dies entspricht der
|
||||
Erwartung, da die maximale Reaktionsgeschwindigkeit bei Substratsättigung in beiden Fällen identisch sein sollte.
|
||||
|
||||
Der beobachtete Abfalls der gemessenen Reaktionsgeschwindigkeit bei einer \acs{ATP}-Konzentration von \SI{2,5}{\milli\Molar} (Abbildung \ref{abb:kinetik_atp}) ist auf
|
||||
Der beobachtete Abfall der gemessenen Reaktionsgeschwindigkeit bei einer \acs{ATP}-Konzentration von \SI{2,5}{\milli\Molar} (Abbildung \ref{abb:kinetik}) ist auf
|
||||
die inhibitorische Wirkung von \acs{ATP}, \acs{ADP} und \acs{AMP} auf die als letzte Stufe des gekoppelten Enzymassays eingesetzte \acs{MDH} zurückzuführen \citep{Harris}. Bei einer \acs{ATP}-Konzentration
|
||||
von \SI{2,5}{\milli\Molar} ist nicht mehr die Pyruvat-Bildung durch die \acs{PPDK}, sondern die Umsetzung des Oxalacetats durch die \acs{MDH} der geschwindigkeitsbestimmende Schritt.
|
||||
|
||||
Zusammenfassend lässt sich festhalten, dass die Aktivität der \acs{PPDK} aus \acs{F. trinervia} in etwa vergleichbar mit anderen bekannten PPDKs ist.
|
||||
Zusammenfassend lässt sich festhalten, dass die Aktivität der rekombinant aus \acs{E. coli} gewonnenen \acs{PPDK} aus \acs{F. trinervia} in etwa vergleichbar mit anderen bekannten rekombinant hergestellten \citep{Ohta1997,Chastain2011}, oder nativ isolierten \citep{Hatch1975,Ohta1997} PPDKs ist.
|
||||
|
||||
\section{Homologiemodelle}
|
||||
Die erstellten Homologiemodelle weisen nach einer Analyse mit PROCHECK keine auffälligen Anomalien auf, so dass die Modelle als hinreichend korrekt angesehen werden können.
|
||||
Die erstellten Homologiemodelle weisen nach einer Analyse mit PROCHECK keine auffälligen Anomalien auf, so dass die Modelle als hinreichend korrekt angesehen werden können. Hierauf deuten auch die zDOPE"=Werte von -0,92803 für das auf \textit{Zea mays} bzw. -0,92815 für das auf \acs{C. symbiosum} basierende Modell hin. Bei Betrachtung der DOPE"=Werte je Position im Alignment (vgl. Abbildung \ref{abb:dope}) zeigt sich, dass die Profile der Modelle und der entsprechenden Template qualitativ ähnlich sind. Es fallen allerdings Verschiebungen mit zunehmender Position im Alignment auf, welche auf einen Versatz des Alignments hindeuten können. Dies ist allerdings unwahrscheinlich, da insbesondere im C-terminalen Bereich innerhalb der \acs{PEP}/Pyruvat"=Bindedomäne (ab Position 517) hoch konservierte Sequenzabschnitte mit bekannter Funktionalität -- beispielsweise in Bezug auf die Substratbindung -- zu finden sind. Diese konservierten Abschnitte sind korrekt aligniert (vgl. Abbildung \ref{abb:ma}), weisen aber im DOPE"=Profil dennoch einen Versatz auf (Abbildung \ref{abb:dope}).
|
||||
|
||||
Da die \acs{PPDK} aus \textit{Zea mays} zudem eine hohe Sequenzidentität von \SI{79}{\percent} zur \acs{PPDK} aus \acs{F. trinervia} aufweist, bietet das hierauf basierende
|
||||
Modell eine gute Annäherung an die tatsächliche dreidimensionale Struktur der \acs{PPDK} aus \acs{F. trinervia}, insbesondere in Hinblick auf die räumliche Ausrichtung
|
||||
der Seitenketten in der \acs{PEP}-Bindetasche. In Kombination mit der Identifikation hoch konservierter Sequenzabschnitte können einige für die \acs{PEP}-Bindung und
|
||||
Umsetzung wichtige Reste identifiziert werden \citep{Nakanishi2005}: Arg562, Arg619, Arg669, Glu748, Asp772 und Asn771, sowie Cys834, welches als Protonen-Donor fungiert (Abbildung \ref{abb:substratbindetasche}).
|
||||
Durch gezielte Mutation dieser Reste kann in zukünftigen Experimenten ihr Einfluss auf die Aktivität und Stabilität der \acs{PPDK} untersucht werden.
|
||||
|
||||
%
|
||||
\clearpage
|
||||
%
|
||||
\section{Ausblick}
|
||||
Die im Rahmen dieser Arbeit gereinigte \acs{PPDK} liegt in hoher Konzentration, monodispers und hoher Reinheit vor, so dass sie in Kristallisationsexperimente eingesetzt
|
||||
werden kann. Eine erfolgreiche Kristallisation ist dann notwendig für die Strukturaufklärung mittels Röntgenkristallographie. Zusätzlich können anhand der erstellten
|
||||
Homologiemodelle \textit{in silico} Analysen durchgeführt werden. Beispielsweise kann nach Bindetaschen für Effektoren gesucht werden, welche das \textit{Domain-Swiveling}
|
||||
in distinkten Zwischenstadien halten. Sobald Kristallisationsbedingungen für die wildtypische Form etabliert sind, können diese für die Co-Kristallisation mit den gefundenen
|
||||
Effektoren adaptiert werden. Letztere können darüber hinaus direkt mit Hilfe des etablierten Aktivitätsassays auf ihren Einfluss auf die \acs{PPDK}-Aktivität hin untersucht werden.
|
||||
Aus den resultierenden Strukturdaten ließen sich dann intermediäre Konformationen ableiten, die zu einem genaueren Verständnis der Funktionalität
|
||||
der \acs{PPDK} führen können. Mittels einer Netzwerkanalyse ließen sich zusätzlich Regionen innerhalb der \acs{PPDK} identifizieren, welche für die Flexibilität der zentralen
|
||||
Phospho"=Histidin"=Domäne verantwortlich sind. Hier bietet sich ein weiterer Ansatzpunkt um beispielsweise über \textit{Cross-Linking} Zwischenkonformationen zu stabilieren.
|
||||
Die im Rahmen dieser Arbeit gereinigte \acs{PPDK} liegt in hoher Konzentration, monodispers und hoher Reinheit vor, so dass sie in Kristallisationsexperimente eingesetzt werden kann. Eine erfolgreiche Kristallisation ist dann notwendig für die Strukturaufklärung mittels Röntgenkristallographie. Zusätzlich können anhand der erstellten Homologiemodelle \textit{in silico} Analysen durchgeführt werden. Beispielsweise kann nach Bindetaschen für Effektoren gesucht werden, welche das \textit{Domain-Swiveling} in distinkten Zwischenstadien halten. Sobald Kristallisationsbedingungen für die wildtypische Form etabliert sind, können diese für die Co-Kristallisation mit den gefundenen Effektoren adaptiert werden. Letztere können darüber hinaus direkt mit Hilfe des etablierten Aktivitätstests auf ihren Einfluss auf die \acs{PPDK}-Aktivität hin untersucht werden. Aus den resultierenden Strukturdaten ließen sich dann intermediäre Konformationen ableiten, die zu einem genaueren Verständnis der Funktionalität der \acs{PPDK} führen können. Mittels einer Netzwerkanalyse ließen sich zusätzlich Regionen innerhalb der \acs{PPDK} identifizieren, welche für die Flexibilität der zentralen Phospho"=Histidin"=Domäne verantwortlich sind. Hier bietet sich ein weiterer Ansatzpunkt um beispielsweise über \textit{Cross-Linking} Zwischenkonformationen zu stabilieren.
|
||||
|
||||
Ein weiterer interessanter Aspekt ist die genauere Untersuchung der Kältelabilität der \acs{PPDK}. Die für die Kältetoleranz bestimmter \acs{PPDK} Spezies verantwortlichen Aminosäurereste sind bekannt und für die Wirkungsweise wurden hydrophobe Wechselwirkungen, sowie eine gesteigerten Affinität zum im Tetramer zentral komplexierten \ce{Mg^{2+}}-Ion postuliert \citep{Ohta1997}. Gelöste Kristallstrukturen, auch von Mutanten, welche die zur Kältetoleranz führenden Punktmutationen tragen, könnten diese Vermutungen bestätigen oder erweitern.
|
||||
|
|
@ -4,40 +4,42 @@ Die \acl{PPDK} (PPDK, EC 2.7.9.1) gehört zur Enzymklasse der Phosphotransferase
|
|||
\ce{\text{Pyruvat} + \text{ATP} + \text{Pi} <=> \text{PEP} + \text{AMP} + \text{PPi}}
|
||||
\end{equation*}
|
||||
Erstmals beschrieben wurde die \acs{PPDK} von \citet{Slack1968,Reeves1968} in tropischen Gräsern und der parasitären Amöbe
|
||||
\textit{Entamoeba histolytica} \citep{Chastain2011}. Strukturdaten der \acs{PPDK} sind verfügbar aus \textit{Clostridium symbiosum} \citep{Herzberg1996}, \textit{Zea mays} \citep{Nakanishi2005} und \textit{Trypanosomas brucei} \citep{Cosenza2002}.
|
||||
\textit{Entamoeba histolytica} \citep{Chastain2011}. Strukturdaten der \acs{PPDK} sind verfügbar aus \textit{Clostridium symbiosum} (\SI{1,94}{\angstrom}; \citet{Herzberg1996}), \textit{Zea mays} (\SI{2,3}{\angstrom}; \citet{Nakanishi2005}) und \textit{Trypanosomas brucei} (\SI{3,0}{\angstrom}; \citet{Cosenza2002}).
|
||||
|
||||
\section{Strukturelle Funktionalität der \acs{PPDK}}
|
||||
Die \acs{PPDK} kann in drei Domänen unterteilt werden:
|
||||
Die \acs{PPDK} kann auf Grund von Sequenzhomologien, sowie funktionellen Überlegungen und Strukturdaten in drei Domänen unterteilt werden:
|
||||
\begin{enumerate}
|
||||
\item \acs{PEP}/Pyruvat-Bindedomäne
|
||||
\item Nukleotid-Bindedomäne
|
||||
\item Zentrale Phosphohistidin-Domäne
|
||||
\item Nukleotid-Bindedomäne (AS 1-380)
|
||||
\item Zentrale Phosphohistidin-Domäne (AS 381-516)
|
||||
\item \acs{PEP}/Pyruvat-Bindedomäne (AS 517-871)
|
||||
\end{enumerate}
|
||||
|
||||
Innerhalb der N-terminalen Nukleotid-Bindedomäne formen 240 Reste eine so genannte \textit{\acs{ATP} grasp}, während 340 Reste innerhalb der C-terminalen \acs{PEP}/Pyruvat"=Bindedomäne ein \textit{TIM barrel}-Motiv bilden. Die Nukleotid"=Bindedomäne wurde über Sequenzhomologien zu bekannten \acs{ATP}"=bindenden Proteinen identifiziert, die \acs{PEP}/Pyruvat"=Bindedomäne über kristallographische Strukturdaten in Anwesenheit von des Substratanalogons Phosphonopyruvate \citep{Herzberg2002}.
|
||||
|
||||
\begin{figure}[H]
|
||||
\centering
|
||||
\includegraphics[height=0.7\textheight,keepaspectratio=true]{./img/einleitung/ppdk_1vbh.png}
|
||||
% ppdk_1vbh.png: 2480x4004 pixel, 300dpi, 21.00x33.90 cm, bb=0 0 595 961
|
||||
\caption[Struktur der \acs{PPDK} aus \textit{Zea mays}]{Struktur der \acs{PPDK} aus \textit{Zea mays} (PDB: 1VBH). Farblich abgesetzt sind die Nukleotid-Bindedomäne (grün), \acs{PEP}/Pyruvat-Bindedomäne (blau) mit dem Substra \acs{PEP} und einem \ce{Mg2+}-Ion, die Phosphohistidin-Domäne (gelb), sowie die Linker-Peptide(rot). Der katalytische Rest His458 ist durch einen Pfeil hervorgehoben. Die Überlagerung (grau) zeigt die \acs{PPDK} aus \acs{C. symbiosum} (PDB: 1KBL). Das katalytische His455 ist ebenfalls durch einen Pfeil markiert. Es zeigt sich die Torsionsbewegung der zentralen Phosphohistidindomäne.}
|
||||
\caption[Struktur der \acs{PPDK} aus \textit{Zea mays}]{Struktur der \acs{PPDK} aus \textit{Zea mays} (PDB: 1VBH). Farblich abgesetzt sind die Nukleotid-Bindedomäne (grün), \acs{PEP}/Pyruvat-Bindedomäne (blau) mit dem Substrat \acs{PEP} und einem \ce{Mg^{2+}}-Ion, die Phosphohistidin-Domäne (gelb), sowie die Linker-Peptide (rot). Der katalytische Rest His458 ist durch einen Pfeil hervorgehoben. Die Überlagerung (grau) zeigt die \acs{PPDK} aus \acs{C. symbiosum} (PDB: 1KBL). Das katalytische His455 ist ebenfalls durch einen Pfeil markiert. Es zeigen sich zwei unterschiedliche Konformationen der zentralen Phosphohistidindomäne.}
|
||||
\label{abb:swivel_domain}
|
||||
\end{figure}
|
||||
|
||||
Verknüpft sind die genannten Domänen über flexible Linker-Peptide. Der Abstand zwischen der Nukleotid-Bindedomäne und der \acs{PEP}/Pyruvat-Bindedomäne beträgt etwa \SI{50}{\angstrom}, so dass eine direkte Interaktion der Substrate mit dem katalytisch
|
||||
aktiven Histidinrest in der zentralen Phosphohistidin-Domäne nicht möglich ist. Daher wurde ein so genannter \textit{Domain-Swiveling}-Mechanismus vorgeschlagen, der eine Torsionsbewegung der Phosphohistidin-Domäne postuliert, wodurch die Übertragung der Phosphatgruppen ermöglicht wird \citep{Herzberg1996,Nakanishi2005}. Das Ausmaß dieser Domänenbewegung ist bei Überlagerung der \acs{PEP}-gebundenen Struktur aus \textit{Zea mays} und der ungebundenen Struktur aus \acs{C. symbiosum} (Abbildung \ref{abb:swivel_domain}).
|
||||
Verknüpft sind die genannten Domänen über flexible Linker-Peptide. Der Abstand zwischen der Nukleotid-Bindedomäne und der \acs{PEP}/Pyruvat-Bindedomäne beträgt etwa \SI{45}{\angstrom}, so dass eine direkte Interaktion der Substrate mit dem katalytisch
|
||||
aktiven Histidinrest in der zentralen Phosphohistidin-Domäne nicht möglich ist. Daher wurde ein so genannter \textit{Domain-Swiveling}-Mechanismus vorgeschlagen, der eine Torsionsbewegung der Phosphohistidin-Domäne postuliert, wodurch die Übertragung der Phosphatgruppen ermöglicht wird \citep{Herzberg1996,Nakanishi2005}. Das Ausmaß dieser Domänenbewegung ist bei Überlagerung der \acs{PEP}-gebundenen Struktur aus \textit{Zea mays} und der ungebundenen Struktur aus \acs{C. symbiosum} (Abbildung \ref{abb:swivel_domain}) erkennbar.
|
||||
|
||||
\section{Funktion in $\text{C}_\text{4}$-Pflanzen}
|
||||
\label{sec:c4_ppdk}
|
||||
Am besten untersucht ist die Funktion der \acs{PPDK} in \ce{C_4}"=Pflanzen. In \ce{C_3}-Pflanzen limitiert die Oxygenase-Aktivität der \ac{RuBisCO} die Effizienz
|
||||
der Photosynthese bei warmen Umgebungstemperaturen oder bei Wasserstress. Bei den genannten Bedingungen werden die Spaltöffnungen der Blätter geschlossen um
|
||||
den Wasserverlust durch Verdunstung zu minimieren. Durch das Schließen der Spaltöffnungen wird aber auch die Diffusion von \ce{CO2} in das Blatt vermindert. Die resultierende Absenkung der \ce{CO2}-Konzentration in den photosynthetisch aktiven Zellen führt zu einer Begünstigung der zur \ce{CO2}-Fixierung konkurrierenden Oxygenaseaktivität der \ac{RuBisCO} \citep{Sharkey1989,Cornic2000,Lawlor2002}. Durch die Fixierung von \ce{O2} statt \ce{CO2} wird entsteht als Zwischenprodukt 2-Phosphoglycolat, welches nicht im Calvin-Zyklus verstoffwechselt werden kann und unter zusätzlichem Energieverbrauch über die Photorespiration in 3-Phosphoglycerat umgesetzt wird.
|
||||
der Photosynthese bei warmen Umgebungstemperaturen oder Wasserstress. Die genannten Bedingungen führen zum Schließen der Spaltöffnungen in den Blättern, um den Wasserverlust durch Verdunstung zu minimieren. Durch das Schließen der Spaltöffnungen wird aber auch die Diffusion von \ce{CO2} in das Blatt vermindert. Die resultierende Absenkung der \ce{CO2}-Konzentration in den photosynthetisch aktiven Zellen führt zu einer Begünstigung der zur \ce{CO2}-Fixierung konkurrierenden Oxygenaseaktivität der \ac{RuBisCO} \citep{Sharkey1989,Cornic2000,Lawlor2002}. Durch die Fixierung von \ce{O2} statt \ce{CO2} wird entsteht als Zwischenprodukt 2-Phosphoglycolat, welches nicht im Calvin-Zyklus verstoffwechselt werden kann und unter zusätzlichem Energieverbrauch über die Photorespiration in 3-Phosphoglycerat umgesetzt wird.
|
||||
|
||||
Die \ce{C_4}"=Kohlenstofffixierung umgeht dieses Problem durch eine räumliche Trennung von \ce{CO2}-Fixierung und Calvin-Zyklus. Hierdurch kann \ce{CO2} konzentriert werden, was der \acs{RuBisCO} eine \ce{CO2} reiche Umgebung zur Verfügung stellt. Hierdurch wird die Oxygenaseaktivität stark reduziert.
|
||||
Die \ce{C_4}"=Kohlenstofffixierung umgeht dieses Problem durch eine räumliche Trennung von \ce{CO2}-Fixierung und Calvin-Zyklus. Hierdurch kann \ce{CO2} konzentriert werden, was der \acs{RuBisCO} eine \ce{CO2} reiche Umgebung zur Verfügung stellt und die Oxygenaseaktivität stark reduziert.
|
||||
Die \acs{PPDK} ist hierbei im Stroma der Chloroplasten der Mesophyllzellen lokalisiert und katalysiert dort die Regeneration des primären \ce{CO2}-Akzeptors \ac{PEP} \citep{Hatch2002}.
|
||||
|
||||
\begin{figure}[H]
|
||||
\centering
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/einleitung/C4_photosynthesis_NADP-ME_type.eps}
|
||||
% C4_photosynthesis_NADP-ME_type.eps: 0x0 pixel, 300dpi, 0.00x0.00 cm, bb=0 -1 713 233
|
||||
\caption[\ce{C_4}"-Kohlenstofffixierung]{\ce{C_4}"-Kohlenstofffixierung nach dem NADP-\acs{ME} Mechanismus. Dargestellt sind eine Mesophyllzelle (links) und eine Bündelscheidezelle (rechts), sowie die Chloroplasten (grün). \ce{CO2} wird auf \ac{PEP} übertragen, welches in Malat umgewandelt und in die Bündelscheidezelle transportiert wird. Dort wird \ce{CO2} abgespalten und das entstandene Pyruvat zurück in die Chloroplasten der Mesophyllzelle transportiert, wo \ac{PEP} durch die \acs{PPDK} aus Pyruvat regeneriert wird. \citep{Raghavendra2011}}
|
||||
\caption[\ce{C_4}"=Kohlenstofffixierung]{\ce{C_4}"-Kohlenstofffixierung nach dem NADP-\acs{ME} Mechanismus. Dargestellt sind eine Mesophyllzelle (links) und eine Bündelscheidezelle (rechts), sowie die Chloroplasten (grün). \ce{CO2} wird auf \ac{PEP} übertragen, welches in Malat umgewandelt und in die Bündelscheidezelle transportiert wird. Dort wird \ce{CO2} abgespalten und das entstandene Pyruvat zurück in die Chloroplasten der Mesophyllzelle transportiert, wo \ac{PEP} durch die \acs{PPDK} aus Pyruvat regeneriert wird. \citep{Raghavendra2011}}
|
||||
\label{abb:c4_cycle}
|
||||
\end{figure}
|
||||
|
||||
|
|
@ -57,12 +59,12 @@ Abbildung \ref{abb:c4_cycle} illustriert die \ce{C_4}"=Kohlenstofffixierung mit
|
|||
\label{abb:aktivierung_ppdk}
|
||||
\end{figure}
|
||||
|
||||
Die Regulation der \acs{PPDK} erfolgt lichtabhängig durch das \ac{PDRP} über die Phosphorylierung eines Threonin-Restes (vgl. Abbildung \ref{abb:aktivierung_ppdk}) im aktiven Zentrum \citep{Burnell1985,Burnell2006,Chastain2011}.
|
||||
Die Regulation der \acs{PPDK} erfolgt lichtabhängig durch das \ac{PDRP} über die Phosphorylierung eines Threonin-Restes (vgl. Abbildung \ref{abb:aktivierung_ppdk}) im aktiven Zentrum \citep{Burnell1985,Chastain2003,Burnell2006,Chastain2011}.
|
||||
|
||||
\section{Funktion in $\text{C}_\text{3}$-Pflanzen}
|
||||
Über die Funktion der \acs{PPDK} in \ce{C_3}-Pflanzen liegen weitaus weniger gesicherte Erkenntnisse vor. Die \acs{PPDK} kann ubiquitär in Geweben aus \ce{C_3}-Pflanzen nachgewiesen werden, liegt dort aber meist nur in sehr geringen Konzentrationen vor \citep{Chastain2003}. Dies erschwert die biochemische Charakterisierung von \acs{PPDK}s aus \ce{C_3}-Pflanzen \textit{in vivo}, da die Umsetzung der Substrate, sowie die Produktbildung nicht zuverlässig verfolgt werden können. Zudem wird der Substratumsatz durch konkurrierende Reaktionen der Pyruvat-Kinase und \acs{PEP}-Carboxykinase maskiert \citep{Chastain2011}. \textit{Knock-out} Linien von \textit{Arabidopsis thaliana} zeigen keinen veränderten Phänotyp, so dass auch hierüber eine Aussage über die Funktion der \acs{PPDK} in \ce{C_3}-Pflanzen nicht möglich ist \citep{Chastain2011}.
|
||||
Über die Funktion der \acs{PPDK} in \ce{C_3}-Pflanzen liegen weitaus weniger gesicherte Erkenntnisse vor. Die \acs{PPDK} kann ubiquitär in Geweben aus \ce{C_3}-Pflanzen nachgewiesen werden, liegt dort aber meist nur in sehr geringen Konzentrationen vor \citep{Chastain2003}. Dies erschwert die biochemische Charakterisierung von \acs{PPDK}s aus \ce{C_3}-Pflanzen \textit{in vivo}, da die Umsetzung der Substrate, sowie die Produktbildung nicht zuverlässig verfolgt werden können. Zudem wird der Substratumsatz durch konkurrierende Reaktionen der Pyruvat-Kinase und \acs{PEP}-Carboxykinase maskiert \citep{Chastain2011}. \textit{Knock-out} Linien von \textit{Arabidopsis thaliana} zeigen keinen veränderten Phänotyp, so dass auch hierüber keine Aussage über die Funktion der \acs{PPDK} in \ce{C_3}-Pflanzen möglich ist \citep{Chastain2011}.
|
||||
|
||||
Untersuchungen an Mais-Samen, in denen die \acs{PPDK} in hohem Maße im Cytoplasma des Endosperms exprimiert wird legen allerdings eine Funktion als ergänzendes Enzym der Glykolyse nahe \citep{Kang2005,Hennen-Bierwagen2009}. Es wurde postuliert, dass die \acs{PPDK} durch die von ihr katalysierte, frei reversible Reaktion den Kohlenstofffluss zwischen verschiedenen Biosynthesewegen
|
||||
Untersuchungen an Mais-Samen, in denen die \acs{PPDK} in hohem Maße im Cytoplasma des Endosperms exprimiert wird, legen allerdings eine Funktion als ergänzendes Enzym der Glykolyse nahe \citep{Kang2005,Hennen-Bierwagen2009}. Es wurde postuliert, dass die \acs{PPDK} durch die von ihr katalysierte, frei reversible Reaktion den Kohlenstofffluss zwischen verschiedenen Biosynthesewegen
|
||||
ausgleicht \citep{Hennen-Bierwagen2009} und \acs{ATP} in hypoxischen Bereichen des Endosperms zur Verfügung stellt \citep{Chastain2006}.
|
||||
|
||||
\section{Funktion in nicht-pflanzlichen Organismen}
|
||||
|
|
@ -74,17 +76,17 @@ Reaktion erlaubt sowohl die Synthese von \acs{ATP}, als auch die Bildung von \ac
|
|||
\centering
|
||||
\includegraphics[width=0.6\textwidth,keepaspectratio=true]{./img/einleitung/ppdk_glycolysis.eps}
|
||||
% ppdk_glycolysis.eps: 0x0 pixel, 300dpi, 0.00x0.00 cm, bb=0 -1 536 475
|
||||
\caption[Einfluss der \acs{PPDK} auf die glykolytische ATP-Ausbeute]{Einfluss der \acs{PPDK} auf die glykolytische ATP-Ausbeute. Durch das Zusammenspiel zwischen \ac{AK} und \ac{PPDK} können im Vergleich zur konventionellen Glykolyse drei zusätzliche Moleküle \acs{ATP} je Glukosemolekül gewonnen werden.}
|
||||
\caption[Einfluss der \acs{PPDK} auf die glykolytische ATP-Ausbeute]{Einfluss der \acs{PPDK} auf die glykolytische ATP-Ausbeute. Durch das Zusammenspiel zwischen \ac{AK} und \ac{PPDK} können im Vergleich zur konventionellen Glykolyse drei zusätzliche Moleküle \acs{ATP} je Glukosemolekül gewonnen werden (nach \citet{Chastain2011}).}
|
||||
\label{abb:glykolyse}
|
||||
\end{figure}
|
||||
%
|
||||
Durch synergetische Effekte zwischen \acl{AK} und \ac{PPDK} kann die \acs{ATP}-Ausbeute von drei Molekülen \acs{ATP} je Molekül Glukose auf fünf Moleküle \acs{ATP} erhöht werden (Abbildung \ref{abb:glykolyse}). Hierbei kann die Bindungsenergie von Pyrophosphat durch die \acs{PPDK} zum Aufbau von \acs{ATP} aus \acs{AMP} genutzt werden \citep{Huang2008}. Die Reaktion läuft dabei in die Pyruvat-formende Richtung ab.
|
||||
Durch synergetische Effekte zwischen \acl{AK} und \ac{PPDK} kann die \acs{ATP}-Ausbeute in der Glykolyse von drei Molekülen \acs{ATP} je Molekül Glukose auf fünf Moleküle \acs{ATP} erhöht werden (Abbildung \ref{abb:glykolyse}). Hierbei kann die Bindungsenergie von Pyrophosphat durch die \acs{PPDK} zum Aufbau von \acs{ATP} aus \acs{AMP} genutzt werden \citep{Huang2008}. Die Reaktion läuft dabei in die Pyruvat-formende Richtung ab.
|
||||
|
||||
\section{Kälteinaktivierung}
|
||||
|
||||
\label{sec:kaelte}
|
||||
Eine besondere Eigenschaft der \acs{PPDK} ist die Kälteinaktivierung. Die funktionelle Form ist ein Tetramer, welches bei Temperaturen unterhalb von \SI{10}{\celsius} in inaktive Di- und Monomere zerfällt \citep{Slack1968,Shirahashi1978,Burnell1990}.
|
||||
Bei der experimentellen Arbeit mit der \acs{PPDK} ergibt sich hieraus die Problematik, dass alle Arbeitsschritte bei Raumtemperatur
|
||||
durchgeführt werden müssen, was aber die Anfälligkeit für die Degradierung durch im Zelllysat enthaltene Proteasen erhöht. Durch Erwärmen auf \SI{30}{\celsius} ist allerdings eine weitgehende Reaktivierung zu erreichen \citep{Burnell1985}.
|
||||
durchgeführt werden müssen, was aber die Anfälligkeit für die Degradierung durch im Zelllysat enthaltene Proteasen erhöht. Durch Erwärmen auf \SI{30}{\celsius} ist allerdings eine weitgehende Reaktivierung zu erreichen \citep{Burnell1985, Ashton1990}.
|
||||
|
||||
Die Kältesensitivität ist zwischen verschiedenen Spezies unterschiedlich stark ausgeprägt. Innerhalb der Gattung \textit{Flaveria} weist die \acs{PPDK} aus \acs{F. trinervia} die höchste Sensitivität auf (vgl. Abbildung \ref{abb:cold_lability}): Nach einer \SI{30}{\minute} Inkubation bei \SI{0}{\celsius} konnte eine Restaktivität von lediglich \SI{10}{\percent} beobachtet werden. Die \acs{PPDK} aus \acs{F. brownii} wies nach der Kältebehandlung eine Restaktivität von \SI{80}{\percent} auf \citep{Burnell1990}.
|
||||
%
|
||||
|
|
@ -96,11 +98,11 @@ Die Kältesensitivität ist zwischen verschiedenen Spezies unterschiedlich stark
|
|||
\label{abb:cold_lability}
|
||||
\end{figure}
|
||||
%
|
||||
Durch Sequenzanalysen konnten gezeigt werden, dass nur wenige Aminosäurereste die Kältesensitivität stark beeinflussen \citep{Ohta1997}. Darüberhinaus kann durch Zusatz von Glycerin und reduzierenden Agenzien wie \acs{DTT} die Aktivität zu einem Großteil erhalten bleiben \citep{Shirahashi1978}.
|
||||
Durch Sequenzanalyse und die Generierung chimärer \acs{PPDK}s konnten gezeigt werden, dass nur drei Aminosäurereste die Kältesensitivität stark beeinflussen. Es handelt sich hierbei um Pro790, Leu806 und Val873 in der \acs{PPDK} aus \textit{F. brownii} (\citet{Ohta1997}; vgl. auch Abbildung \ref{abb:ma}). \citet{Ohta1997} postulieren eine erhöhte Affinität der \acs{PPDK}"=Monomere zum zentralen \ce{Mg^{2+}}-Ion, sowie stärkere hydrophobe Wechselwirkungen zwischen den einzelnen Monomeren als Ursache der beobachteten Kältetoleranz durch die oben genannten Reste. Erstere Annahme wird dadurch gestützt, dass \acs{PPDK}s, welche diese Reste aufweisen gleichzeitig toleranter gegenüber einer Inaktivierung durch chelatierende Substanzen wie \acs{EDTA} sind \citep{Ohta1997}. Darüberhinaus kann durch Zusatz von Glycerin und reduzierenden Agenzien wie \acs{DTT} die Aktivität zu einem Großteil erhalten bleiben \citep{Shirahashi1978}.
|
||||
|
||||
\section{Zielsetzung}
|
||||
|
||||
Die \acs{PPDK} aus \textit{Zea mays} wurde bereits heterolog in \acs{E. coli} exprimiert \citep{Chastain1996,Nakanishi2003} und gereinigt. Ebenfalls etabliert ist ein photometrischer Aktivitätsassay über die \acs{PEP}-Carboxylase und die Malatdehydrogenase \citep{Jenkins1985,Salahas1990}.
|
||||
Die \acs{PPDK} aus \textit{Zea mays} wurde bereits heterolog in \acs{E. coli} exprimiert \citep{Chastain1996,Nakanishi2003} und gereinigt. Ebenfalls etabliert ist ein photometrischer Aktivitätstest über die \acs{PEP}-Carboxylase und die Malatdehydrogenase \citep{Jenkins1985,Salahas1990}.
|
||||
|
||||
Auf diesen Ergebnissen aufbauend war es Ziel dieser Arbeit, ein Expressions- und Reinigungsprotokoll für die \acs{PPDK} aus \acs{F. trinervia} zu etablieren, sowie nachzuweisen, dass das gereinigte Enzym funktionell gefalten ist. Darüber hinaus sollten Homologiemodelle erstellt werden, um im Vorfeld zukünftiger Experimente die Identifikation funktionell und strukturell bedeutender Reste zu ermöglichen.
|
||||
|
||||
|
|
@ -4,10 +4,7 @@
|
|||
\section{Klonierung}
|
||||
\label{sec:erg_klonierung}
|
||||
%
|
||||
Sie \acs{SLIC}-Klonierung erfolgte wie in \ref{sec:slic} beschrieben. Die mittels \acs{PCR} synthetisierten \textit{Inserts}
|
||||
(vgl.~\ref{sec:inserts_slic}), sowie der linearisierte Vektor (vgl.~\ref{sec:restriktionsverdau_dna}) wurden zur Reinigung auf ein
|
||||
Agarosegel aufgetragen (vgl. \ref{sec:agarose_gelelektrophorese}). Es ergab sich das in Abbildung \ref{abb:agarosegel_vektor_insert} gezeigte
|
||||
Auftrennungsmuster.
|
||||
Sie \acs{SLIC}-Klonierung erfolgte wie in \ref{sec:slic} beschrieben. Zur Erhöhung der Translationsgeschwindigkeit und somit der Expressionsrate lag die für die \acs{PPDK} kodierende \acs{DNA} Sequenz Codon optimiert für \acs{E. coli} vor \citep{Ikemura1981}. Die mittels \acs{PCR} synthetisierten \textit{Inserts} (vgl.~\ref{sec:inserts_slic}), sowie der linearisierte Vektor (vgl.~\ref{sec:restriktionsverdau_dna}) wurden zur Reinigung auf ein Agarosegel aufgetragen (vgl. \ref{sec:agarose_gelelektrophorese}). Es ergab sich das in Abbildung \ref{abb:agarosegel_vektor_insert} gezeigte Auftrennungsmuster.
|
||||
%
|
||||
\begin{figure}[htb]
|
||||
\centering
|
||||
|
|
@ -30,8 +27,8 @@ Auftrennungsmuster.
|
|||
\end{subfigure}
|
||||
\caption[Agarosegel zur Reinigung von Vektor und dem Insert]{Exemplarischer Ausschnitt aus dem Agarosegel zur Reinigung von
|
||||
linearisiertem Vektor (a) und dem Insert (b) zur SLIC-Klonierung.
|
||||
Aufgetragen wurden \SI{5}{\micro\liter} \SI{1}{\kb}-Größenstandard und
|
||||
je \SI{20}{\micro\liter} Probe. Die erwarteten Größen sind \SI{5720}{\bp} (Vektor)
|
||||
Aufgetragen wurden \SI{5}{\micro\liter} \SI{1}{\kb}-Größenstandard (M) und
|
||||
je \SI{20}{\micro\liter} Probe (V bzw. I). Die erwarteten Größen sind \SI{5720}{\bp} (Vektor)
|
||||
und \SI{2691}{\bp} (Insert).}
|
||||
\label{abb:agarosegel_vektor_insert}
|
||||
\end{figure}
|
||||
|
|
@ -45,7 +42,7 @@ das korrekte Insert trägt. Das enstsprechende Gelbild ist in Abbildung \ref{abb
|
|||
\centering
|
||||
\includegraphics[width=0.8\textwidth,keepaspectratio=true]{./img/ergebnisse/agarose_gele/colony_pcr.png}
|
||||
% colony_pcr.png: 1586x1474 pixel, 300dpi, 13.43x12.48 cm, bb=0 0 381 354
|
||||
\caption[Agarosegel nach Kolonie-PCR]{Agarosegel nach Kolonie-PCR. Es wurden \SI{5}{\micro\liter} \SI{1}{\kb}-Größenstandard und je \SI{20}{\micro\liter} Probe aufgetragen.
|
||||
\caption[Agarosegel nach Kolonie-PCR]{Agarosegel nach Kolonie-PCR. Es wurden \SI{5}{\micro\liter} \SI{1}{\kb}-Größenstandard (M) und je \SI{20}{\micro\liter} Probe aufgetragen.
|
||||
Untersucht wurden 24 Klone, von denen fünf (10, 13, 22, 23 und 24) ein Plasmid mit der korrekten Größe tragen.}
|
||||
\label{abb:kolonie_pcr}
|
||||
\end{figure}
|
||||
|
|
@ -58,7 +55,7 @@ aufgeführt.
|
|||
%
|
||||
\begin{figure}[htb]
|
||||
\centering
|
||||
\includegraphics[width=0.8\textwidth,keepaspectratio=true]{./img/ergebnisse/pETEV-16b-ppdk.pdf}
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/ergebnisse/pETEV-16b-ppdk.pdf}
|
||||
% pETEV-16b-ppdk.pdf: 611x480 pixel, 72dpi, 21.55x16.93 cm, bb=0 0 611 480
|
||||
\caption[Plasmidkarte von pETEV-16b-ppdk]{Plasmidkarte von pETEV-16b-ppdk. Der für die \acs{PPDK} kodierende Bereich liegt zwischen Position 5392 und 8022.
|
||||
\textit{Upstream} befinden sich die kodierenden Sequenzen für die \acs{TEV}-Schnittstelle und den Hexa-Histidin-Tag. Die Plasmidkarte wurde mit
|
||||
|
|
@ -66,6 +63,7 @@ aufgeführt.
|
|||
\label{abb:plasmidkarte}
|
||||
\end{figure}
|
||||
|
||||
\clearpage
|
||||
\section{Expressionsstudien}
|
||||
\label{sec:Expressionsstudien}
|
||||
Die Expressionsstudien (vgl. \ref{sec:expression_ecoli_studien}) zeigten eine deutliche Überexpression der \acs{PPDK} in \acs{E. coli} BL21 (DE3) bei einer Temperatur von \SI{30}{\celsius} und
|
||||
|
|
@ -84,9 +82,9 @@ gleichzeitig geringerer IPTG-Konzentration. Eine Expression über Nacht führte
|
|||
\label{abb:expressionsstudie}
|
||||
\end{figure}
|
||||
%
|
||||
\begin{figure}[htb]
|
||||
\begin{figure}[H]
|
||||
\centering
|
||||
\begin{subfigure}[b]{0.4\textwidth}
|
||||
\begin{subfigure}[b]{0.48\textwidth}
|
||||
\centering
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/ergebnisse/sds_gele/Expressionsstudie_19042012_klein.png}
|
||||
% Expressionsstudie_19042012_klein.png: 2480x2894 pixel, 241dpi, 26.13x30.49 cm, bb=0 0 741 864
|
||||
|
|
@ -96,7 +94,7 @@ gleichzeitig geringerer IPTG-Konzentration. Eine Expression über Nacht führte
|
|||
%
|
||||
~
|
||||
%
|
||||
\begin{subfigure}[b]{0.4\textwidth}
|
||||
\begin{subfigure}[b]{0.48\textwidth}
|
||||
\centering
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/ergebnisse/sds_gele/Expressionsstudie_19042012_klein_blot.png}
|
||||
% Expressionsstudie_19042012_klein_blot.png: 2480x2894 pixel, 241dpi, 26.13x30.49 cm, bb=0 0 741 864
|
||||
|
|
@ -108,6 +106,7 @@ gleichzeitig geringerer IPTG-Konzentration. Eine Expression über Nacht führte
|
|||
Expressionsergebnis in BL21 (DE3) bzw. BL21 Gold (DE3). Die Induktion erfolgte mit \SI{0,1}{\milli\Molar} bzw. \SI{1}{\milli\Molar} IPTG.}
|
||||
\label{abb:expressionsstudie_klein}
|
||||
\end{figure}
|
||||
\clearpage
|
||||
|
||||
\section{Differentielle Zentrifugation}
|
||||
\label{sec:ergebnisse_dz}
|
||||
|
|
@ -117,9 +116,9 @@ und einer differentiellen Zentrifugation unterzogen (vgl. \ref{sec:differentiell
|
|||
(Abbildung \ref{abb:dz}). Hierbei zeigte sich, dass der überwiegende Anteil der \acs{PPDK} in den Überstandsfraktionen lokalisiert und somit löslich ist.
|
||||
Nur ein geringer Anteil befindet sich in den Pellets nach der Zentrifugation.
|
||||
|
||||
\begin{figure}[htb]
|
||||
\begin{figure}[H]
|
||||
\centering
|
||||
\begin{subfigure}[b]{0.4\textwidth}
|
||||
\begin{subfigure}[b]{0.48\textwidth}
|
||||
\centering
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/ergebnisse/sds_gele/03052012_4h_2min.png}
|
||||
% 03052012_4h_2min.png: 2480x2254 pixel, 300dpi, 21.00x19.08 cm, bb=0 0 595 541
|
||||
|
|
@ -129,7 +128,7 @@ Nur ein geringer Anteil befindet sich in den Pellets nach der Zentrifugation.
|
|||
%
|
||||
~
|
||||
%
|
||||
\begin{subfigure}[b]{0.4\textwidth}
|
||||
\begin{subfigure}[b]{0.48\textwidth}
|
||||
\centering
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/ergebnisse/sds_gele/03052012_üN_2min.png}
|
||||
% 03052012_üN_2min.png: 2480x2141 pixel, 300dpi, 21.00x18.13 cm, bb=0 0 595 514
|
||||
|
|
@ -141,27 +140,24 @@ Nur ein geringer Anteil befindet sich in den Pellets nach der Zentrifugation.
|
|||
Zentrifugationsschritte (jeweils \SI{10}{\micro\liter}).}
|
||||
\label{abb:dz}
|
||||
\end{figure}
|
||||
\clearpage
|
||||
|
||||
\section{Native Reinigung der \acs{PPDK}}
|
||||
\label{sec:ergebnisse_reinigung}
|
||||
|
||||
Die Reinigung der \acs{PPDK} erfolgte wie in \ref{sec:affinitaetschromatographie} beschrieben. Im Verlauf der Reinigung konnten vier Proteinfraktionen bei Elution
|
||||
mit \SIlist{50;150;200;250}{\milli\Molar} Imidazol identifiziert werden (vgl. Abbildung \ref{abb:chromatogramm_aff}). In einer nachfolgend durchgeführten
|
||||
\acs{SDS}-\acs{PAGE} mit Westernblot zeigte sich, dass drei Fraktionen (\SIlist{150;200;250}{\milli\Molar}) \acs{PPDK} in hoher Reinheit enthielten.
|
||||
\acs{SDS}-\acs{PAGE} mit Westernblot zeigte sich, dass drei Fraktionen (\SIlist{150;200;250}{\milli\Molar}) \acs{PPDK} in hoher Reinheit enthielten (Abbildung \ref{abb:reinigung_sds}).
|
||||
%
|
||||
\begin{figure}[htb]
|
||||
\begin{figure}[H]
|
||||
\centering
|
||||
\includegraphics[width=0.9\textwidth,keepaspectratio=true]{img/ergebnisse/aekta/20062012.eps}
|
||||
\caption[Chromatogramm der \acs{PPDK}-Reinigung mittels \acs{IMAC}]{Chromatogramm der \acs{PPDK}-Reinigung mittels \acs{IMAC}. Dargestellt sind die Absorption bei
|
||||
\SI{280}{\nano\meter} (blau) und die Imidazolkonzentration (rot). Die gesammelten \acs{PPDK}-Fraktionen sind durch Pfeile markiert.}
|
||||
\SI{280}{\nano\meter} (schwarz) und die Imidazolkonzentration (rot). Die gesammelten \acs{PPDK}-Fraktionen sind durch Pfeile markiert.}
|
||||
\label{abb:chromatogramm_aff}
|
||||
\end{figure}
|
||||
%
|
||||
Die gesammelte PPDK-Fraktionen bei Elution mit \SI{250}{\milli\Molar} Imidazol ließ sich bis auf \SI{37,54(134)}{\milli\gram\per\milli\liter} konzentrieren.
|
||||
In der Expression konnten aus \SI{2}{\liter} Kultur \SI{20}{\gram} Zellen geerntet werden. Da im Zuge der Reinigung \SI{4}{\gram} Zellen aufgeschlossen wurden, ergibt sich eine Ausbeute von etwa
|
||||
\SI{47}{\milli\gram\per\liter}~Kultur (vgl. Tabelle \ref{tab:ausbeute}).
|
||||
%
|
||||
\begin{table}[htb]
|
||||
\begin{table}[H]
|
||||
\centering
|
||||
\caption[\acs{PPDK}-Konzentration und Ausbeute nach Reinigung]{\acs{PPDK}-Konzentration und Ausbeute nach Reinigung. Die Konzentrationen beziehen sich auf den erreichten
|
||||
Wert nach Einengen der fraglichen Fraktionen auf ein Volumen von \SI{500}{\micro\liter}.}
|
||||
|
|
@ -177,9 +173,13 @@ Wert nach Einengen der fraglichen Fraktionen auf ein Volumen von \SI{500}{\micro
|
|||
\end{tabular}
|
||||
\end{table}
|
||||
%
|
||||
\begin{figure}[htb]
|
||||
Die gesammelte PPDK-Fraktionen bei Elution mit \SI{250}{\milli\Molar} Imidazol ließ sich bis auf \SI[seperr]{37,54(134)}{\milli\gram\per\milli\liter} konzentrieren.
|
||||
In der Expression konnten aus \SI{2}{\liter} Kultur \SI{20}{\gram} Zellen geerntet werden. Da im Zuge der Reinigung \SI{4}{\gram} Zellen aufgeschlossen wurden, ergibt sich eine Ausbeute von etwa
|
||||
\SI{47}{\milli\gram\per\liter}~Kultur (vgl. Tabelle \ref{tab:ausbeute}).
|
||||
|
||||
\begin{figure}[H]
|
||||
\centering
|
||||
\begin{subfigure}[b]{0.4\textwidth}
|
||||
\begin{subfigure}[b]{0.48\textwidth}
|
||||
\centering
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/ergebnisse/sds_gele/Reinigung_02072012.png}
|
||||
% Reinigung_02072012.png: 2480x2338 pixel, 300dpi, 21.00x19.80 cm, bb=0 0 595 561
|
||||
|
|
@ -189,7 +189,7 @@ Wert nach Einengen der fraglichen Fraktionen auf ein Volumen von \SI{500}{\micro
|
|||
%
|
||||
~
|
||||
%
|
||||
\begin{subfigure}[b]{0.4\textwidth}
|
||||
\begin{subfigure}[b]{0.48\textwidth}
|
||||
\centering
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/ergebnisse/sds_gele/Reinigung_02072012_blot.png}
|
||||
% Reinigung_02072012.png: 2480x2338 pixel, 300dpi, 21.00x19.80 cm, bb=0 0 595 561
|
||||
|
|
@ -198,44 +198,43 @@ Wert nach Einengen der fraglichen Fraktionen auf ein Volumen von \SI{500}{\micro
|
|||
\end{subfigure}
|
||||
\caption[\acs{SDS}-\acs{PAGE} und Westernblot der nativen Reinigung]{\acs{SDS}-\acs{PAGE} (a) und Westernblot (b) der nativen Reinigung. Aufgetragen wurden \SI{3}{\micro\liter} Marker (M), \SI{1}{\micro\liter}
|
||||
der Proben des Zelllysates (A), sowie der Zentrifugationen bei \SI{10000}{\xg} (10kÜ) bzw \SI{100000}{\xg} und \SI{10}{\micro\liter} des Durchflusses (D) und nachfolgenden Elutionsfraktionen.
|
||||
Die \acs{PPDK}-Banden sind rot hervorgehoben (MW: \SI{98}{\kilo\dalton})}
|
||||
Die \acs{PPDK}-Banden sind rot hervorgehoben (MW: \SI{98}{\kilo\dalton}). Beim Westernblot wurden Anti"=His"=HRP"=Antikörper in einer Verdünnung von 1:10000 verwendet.}
|
||||
\label{abb:reinigung_sds}
|
||||
\end{figure}
|
||||
%
|
||||
\begin{figure}[H]
|
||||
\centering
|
||||
\includegraphics[width=0.87\textwidth,keepaspectratio=true]{./img/ergebnisse/aekta/11072012.eps}
|
||||
% 11072012.eps: 0x0 pixel, 300dpi, 0.00x0.00 cm, bb=5 4 461 375
|
||||
\caption[Chromatogramm der Größenausschlusschromatographie]{Chromatogramm der Größenausschlusschromatographie. Die Kurvenverläufe wurden auf die jeweilige Konzentration normalisiert. Fraktion 3 zeigt ein monodisperses Profil,
|
||||
während die \acs{PPDK} in den Fraktionen 1 und 2 in verschiedenen Oligomerisierungszuständen vorliegt. Vertikale Linien markieren die Position der \textit{Peaks}. Es wurde eine Superdex 200 5/150 GL"=Säule mit einem Volumen von \SI{3}{\milli\liter} eingesetzt.}
|
||||
\label{abb:chromatogramm_gefi}
|
||||
\end{figure}
|
||||
%
|
||||
Zur Bestimmung der Dispersität der gereinigten \acs{PPDK} wurden Proben aller drei Fraktionen mittels einer Größenausschlusschromatographie (vgl. \ref{sec:groessenausschluss}) analysiert.
|
||||
Hierbei zeigte sich, dass lediglich die mit \SI{250}{\milli\Molar} Imidazol eluierte Fraktion monodispers ist, während die mit \SIlist{150;200}{\milli\Molar} eluierten
|
||||
\acs{PPDK}-Fraktionen einen diversen Oligomerisierungsgrad aufwiesen (vgl. Abbildung \ref{abb:chromatogramm_gefi}).
|
||||
|
||||
\begin{figure}[htb]
|
||||
\centering
|
||||
\includegraphics[width=0.8\textwidth,keepaspectratio=true]{./img/ergebnisse/aekta/11072012.eps}
|
||||
% 11072012.eps: 0x0 pixel, 300dpi, 0.00x0.00 cm, bb=5 4 461 375
|
||||
\caption[Chromatogramm der Größenausschlusschromatographie]{Chromatogramm der Größenausschlusschromatographie. Die Kurvenverläufe wurden auf die jeweilige Konzentration normalisiert. Fraktion 3 zeigt ein monodisperses Profil,
|
||||
während die \acs{PPDK} in den Fraktionen 1 und 2 in verschiedenen Oligomerisierungszuständen vorliegt. Vertikale Linien markieren die Position der \textit{Peaks}.}
|
||||
\label{abb:chromatogramm_gefi}
|
||||
\end{figure}
|
||||
\clearpage
|
||||
\acs{PPDK}-Fraktionen in multiplen Oligomerisierungsgraden vorlagen (vgl. Abbildung \ref{abb:chromatogramm_gefi}). Da einige der eingesetzten Eichproteine im verwendeten Puffer nicht stabil waren, konnte eine zuverlässige Größenzuordnung nicht vorgenommen werden. Somit können lediglich die \acs{PPDK}-Eluate untereinander verglichen werden. Deutlich zu erkennen sind aber insgesamt drei distinkte \textit{Peaks} bei einem Elutionsvolumen von \SIlist{1,28;1,68;1,97}{\milli\liter}. Das Ausschlussvolumen der Säule beträgt \SI{1,2}{\milli\liter}.
|
||||
|
||||
\section{\acs{CD}-Spektroskopie}
|
||||
\label{sec:ergebnisse_cd}
|
||||
Das \acs{CD}-Spektrum wurde wie in \ref{sec:cd_spektroskopie} beschrieben aufgenommen. Abbildung \ref{abb:cd_spektrum} zeigt das Spektrum nach Abzug des Pufferspektrums. Deutlich zu erkennen ist
|
||||
Das \acs{CD}-Spektrum wurde wie in \ref{sec:cd_spektroskopie} beschrieben aufgenommen. Abbildung \ref{abb:cd_spektrum} zeigt das Spektrum nach Pufferkorrektur. Deutlich zu erkennen ist
|
||||
ein negativer Cotton-Effekt im Bereich um \SI{210}{\nano\meter}, welcher auf \textalpha-helikale Strukturen hindeutet.
|
||||
Anhand des experimentellen Spektrums wurde eine Sekundärstrukturanalyse mit den Programmen SELCON3 \citep{Sreerama1993}, CONTINLL \citep{Provencher1981}, CDSSTR \citep{Johnson1999} und K2D3 \citep{Louis-Jeune2011} durchgeführt.
|
||||
Die daraus resultierenden, vorhergesagten Spektren sind ebenfalls in Abbildung \ref{abb:cd_spektrum} dargestellt. Alle verwendeten Algorithmen sagen das Spektrum qualitativ
|
||||
korrekt vorher, die geringsten Abweichungen vom experimentellen Spektrum ergeben sich für CONTINLL und CDSSTR. Für die \acs{PPDK} werden in allen Fällen hohe \textalpha"=helikale
|
||||
Strukturanteile vorhergesagt, im Fall von CONTINLL jedoch nur ein sehr geringer Anteil an \textbeta"=Strands (vgl. Tabelle \ref{tab:cd}). Die \textit{ab initio} Vorhersage mit SOPMA,
|
||||
sowie die Ergebnisse von K2D3 und CDSSTR sind weitestgehend deckungsgleich mit den Strukturanteilen der PPDK aus \textit{Zea mays} (Tabelle \ref{tab:cd}).
|
||||
\begin{figure}[htb]
|
||||
%
|
||||
\begin{figure}[H]
|
||||
\centering
|
||||
\includegraphics[width=0.8\textwidth,keepaspectratio=true]{./img/ergebnisse/cd/cd.eps}
|
||||
\includegraphics[width=0.9\textwidth,keepaspectratio=true]{./img/ergebnisse/cd/cd.eps}
|
||||
% cd.eps: 0x0 pixel, 300dpi, 0.00x0.00 cm, bb=2 4 468 375
|
||||
\caption[\acs{CD}-Spektrum von gereinigter PPDK]{\acs{CD}-Spektrum von gereinigter PPDK. Die \acs{PPDK} lag in einer Konzentration von \SI{0,1}{\milli\gram\per\milli\liter} in \SI{50}{\milli\Molar} Kaliumphosphat"=Puffer mit
|
||||
\SI{10}{\milli\Molar} Magnesiumsulfat vor. Es wurden 15 Spektren mit einer Auflösung von \SI{1}{\nano\meter} akkumuliert. Im Bereich um \SI{210}{\nano\meter} zeigt sich ein negativer
|
||||
Cotton-Effekt, welcher charakteristisch für \textalpha-helikale Strukturanteile ist. Farbig dargestellt sind die mit unterschiedlichen Programmen vorhergesagten Spektren.}
|
||||
\label{abb:cd_spektrum}
|
||||
\end{figure}
|
||||
|
||||
\begin{table}[htb]
|
||||
%
|
||||
\clearpage
|
||||
Die daraus resultierenden, vorhergesagten Spektren sind ebenfalls in Abbildung \ref{abb:cd_spektrum} dargestellt. Alle verwendeten Algorithmen sagen das Spektrum qualitativ korrekt vorher, die geringsten Abweichungen vom experimentellen Spektrum ergeben sich für CONTINLL und CDSSTR, wobei ersteres allerdings die geringste Übereinstimmung mit den Sekundärstrukturanteilen aus der \textit{ab initio} Vorhersage und den Strukturdaten aus \textit{Zea mays} zeigt. Für die \acs{PPDK} werden in allen Fällen hohe \textalpha"=helikale Strukturanteile vorhergesagt, im Fall von CONTINLL jedoch nur ein sehr geringer Anteil an \textbeta"=Strands (vgl. Tabelle \ref{tab:cd}). Die \textit{ab initio} Vorhersage mit SOPMA, sowie die Ergebnisse von K2D3 und CDSSTR sind weitestgehend deckungsgleich mit den Strukturanteilen der PPDK aus \textit{Zea mays} (Tabelle \ref{tab:cd}).
|
||||
%
|
||||
\begin{table}[H]
|
||||
\caption[Vorhersage der Sekundärstrukturanteile]{Vorhersage der Sekundärstrukturanteile. Aufgeführt sind die vorhergesagten Strukturelemente anhand des \acs{CD}-Spektrums. Zum Vergleich dienen die Ergebnisse der sequenzbasierten \textit{ab initio} Vorhersage (SOPMA),
|
||||
sowie die Sekundärstrukturanteile aus der Kristallstruktur der \acs{PPDK} aus \textit{Zea mays} (PDB: 1VBG).}
|
||||
\label{tab:cd}
|
||||
|
|
@ -254,12 +253,38 @@ sowie die Ergebnisse von K2D3 und CDSSTR sind weitestgehend deckungsgleich mit d
|
|||
\bottomrule
|
||||
\end{tabular}
|
||||
\end{table}
|
||||
\clearpage
|
||||
|
||||
\section{Aktivitätsassay}
|
||||
\section{Aktivitätstest}
|
||||
\label{sec:ergebnisse_aktivitaetsassay}
|
||||
Um die Aktivität der gereinigten PPDK zu quantifizieren, wurden zunächst die beiden Fraktionen mit der höchsten \acs{PPDK}-Konzentration -- Fraktion 2 und
|
||||
Fraktion 3 (\SIlist{200;250}{\milli\Molar} Imidazol) -- untersucht (vgl. \ref{sec:aktivitaetsassay}). Hierbei zeigte sich im Vergleich zur Negativkontrolle,
|
||||
dass in beiden Fraktionen eine Aktivität zu verzeichnen ist (siehe Abbildung \ref{abb:aktivitaet}). Da hinsichtlich zukünftiger Kristallisationsexperimente
|
||||
Um die Aktivität der gereinigten PPDK zu quantifizieren, wurden zunächst die beiden Fraktionen mit der höchsten \acs{PPDK}-Konzentration -- Fraktion~2 und Fraktion~3 (\SIlist{200;250}{\milli\Molar} Imidazol) -- untersucht (vgl. \ref{sec:aktivitaetsassay}). Hierbei zeigte sich im Vergleich zur Negativkontrolle,
|
||||
dass in beiden Fraktionen eine Aktivität zu verzeichnen ist (siehe Tabelle \ref{tab:aktivitaet}).
|
||||
\begin{table}[H]
|
||||
\centering
|
||||
\caption[Aktivität der gereinigten PPDK-Fraktionen]{Aktivität der gereinigten PPDK-Fraktionen 2 und 3. Die Absorption bei \SI{340}{\nano\meter} wurde über einen Zeitraum von \SI{80}{\second} in Dreifachbestimmung aufgenommen. Anschließend wurde eine Tangente an die Messpunkte gelegt um die Reaktionsgeschwindigkeit zu bestimmen. Der Vergleich der Negativkontrolle mit den beiden vermessenen Fraktionen zeigt eine deutliche Aktivität.}
|
||||
\label{tab:aktivitaet}
|
||||
\begin{tabular}{cS[seperr,table-format = 1.4(2)]S[seperr,table-format = 1.2(2)]}
|
||||
\toprule
|
||||
\textbf{Fraktion} & \textbf{Aktivität [\si{\micro\mole\per\minute}]} &\textbf{spez. Aktivität [\si{\Unit\per\milli\gram}]}\\
|
||||
\midrule
|
||||
Negativkontrolle & 0,0005(1) & \\
|
||||
2 (\SI{200}{\milli\Molar} Imidazol) & 0,065(24) & 0,31(12) \\
|
||||
3 (\SI{250}{\milli\Molar} Imidazol) & 0,037(6) & 0,99(9) \\
|
||||
\bottomrule
|
||||
\end{tabular}
|
||||
|
||||
\end{table}
|
||||
|
||||
% \begin{figure}[H]
|
||||
% \centering
|
||||
% \includegraphics[width=0.7\textwidth,keepaspectratio=true]{./img/ergebnisse/kinetik/aktivitaet.eps}
|
||||
% % aktivitaet.eps: 0x0 pixel, 300dpi, 0.00x0.00 cm, bb=6 4 466 375
|
||||
% \caption[Aktivität der gereinigten PPDK]{Aktivität der gereinigten PPDK. Die Absorption bei \SI{340}{\nano\meter} wurde über einen Zeitraum von \SI{80}{\second}
|
||||
% aufgenommen und auf die jeweilige PPDK-Konzentration, sowie das absolute Absorptionsmaximum normiert. Die Kontrolle enthielt anstelle der PPDK ein identisches
|
||||
% Volumen Puffer. Die beiden PPDK-Fraktionen weisen eine deutliche Absorptionsabnahme auf, während die Absorption der Kontrolle nahezu unverändert bleibt.}
|
||||
% \label{abb:aktivitaet}
|
||||
% \end{figure}
|
||||
Da hinsichtlich zukünftiger Kristallisationsexperimente
|
||||
in erster Linie die monodispers vorliegende Fraktion 3 von Interesse ist, wurde von dieser Fraktion eine vollständige Reaktionskinetik aufgenommen. Hierbei ergaben
|
||||
sich durch Anpassen einer Sättigungsfunktion durch nichtlineare Regression an die Michaelis"=Menten"=Gleichung \eqref{eq:mm} für \acs{ATP} und Pyruvat ein \ce{K_M} von
|
||||
\SI[seperr]{50(9)}{\micro\Molar} bzw. \SI[seperr]{270(44)}{\micro\Molar}, sowie ein \ce{V_{max}} von \SI[seperr]{0,095(5)}{\milli\Molar\per\minute} (ATP)
|
||||
|
|
@ -269,7 +294,15 @@ sich durch Anpassen einer Sättigungsfunktion durch nichtlineare Regression an d
|
|||
\label{eq:mm}
|
||||
v &= \frac{V_\text{max} \cdot [S]}{K_m + [S]}
|
||||
\end{align}
|
||||
|
||||
%
|
||||
\begin{figure}[H]
|
||||
\centering
|
||||
\includegraphics[width=0.7\textwidth,keepaspectratio=true]{./img/ergebnisse/kinetik/kinetik_combined.eps}
|
||||
\caption[Reaktionskinetik der \acs{PPDK}]{Reaktionskinetik der \acs{PPDK} mit \acs{ATP} (A) und Pyruvat (B) als Substrat. Der inhibierende Effekt von \acs{ATP} auf die im gekoppelten Enzymassay eingesetzte \acs{MDH} ist in (A) ersichtlich. Die Ordinatenachse ist der besseren Übersichtlichkeit wegen logarithmisch skaliert.}
|
||||
\label{abb:kinetik}
|
||||
\end{figure}
|
||||
%
|
||||
\begin{samepage}
|
||||
Die Wechselzahl \ce{k_{cat}} wurde anhand von Gleichung \eqref{eq:kcat} aus \ce{V_{max}} und der PPDK-Konzentration von \SI[seperr]{0,38(2)}{\milli\Molar} mit
|
||||
\SI[seperr]{1,63(9)}{\per\second} bestimmt. Die spezifische Aktivität der \acs{PPDK} beträgt \SI[seperr]{0,99(9)}{\Unit\per\milli\gram} und konnte ebenfalls unter Berücksichtigung der
|
||||
Proteinkonzentration mittels Gleichung \ref{eq:spez_akt} berechnet werden.
|
||||
|
|
@ -278,13 +311,13 @@ Proteinkonzentration mittels Gleichung \ref{eq:spez_akt} berechnet werden.
|
|||
\label{eq:kcat}
|
||||
k_\text{cat} &= \frac{V_\text{max}}{[E_0]}
|
||||
\end{align}
|
||||
\end{samepage}
|
||||
|
||||
Die katalytische Effizient {\ce{k_{cat}}/\ce{K_M}} beträgt \SI[seperr]{32,60(936)}{\milli\Molar\second} (ATP) bzw.
|
||||
\SI[seperr]{6,04(154)}{\milli\Molar\second} (Pyruvat). Eine Auflistung der kinetischen Parameter ist in Tabelle \ref{tab:kinetische_parameter} zu finden.
|
||||
Die katalytische Effizienz {\ce{k_{cat}}/\ce{K_M}} beträgt \SI[seperr]{32,60(936)}{\per\second\per\milli\Molar} (ATP) bzw.\\ \SI[seperr]{6,04(154)}{\per\second\per\milli\Molar} (Pyruvat). Eine Auflistung der kinetischen Parameter ist in Tabelle \ref{tab:kinetische_parameter} zu finden.
|
||||
%
|
||||
\begin{align}
|
||||
\label{eq:spez_akt}
|
||||
\text{spez. Aktivität \si{\Unit\per\milli\gram}} &= \frac{V_\text{max}~[\si{\micro\Molar\per\minute}] \cdot V(\text{Ansatz})~[\si{\liter}]}{m(\text{Protein})~[\si{\milli\gram}]}
|
||||
\text{spez. Aktivität [\si{\Unit\per\milli\gram}]} &= \frac{V_\text{max}~[\si{\micro\Molar\per\minute}] \cdot V(\text{Ansatz})~[\si{\liter}]}{m(\text{Protein})~[\si{\milli\gram}]}
|
||||
\end{align}
|
||||
|
||||
\begin{table}[htb]
|
||||
|
|
@ -301,80 +334,51 @@ Die katalytische Effizient {\ce{k_{cat}}/\ce{K_M}} beträgt \SI[seperr]{32,60(93
|
|||
\ce{K_m} (ATP) & 50(9) & \micro\Molar \\
|
||||
\ce{K_m} (Pyruvat) & 270(44) & \micro\Molar \\
|
||||
\midrule
|
||||
\ce{k_{cat}}/\ce{K_M} (ATP) & 32,60(936)& \milli\Molar\second \\
|
||||
\ce{k_{cat}}/\ce{K_M} (Pyruvat) & 6,04(154) & \milli\Molar\second \\
|
||||
\ce{k_{cat}}/\ce{K_M} (ATP) & 32,60(936)& \per\second\per\milli\Molar \\
|
||||
\ce{k_{cat}}/\ce{K_M} (Pyruvat) & 6,04(154) & \per\second\per\milli\Molar \\
|
||||
\midrule
|
||||
spez. Aktivität & 0,99(9) & \Unit\per\milli\gram \\
|
||||
\bottomrule
|
||||
\end{tabular}
|
||||
\end{table}
|
||||
|
||||
|
||||
\begin{figure}[htb]
|
||||
\centering
|
||||
\includegraphics[width=0.7\textwidth,keepaspectratio=true]{./img/ergebnisse/kinetik/aktivitaet.eps}
|
||||
% aktivitaet.eps: 0x0 pixel, 300dpi, 0.00x0.00 cm, bb=6 4 466 375
|
||||
\caption[Aktivität der gereinigten PPDK]{Aktivität der gereinigten PPDK. Die Absorption bei \SI{340}{\nano\meter} wurde über einen Zeitraum von \SI{80}{\second}
|
||||
aufgenommen und auf die jeweilige PPDK-Konzentration, sowie das absolute Absorptionsmaximum normiert. Die Kontrolle enthielt anstelle der PPDK ein identisches
|
||||
Volumen Puffer. Die beiden PPDK-Fraktionen weisen eine deutliche Absorptionsabnahme auf, während die Absorption der Kontrolle nahezu unverändert bleibt.}
|
||||
\label{abb:aktivitaet}
|
||||
\end{figure}
|
||||
|
||||
\begin{figure}[htb]
|
||||
\centering
|
||||
\begin{subfigure}[b]{0.45\textwidth}
|
||||
\centering
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/ergebnisse/kinetik/atp.eps}
|
||||
% atp.eps: 0x0 pixel, 300dpi, 0.00x0.00 cm, bb=2 4 467 375
|
||||
\caption{}
|
||||
\label{abb:kinetik_atp}
|
||||
\end{subfigure}
|
||||
%
|
||||
~
|
||||
%
|
||||
\begin{subfigure}[b]{0.45\textwidth}
|
||||
\centering
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/ergebnisse/kinetik/pyruvat.eps}
|
||||
% pyruvat.eps: 0x0 pixel, 300dpi, 0.00x0.00 cm, bb=2 3 467 375
|
||||
\caption{}
|
||||
\label{abb:kinetik_pyruvat}
|
||||
\end{subfigure}
|
||||
\caption[Reaktionskinetik der \acs{PPDK}]{Reaktionskinetik der \acs{PPDK} mit \acs{ATP} (a) und Pyruvat (b) als Substrat. Der inhibierende Effekt von \acs{ATP} auf
|
||||
die im gekoppelten Enzymassay eingesetzte \acs{MDH} ist in (a) ersichtlich. Die Ordinatenachse ist der besseren Übersichtlichkeit wegen logarithmisch skaliert.}
|
||||
\label{abb:kinetik}
|
||||
\end{figure}
|
||||
|
||||
\clearpage
|
||||
|
||||
\section{Homologiemodelle}
|
||||
\label{sec:ergebnisse_homologemodell}
|
||||
Die erzeugten Homologiemodelle (vgl. \ref{sec:erstellung_homologiemodell}) der \acs{PPDK} aus \acs{F. trinervia} zeigen eine gute Übereinstimmung mit
|
||||
den zu Grunde liegenden Templat-Strukturen: \SI{0,708}{\angstrom} für das auf der Struktur aus \acs{C. symbiosum} und \SI{0,705}{\angstrom} für das auf der Struktur aus
|
||||
\textit{Zea mays} basierende Modell. Die Sequenzidentität zur zwischen \acs{F. trinervia} und \textit{Zea mays} beträgt \SI{79}{\percent}, zwischen \acs{F. trinervia} und
|
||||
\acs{C. symbiosum} \SI{55}{\percent}. Das jeweils beste Modell wurde anhand des zDOPE Wertes, sowie der Ergebnisse der PROCHECK-Analyse ausgewählt. Im Ramachandran-Plot
|
||||
zeigt keines der beiden ausgewählten Modelle eine Kombination von ψ- und φ-Winkel, die nicht in einem der erlaubten Bereiche liegt (vgl. Abbildungen \ref{abb:ramachandran_Zm}
|
||||
Die erzeugten Homologiemodelle (vgl. \ref{sec:erstellung_homologiemodell}) der \acs{PPDK} aus \acs{F. trinervia} zeigen eine gute Übereinstimmung mit den zu Grunde liegenden Templat-Strukturen: Es ergab sich ein \acs{RMSD} von \SI{0,708}{\angstrom} für das auf der Struktur aus \acs{C. symbiosum} und \SI{0,705}{\angstrom} für das auf der Struktur aus \textit{Zea mays} basierende Modell. Die Sequenzidentität zur zwischen \acs{F. trinervia} und \textit{Zea mays} beträgt \SI{79}{\percent}, zwischen \acs{F. trinervia} und \acs{C. symbiosum} \SI{55}{\percent}. Das jeweils beste Modell wurde anhand des zDOPE Wertes \citep{Shen2006,Pieper2011}, sowie der Ergebnisse der PROCHECK-Analyse ausgewählt. Der \ac{DOPE} Wert stellt ein statistisch ermitteltes Potential dar, welches die paarweisen atomaren Abstände innerhalb eines Modells im Vergleich zu einer definierten Menge bekannter Proteinstrukturen beurteilt.
|
||||
|
||||
In der normalisierten Variante (zDOPE) stehen Werte gleich oder kleiner als -1,0 für ein sehr exaktes Modell, bei dem sich mehr als \SI{80}{\percent} der \ce{C_α}"=Atome innerhalb eines Abstands von \SI{3,5}{\angstrom} zu ihrer korrekten Position befinden \citep{Lasker2012}. Der zDOPE für das auf \textit{Zea mays} basierende Modell beträgt -0,92803, für das auf \acs{C. symbiosum} basierende Modell -0,92815. Da das Templat Strukturen aufweisen kann, welche nicht in der verwendeten Vergleichsmenge bekannter Strukturen vorhanden ist, kann der zDOPE-Wert hierdurch fälschlich erhöht werden. Daher können die DOPE-Werte je Aminosäurerest für das Templat und das Homologiemodell verglichen werden. Eine vergleichende Darstellung der DOPE-Profile der im Rahmen dieser Arbeit generierten Modelle findet sich in Abbildung \ref{abb:dope}. Die Profile weisen einen qualitativ ähnlichen Verlauf auf, was für die Korrektheit der erstellen Modelle spricht. Allerdings zeigt sich in beiden Fällen ein zunehmender Versatz der Kurvenverläufe, was auf eine Verschiebung des Alignments in den entsprechenden Sequenzabschnitten hindeuten kann.
|
||||
%
|
||||
\begin{figure}[H]
|
||||
\centering
|
||||
\includegraphics[width=0.7\textwidth,keepaspectratio=true]{./img/ergebnisse/homologiemodell/DOPE_combined.eps}
|
||||
\caption[\acs{DOPE}-Profile der Homologiemodelle und ihrer Template]{\acs{DOPE}-Profile der von \textit{Zea mays} (A) bzw \acs{C. symbiosum} (B) abgeleiteten Homologiemodelle und ihrer Template je Position im Alignment. Der Verlauf ist in beiden Fällen für das Modell und das Templat ähnlich, was auf eine gute Qualität der Homologiemodelle schließen lässt. Allerdings zeigen sich Verschiebungen der Profile um einige Reste, was auf einen Versatz des Alignments hindeuten kann.}
|
||||
\label{abb:dope}
|
||||
\end{figure}
|
||||
%
|
||||
Im Ramachandran-Plot zeigt keines der beiden ausgewählten Modelle eine Kombination von ψ- und φ-Winkel, die nicht in einem der erlaubten Bereiche liegt (vgl. Abbildungen \ref{abb:ramachandran_Zm}
|
||||
und \ref{abb:ramachandran_Cs}).
|
||||
|
||||
Anhand der Modelle wurde eine Visualisierung des \textit{Domain-Swiveling} Mechanismus für die \acs{PPDK} aus \acs{F. trinervia} (Abbildung \ref{abb:overlay_homologiemodell}), sowie
|
||||
der \acs{PEP}-Bindestelle (Abbildung \ref{abb:substratbindetasche}) erstellt. Es zeigt sich eine deutliche Torsion der zentralen Phospo-Histidindomäne und des katalytischen
|
||||
His458.
|
||||
der \acs{PEP}-Bindestelle (Abbildung \ref{abb:substratbindetasche}) erstellt. Es zeigt sich eine deutliche Torsion der zentralen Phospo-Histidindomäne und des katalytischen His458.
|
||||
%
|
||||
\begin{figure}[htb]
|
||||
\centering
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/ergebnisse/homologiemodell/swiveling_domain2.png}
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/ergebnisse/homologiemodell/swiveling_domain3.png}
|
||||
% swiveling_domain2.png: 2480x976 pixel, 119dpi, 53.13x20.91 cm, bb=0 0 1506 593
|
||||
\caption[Homologiemodelle der \acs{PPDK}]{Homologiemodelle der \acs{PPDK} aus \acs{F. trinervia}. (A) zeigt die \acs{PEP} gebundene Konformation basierend auf der Struktur aus
|
||||
\textit{Zea mays}, (B) das auf \acs{C. symbiosum} basierende Modell. Beide Modelle stellen die jeweiligen Extremkonformationen des \textit{Swiveling-domain} Mechanismus dar. Das
|
||||
an der Übertragung der Phosphatgruppe beteiligte His458 ist als Stabmodell rot eingefärbt und durch einen schwarzen Pfeil markiert. Die einzelnen Domänen der \acs{PPDK} sind ebenfalls
|
||||
farblich hervorgehoben: Nukleotidbindedomäne (grün), Pyruvat/PEP-Bindedomäne (blau), Phosphohistidin-Domäne (gelb), Linker-Peptide (magenta und rot).}
|
||||
\caption[Homologiemodelle der \acs{PPDK}]{Homologiemodelle der \acs{PPDK} aus \acs{F. trinervia}. Es zeigt die \acs{PEP} gebundene Konformation basierend auf der Struktur aus
|
||||
\textit{Zea mays}, sowie das auf \acs{C. symbiosum} basierende Modell (transparent, grau). Beide Modelle stellen die jeweiligen Extremkonformationen des \textit{Swiveling-domain} Mechanismus dar. Das
|
||||
an der Übertragung der Phosphatgruppe beteiligte His458 ist als Stabmodell rot eingefärbt und durch einen Stern markiert. Die einzelnen Domänen der \acs{PPDK} sind farblich hervorgehoben: Nukleotidbindedomäne (grün), Pyruvat/PEP-Bindedomäne (blau), Phosphohistidin-Domäne (gelb), Linker-Peptide (magenta und rot).}
|
||||
\label{abb:overlay_homologiemodell}
|
||||
\end{figure}
|
||||
|
||||
In der Darstellung der modellierten Substratbindestelle sind die für die Koordination von \acs{PEP} wichtigen Reste Arg562, Arg619, Arg669, Glu748, Asp772 und
|
||||
Asn771 sichtbar. Ebenfalls erkennbar ist das als Protonen-Donor fungierende Cys834. Die genannten Reste befinden sich in hoch konservierten Bereichen (siehe Abbildung \ref{abb:ma}).
|
||||
Asn771 sichtbar. Ebenfalls erkennbar ist das Cys834, welches als Protonendonor/"=akzeptor zusammen mit Ser767 an der Enolisierung des Pyruvats beteiligt ist \citep{Yankie1995}. Die genannten Reste befinden sich in hoch konservierten Bereichen (Abbildung \ref{abb:ma}).
|
||||
%
|
||||
\begin{figure}[htb]
|
||||
\centering
|
||||
\includegraphics[width=0.8\textwidth,keepaspectratio=true]{./img/ergebnisse/homologiemodell/substratbindung.png}
|
||||
\includegraphics[width=\textwidth,keepaspectratio=true]{./img/ergebnisse/homologiemodell/substratbindung.png}
|
||||
% substratbindung.png: 2480x1681 pixel, 90dpi, 70.00x47.45 cm, bb=0 0 1984 1345
|
||||
\caption[Substratbindetasche für \acs{PEP}]{Substratbindetasche für \acs{PEP}. Die Ansicht zeigt die Bindestelle für \acs{PEP} im
|
||||
Homologiemodell der \acs{PPDK} aus \acs{F. trinervia}. Seitenketten in räumlicher Nähe zum Substrat sind als Linienmodell dargestellt und benannt. Die
|
||||
|
|
|
|||
|
|
@ -61,7 +61,7 @@
|
|||
Agar & & Becton Dickinson, Heidelberg\\
|
||||
Ampicillin-Natriumsalz & 69-52-3 & AppliChem, Darmstadt\\
|
||||
Bromphenolblau & 62625-28-9 & Sigma-Aldrich, München\\
|
||||
\ac{CBB} & 6104-58-1 & \\
|
||||
\ac{CBB} & 6104-58-1 & Serva, Heidelberg\\
|
||||
Dikaliumhydrogenphosphat & 16788-57-1 & Grüssing, Filsum\\
|
||||
\acf{DTT} & 3483-12-3 & Sigma-Aldrich, München\\
|
||||
\acf{EDTA} & 60-00-4 & AppliChem, Darmstadt\\
|
||||
|
|
@ -72,7 +72,7 @@
|
|||
\acf{IPTG} & 367-93-1 & PEQLAB Biotechnologie, Erlangen\\
|
||||
Kaliumdihydrogenphosphat & 7778-77-0 & Grüssing, Filsum\\
|
||||
Magnesiumchlorid & 7791-18-6 & VWR, Darmstadt\\
|
||||
Magnesiumsulfat-Heptahydrat & 10034-99-8 & \\
|
||||
Magnesiumsulfat-Heptahydrat & 10034-99-8 & Sigma-Aldrich, München\\
|
||||
Natriumchlorid & 7647-14-5 & VWR, Damrstadt\\
|
||||
Natriumdodecylsulfat (SDS) & 151-21-3 & Serva, Heidelberg\\
|
||||
Natriumhydrogencarbonat & 144-55-8 & VWR, Darmstadt\\
|
||||
|
|
@ -324,7 +324,7 @@
|
|||
\SI{10}{\milli\Molar} Magnesiumsulfat
|
||||
\end{description}
|
||||
|
||||
\subsection{Puffer für den Aktivitätsassay}
|
||||
\subsection{Puffer für den Aktivitätstest}
|
||||
\label{sec:puffer_aktivitaetsassay}
|
||||
\begin{samepage}
|
||||
\begin{description}
|
||||
|
|
@ -349,7 +349,7 @@
|
|||
|
||||
\subsection{Konzentrationsbestimmung von Nukleinsäuren}
|
||||
\label{sec:konzentrationsbestimmung_nukleinsaeuren}
|
||||
Nucleinsäuren besitzen aufgrund der aromatischen Basen ein Absorptionsmaximum
|
||||
Nukleinsäuren besitzen aufgrund der aromatischen Basen ein Absorptionsmaximum
|
||||
bei einer Wellenlänge von \SI{260}{\nano\meter}. Die DNA-Konzentration kann daher spektrometrisch
|
||||
durch eine Absorptionsmessung bestimmt werden. Es gilt hierbei:
|
||||
\begin{align}
|
||||
|
|
@ -406,7 +406,7 @@ nach Herstellerangaben.
|
|||
|
||||
\subsection{\acl{PCR}}
|
||||
\label{sec:pcr}
|
||||
Mit Hilfe der \ac{PCR} konnen Nukleinsäurefragmente gezielt
|
||||
Mit Hilfe der \ac{PCR} können Nukleinsäurefragmente gezielt
|
||||
vervielfältigt werden. Die Spezifität der Reaktion ist hierbei durch die Auswahl der
|
||||
eingesetzten Primer gegeben.
|
||||
Eine PCR gliedert sich grundsätzlich in drei aufeinanderfolgende Phasen: Während
|
||||
|
|
@ -421,10 +421,10 @@ vervielfacht werden.
|
|||
|
||||
\subsubsection{Herstellung von Inserts für die \acs{SLIC}}
|
||||
\label{sec:inserts_slic}
|
||||
\begin{samepage}
|
||||
Die Synthese von Inserts für eine \ac{SLIC} (vgl.~\ref{sec:slic}) wurde mittels einer \ac{PCR} nach untenstehendem
|
||||
Ansatz durchgeführt. Als Primer kamen die in \ref{sec:synthetische_oligonukleotide} aufgeführten Oligonukleotide zum Einsatz. Diese
|
||||
wurden so gewählt, dass jeweils \SI{30}{\bp} zum Zielvektor und \SI{20}{\bp} zum Zielgen homolog sind.
|
||||
wurden so gewählt, dass jeweils \SI{30}{\bp} zum Zielvektor und \SI{20}{\bp} zum Zielgen homolog waren.
|
||||
\begin{samepage}
|
||||
\begin{description}
|
||||
\item[\ac{PCR}-Ansatz] \hfill \\
|
||||
\SI{1}{\micro\liter} DNA (Templat) \\
|
||||
|
|
@ -436,11 +436,7 @@ wurden so gewählt, dass jeweils \SI{30}{\bp} zum Zielvektor und \SI{20}{\bp} zu
|
|||
\SI{50}[ad~]{\micro\liter} \acs{ddH2O}
|
||||
\end{description}
|
||||
\end{samepage}
|
||||
Das verwendete Cyclerprogramm ist in Tabelle \ref{tab:slic_cycler} aufgeführt. Bei der Berechnung
|
||||
der Annealing-Temperatur wurde im Fall der ersten zehn Zyklen die Schmelztemperatur
|
||||
des zum \acs{PPDK}-kodierenden Bereich homologen Primerabschnitts zu Grunde gelegt. In den letzten
|
||||
zwanzig Zyklen die Schmelztemperatur des zum Zielvektor homologen Primerbereichs.
|
||||
|
||||
%
|
||||
\begin{table}[hbt]
|
||||
\centering
|
||||
\caption[Cyclerprogramm \acs{SLIC}]{Cyclerprogramm für die Synthese von Inserts zur \acs{SLIC}}
|
||||
|
|
@ -462,6 +458,11 @@ zwanzig Zyklen die Schmelztemperatur des zum Zielvektor homologen Primerbereichs
|
|||
\end{tabular}
|
||||
\label{tab:slic_cycler}
|
||||
\end{table}
|
||||
%
|
||||
Das verwendete Cyclerprogramm ist in Tabelle \ref{tab:slic_cycler} aufgeführt. Bei der Berechnung
|
||||
der Annealing-Temperatur wurde im Fall der ersten zehn Zyklen die Schmelztemperatur
|
||||
des zum \acs{PPDK}-kodierenden Bereich homologen Primerabschnitts zu Grunde gelegt. In den letzten
|
||||
zwanzig Zyklen die Schmelztemperatur des zum Zielvektor homologen Primerbereichs.
|
||||
|
||||
\subsubsection{Kolonie-\acs{PCR}}
|
||||
\label{sec:kolonie_pcr}
|
||||
|
|
@ -470,6 +471,7 @@ untersucht. Hierzu wurden je Kolonie \SI{5}{\micro\liter} \acs{ddH2O} in einem \
|
|||
vorgelegt. Mit einem sterilen Zahnstocher wurde eine Kolonie gepickt, in das vorgelegte Wasser getaucht
|
||||
und anschließend zum Animpfen eines \SI{5}{\milli\liter} Kulturröhrchens mit \acs{2YT}-Medium verwendet.
|
||||
%
|
||||
\begin{samepage}
|
||||
\begin{description}
|
||||
\item[Kolonie-PCR-Ansatz] \hfill \\
|
||||
\SI{1}{\micro\liter} T7-Pro-Primer (\SI{10}{\micro\Molar})\\
|
||||
|
|
@ -479,6 +481,7 @@ und anschließend zum Animpfen eines \SI{5}{\milli\liter} Kulturröhrchens mit \
|
|||
\SI{0,25}{\micro\liter} dNTPs (\SI{10}{\milli\Molar})\\
|
||||
\SI{25}[ad~]{\micro\liter} \acs{ddH2O}
|
||||
\end{description}
|
||||
\end{samepage}
|
||||
%
|
||||
Die Kolonie-\acs{PCR} wurde dann gemäß des in Tabelle \ref{tab:kolonie_pcr_cycler} dargelegten Programms durchgeführt.
|
||||
|
||||
|
|
@ -566,7 +569,7 @@ Die optimalen Bedingungen zur heterologen Expression der \acs{PPDK} in \acs{E. c
|
|||
unterschiedliche Konzentrationen von \ac{IPTG} zur Induktion verwendet wurden. Es kamen hierbei die \acs{E. coli}"=Stämme BL21 (DE3) und BL21 Gold (DE3)
|
||||
zum Einsatz.
|
||||
|
||||
Von den Agarplatten (vgl.~\ref{sec:transformation}) wurden Vorkulturen in \SI{5}{\milli\liter} Volumen im Kulturröhrchen angesetzt. Die Vorkulturen wurden über Nacht bei
|
||||
Von den Agarplatten (vgl.~\ref{sec:transformation}) wurden Vorkulturen mit einem Volumen von \SI{5}{\milli\liter} im Kulturröhrchen angesetzt. Die Vorkulturen wurden über Nacht bei
|
||||
\SI{37}{\celsius} und \SI{180}{\rpm} im Schütler inkubiert und am folgenden Tag zur Inokulation der Hauptkulturen eingesetzt.
|
||||
|
||||
Hierfür wurden \SI{250}{\milli\liter}-Kolben mit Schikane und \SI{100}{\milli\liter} Kulturmedium mit \SI{1}{\milli\liter} der Vorkultur inokuliert
|
||||
|
|
@ -581,7 +584,7 @@ wurden die Zellen durch Zentrifugation bei \SI{7000}{\xg} für \SI{10}{\minute}
|
|||
Die heterologe Expression der \acs{PPDK} in \acs{E. coli} erfolgte mit den in den Expressionsstudien als besonders geeignet explorierten Bedingungen.
|
||||
Als Expressionsstamm kam \acs{E. coli} BL21 (DE3) zum Einsatz.
|
||||
|
||||
Von den Agarplatten wurden Vorkulturen in \SI{100}{\milli\liter} Volumen in unschikanierten \SI{250}{\milli\liter}-Kolben angesetzt. Die
|
||||
Von den Agarplatten wurden Vorkulturen mit einem Volumen von \SI{100}{\milli\liter} in unschikanierten \SI{250}{\milli\liter}-Kolben angesetzt. Die
|
||||
Vorkulturen wurden über Nacht bei \SI{37}{\celsius} und \SI{180}{\rpm} im Schütler inkubiert und am folgenden Tag zur Inokulation der
|
||||
Hauptkulturen eingesetzt.
|
||||
|
||||
|
|
@ -596,7 +599,7 @@ in flüssigem Stickstoff schockgefroren und für weitere Versuche bei \SI{-80}{\
|
|||
\section{Präparative Methoden}
|
||||
\label{sec:praeparative_methoden}
|
||||
|
||||
Aufgrund der Kältelabilität der \acs{PPDK}, welche bei der \acs{PPDK} aus \acs{F. trinervia} besonder ausgeprägt ist \citep{Burnell1990}, wurden alle
|
||||
Aufgrund der Kältelabilität der \acs{PPDK} (vgl. \ref{sec:kaelte}), welche bei der \acs{PPDK} aus \acs{F. trinervia} besonder ausgeprägt ist \citep{Burnell1990}, wurden alle
|
||||
Schritte des Zellaufschlusses und der Reinigung -- wenn nicht abweichend angegeben -- bei Raumtemperatur durchgeführt.
|
||||
|
||||
\subsection{Zellaufschluss}
|
||||
|
|
@ -609,25 +612,24 @@ bei einem Druck von \SI{1,35}{\kilo\bar} und einer Temperatur von \SI{15}{\celsi
|
|||
\label{sec:affinitaetschromatographie}
|
||||
Proteine, die mit einem Poly-Histidin-Tag markiert sind, lassen sich über eine \acf{IMAC} aus
|
||||
einem Proteingemisch isolieren. Im Rahmen dieser Arbeit wurden HisTrap$^\text{\textregistered}$ HP-Säulen mit einem Volumen von \SI{5}{\milli\liter}
|
||||
eingesetzt. Als Säulenmaterial dient quervernetzte Agarose an welche \acf{IDA} immobilisiert ist. \ce{Ni2+}-Ionen werden von \acs{IDA} dreifach koordinativ
|
||||
komplexiert, so dass drei Koordinationsstellen für die Interaktion Poly-Histidin-markierter Proteine mit den immobilisierten \ce{Ni2+}-Ionen zur
|
||||
eingesetzt. Als Säulenmaterial dient quervernetzte Agarose an welche \acf{IDA} immobilisiert ist. \ce{Ni^{2+}}-Ionen werden von \acs{IDA} dreifach koordinativ
|
||||
komplexiert, so dass drei Koordinationsstellen für die Interaktion Poly-Histidin-markierter Proteine mit den immobilisierten \ce{Ni^{2+}}-Ionen zur
|
||||
Verfügung stehen. Die Elution der spezifisch an das Säulenmaterial gebundenen Proteine erfolgt über die Zugabe von Imidazol, welches als Strukturanalogon zu
|
||||
Histidin in der Lage ist, dieses kompetitiv aus der Bindung mit \ce{Ni2+} zu verdrängen. Das nachfolgend beschriebene Reinigungsprotokoll wurde nach \citet{Nakanishi2003,Chastain1996}
|
||||
Histidin in der Lage ist, dieses kompetitiv aus der Bindung mit \ce{Ni^{2+}} zu verdrängen. Das nachfolgend beschriebene Reinigungsprotokoll wurde nach \citet{Nakanishi2003,Chastain1996}
|
||||
adaptiert.
|
||||
|
||||
Die wie in \ref{sec:zellaufschluss} beschrieben aufgeschlossenen Zellen wurden zunächst bei \SI{10000}{\xg} und \SI{15}{\celsius} für \SI{30}{\minute}
|
||||
zentrifugiert um Zelltrümmer und \textit{Inclusion-Bodies} zu entfernen. Der Überstand wurde anschließend für \SI{1}{\hour} bei \SI{100000}{\xg} und \SI{15}{\celsius}
|
||||
ulrazentrifugiert um lediglich lösliche Proteine im Überstand zu halten und Membranfragmente zu präzipitieren.
|
||||
|
||||
Die mit \ce{Ni2+} beladene Säule wurde zunächst mit \SI{5}{\CV} \acs{ddH2O} und \SI{20}{\CV} Waschpuffer \emph{ohne} \acs{DTT} gewaschen, um schwach bindende
|
||||
\ce{Ni2+} von der Säule zu eluieren und die Bildung von amorphem Nickel bei der nachfolgenden Benutzung der Puffer mit reduzierend wirksamen \acs{DTT}
|
||||
Die mit \ce{Ni^{2+}} beladene Säule wurde zunächst mit \SI{5}{\CV} \acs{ddH2O} und \SI{20}{\CV} Waschpuffer \emph{ohne} \acs{DTT} gewaschen, um schwach bindende
|
||||
\ce{Ni^{2+}} von der Säule zu eluieren und die Bildung von amorphem Nickel bei der nachfolgenden Benutzung der Puffer mit reduzierend wirksamen \acs{DTT}
|
||||
zu minimieren.
|
||||
|
||||
Die Säule wurde mit Waschpuffer äquilibriert und das Zelllysat mit einer Flussrate von \SI{1,5}{\milli\liter\per\minute} auf die Säule geladen. Im Anschluss
|
||||
Unspezifisch bindende Proteine wurde mit \SI{20}{\CV} Waschpuffer + \SI{50}{\milli\Molar} Imidazol von der Säule gelöst. Die Elution der \acs{PPDK} erfolgte dann mit je \SI{10}{\CV} Waschpuffer + \SI{150}{\milli\Molar}, \SI{200}{\milli\Molar} und \SI{250}{\milli\Molar} Imidazol. Es wurden Fraktionen
|
||||
Die Säule wurde mit Waschpuffer äquilibriert und das Zelllysat mit einer Flussrate von \SI{1,5}{\milli\liter\per\minute} auf die Säule geladen. Unspezifisch bindende Proteine wurden im Anschluss mit \SI{20}{\CV} Waschpuffer + \SI{50}{\milli\Molar} Imidazol von der Säule gelöst. Die Elution der \acs{PPDK} erfolgte dann mit je \SI{10}{\CV} Waschpuffer + \SI{150}{\milli\Molar}, \SI{200}{\milli\Molar} und \SI{250}{\milli\Molar} Imidazol. Es wurden Fraktionen
|
||||
mit einem Volumen von \SI{5}{\milli\liter} gesammelt und ggf. vereinigt. Zur Detektion der Proteinfraktionen wurde die Absorption bei \SI{280}{\nano\meter} verfolgt.
|
||||
|
||||
Nach Abschluss der Reinigung wurde die Säule nach Herstellerangaben gereinigt und neu mit \ce{Ni2+} beladen.
|
||||
Nach Abschluss der Reinigung wurde die Säule nach Herstellerangaben gereinigt und neu mit \ce{Ni^{2+}} beladen.
|
||||
|
||||
\subsection{Konzentrierung von Proteinlösungen}
|
||||
\label{sec:konzentrierung}
|
||||
|
|
@ -658,13 +660,9 @@ Langfristig wurden \acs{PPDK}-Lösungen nach Zugabe von \SI{20}{\percent}~(w/v)
|
|||
\subsection{Differentielle Zentrifugation}
|
||||
\label{sec:differentielle_zentrifugation}
|
||||
|
||||
Nach dem Zellaufschluss (vgl.~\ref{sec:zellaufschluss}) wurde eine Probe von \SI{10}{\micro\liter} aus dem Homogenisat als Kontrolle entnommen.
|
||||
Anschließend wurde das Homogenisat bei \SI{2000}{\xg} für \SI{15}{\minute} bei \SI{15}{\celsius} zentrifugiert. Das resultierende Pellet
|
||||
wurde im gleichen Volumen Aufschlusspuffer unter Zusatz von \SI{0,1}{\percent} (w/v) \acs{SDS} bei Raumtemperatur und unter Rühren rückgelöst.
|
||||
Nach dem Zellaufschluss (vgl.~\ref{sec:zellaufschluss}) wurde eine Probe von \SI{10}{\micro\liter} aus dem Zelllysat als Kontrolle entnommen. Anschließend wurde das Zelllysat bei \SI{2000}{\xg} für \SI{15}{\minute} bei \SI{15}{\celsius} zentrifugiert. Das resultierende Pellet wurde im gleichen Volumen Aufschlusspuffer unter Zusatz von \SI{0,1}{\percent} (w/v) \acs{SDS} bei Raumtemperatur und unter Rühren rückgelöst.
|
||||
|
||||
Es wurden jeweils vom Überstand, als auch vom resuspendierten Pellet weitere Proben von \SI{10}{\micro\liter} Volumen entnommen. Diese
|
||||
wurden mit \SI{25}{\micro\liter} \acs{SDS}-Probenpuffer und \SI{65}{\micro\liter} \acs{ddH2O} versetzt. Alle weiteren Zentrifugationsschritte
|
||||
erfolgten hierzu analog und sind in Tabelle \ref{tab:differentielle_zentrifugation} aufgeführt.
|
||||
Sowohl vom Überstand, als auch vom resuspendierten Pellet wurden jeweils weitere Proben von \SI{10}{\micro\liter} Volumen entnommen. Diese wurden mit \SI{25}{\micro\liter} \acs{SDS}-Probenpuffer und \SI{65}{\micro\liter} \acs{ddH2O} versetzt. Alle weiteren Zentrifugationsschritte erfolgten hierzu analog und sind in Tabelle \ref{tab:differentielle_zentrifugation} aufgeführt.
|
||||
%
|
||||
\begin{table}[htb]
|
||||
\centering
|
||||
|
|
@ -699,7 +697,7 @@ Detektion erfolgte durch Absorptionsmessung bei \SI{280}{\nano\meter}. Eluiert w
|
|||
\subsection{SDS-\acl{PAGE}}
|
||||
\label{sec:sds_page}
|
||||
Die Proteinproben wurden auf Polyacrylamid-Gele aufgetragen und dort nach ihrer Masse aufgetrennt
|
||||
\citep{Laemmli1970}. Durch die Zugabe von \ac{SDS} werden die Proteine denaturiert und mit einr negativen
|
||||
\citep{Laemmli1970}. Durch die Zugabe von \ac{SDS} werden die Proteine denaturiert und mit einer negativen
|
||||
Ladung maskiert, wodurch sie ein einheitliches Ladungs-Masse-Verhältnis aufweisen. Somit ist die Wanderungsgeschwindigkeit
|
||||
im elektrischen Feld allein von der Proteinmasse abhängig. Vor dem Auftragen auf das Geld wurden alle Proben mit
|
||||
4\texttimes-Probenpuffer versetzt. Expressionsproben wurden darüber hinaus für \SI{10}{\minute} auf \SI{95}{\celsius} erhitzt.
|
||||
|
|
@ -743,7 +741,7 @@ Pipettierschema für drei kleine Gele (\SI{9}{\centi\meter}~\texttimes~\SI{10}{\
|
|||
%
|
||||
Um die Größenzuordnung der Proteinbanden zu gewährleisten, wurden die in \ref{sec:standards_proteine_nukleinsaeuren} genannten
|
||||
Standards eingesetzt. Bei kleinen Gelen wurde nach dem Beladen für \SI{1}{\hour} eine Stromstärke von \SI{35}{\milli\ampere} je Gel angelegt.
|
||||
Größe Gele liefen über Nacht bei \SI{50}{\milli\ampere}.
|
||||
Große Gele liefen über Nacht bei \SI{50}{\milli\ampere}.
|
||||
|
||||
\subsection{Kolloidale Coomassie-Färbung}
|
||||
\label{sec:faerbung_coomassie}
|
||||
|
|
@ -760,27 +758,27 @@ Waschen mit \acs{ddH2O} erreicht werden.
|
|||
Über eine Immunfärbung kann anschließend eine Visualisierung der Proteine auf der Membran erfolgen. Im Rahmen dieser Arbeit kam das
|
||||
Semi-Dry-Blotverfahren, sowie eine Nitrozellulosemembran mit einer Porengröße von \SI{0,2}{\micro\meter} zum Einsatz.
|
||||
|
||||
Bei Gelen, welche für einen Westernblot vorgesehen waren, kam ein gefärbter Proteingrößenstandard zum Einsatz. Das Gel wurde für etwa
|
||||
\SI{10}{\minute} in Transferpuffer inkubiert. Die benötigten Filterpapiere, sowie die Nitrozellulosemembran wurden ebenfalls kurz in
|
||||
Transferpuffer getränkt.
|
||||
Es wurde ein gefärbter Proteingrößenstandard bei Gelen verwendet, welche für einen Westernblot vorgesehen waren. Das Gel wurde für etwa
|
||||
\SI{10}{\minute} in Transferpuffer inkubiert. Die Nitrozellulosemembran und, sowie die Filterpapiere wurden ebemfalls
|
||||
kurz mit Transferpuffer getränkt.
|
||||
|
||||
Auf die Anode der Blotapparatur wurden zunächst drei Lagen Filterpapier, gefolgt von der Blotmembran, dem Gel sowie drei weiteren Lagen
|
||||
Filterpapier gegeben. Anschließend wurde die Apparatur geschlossen und für \SI{2}{\hour} eine Stromstärke von
|
||||
\SI{1}{\milli\ampere\per\square\centi\meter} angelegt.
|
||||
|
||||
Nach Abschluss des Blotvorgangs wurde die Membran entnommen und \SI{1}{\hour} in einer \SI{1}{\percent}igen Caseinlösung in \acs{TBS} auf einem
|
||||
Rotationsschüttler inkubiert. Es schlossen sich zwei Waschschritte mit \acs{TBT} und einer mit \acs{TBS} zu jeweils \SI{10}{\minute} an.
|
||||
Rotationsschüttler inkubiert. Im Anschluss erfolgten zwei Waschschritte mit \acs{TBT} und einer mit \acs{TBS} zu jeweils \SI{10}{\minute}.
|
||||
|
||||
Die Membran wurde dann zusammen mit einer \SI{1}{\percent}igen Caseinlösung in TBS, welche den Anti-His-\acs{HRP}-Antikörper im Verhältnis 1:10000
|
||||
enthielt, in Folie eingeschweißt und über Nacht bei \SI{4}{\celsius} auf einem Taumelschüttler inkubiert. Am nächsten Tag erfolgten
|
||||
zwei Waschschritte mit \acs{TBT} und einer mit \acs{TBS} zu jeweils \SI{10}{\minute}. Der gebundene Antikörper ließ sich über die gekoppelte
|
||||
Meerrettich-Peroxidase (\acs{HRP}) mit Hilfe eines Chemilumineszenzreagenzes nachweisen. die \acs{HRP} oxidiert in Anwesenheit von
|
||||
wiederum zwei Waschschritte mit \acs{TBT} und einer mit \acs{TBS} zu jeweils \SI{10}{\minute}. Der gebundene Antikörper konnte dann über die gekoppelte
|
||||
Meerrettich-Peroxidase (\acs{HRP}) mit Hilfe eines Chemilumineszenzreagenzes nachweisen. Die \acs{HRP} oxidiert in Anwesenheit von
|
||||
Wasserstoffperoxid das Substrat Luminol, wobei es zu einer Lichtemission kommt.
|
||||
|
||||
Hierfür wurde die Membran in Folie eingeschlagen und mit dem Reagenz überschichtet. Für die Visualisierung wurde ein Lumineszenzdetektor
|
||||
(LAS 4000 mini, Fujifilm) eingesetzt.
|
||||
|
||||
|
||||
Hierfür wurde die Membran in Folie eingeschlagen und mit dem Reagenz überschichtet. Für die Visualisierung wurde ein Lumineszenzdetektor (LAS 4000 mini, Fujifilm) eingesetzt.
|
||||
%
|
||||
\clearpage
|
||||
%
|
||||
\subsection{Konzentrationsbestimmung von Proteinen}
|
||||
\label{sec:konzentrationsbestimmung_proteine}
|
||||
Die Konzentration von Proteinen wurde nach \citet{Bradford1976} bestimmt. Hierzu wurde in einer Mikrotiterplatte \SI{50}{\micro\liter} einer
|
||||
|
|
@ -808,13 +806,13 @@ empfindlich auf Änderungen der Sekundärstruktur \citep{Greenfield2007}. Die Me
|
|||
von \SI{0,1}{\milli\gram\per\milli\liter}. Von den Rohdaten wurde das Pufferspektrum abgezogen und unter Berücksichtigung von Konzentration und
|
||||
Molekulargewicht in molaren \ac{CD} (\textDelta\textepsilon) umgerechnet.
|
||||
|
||||
\subsection{Aktivitätsassay}
|
||||
\subsection{Aktivitätstest}
|
||||
\label{sec:aktivitaetsassay}
|
||||
Um die Aktivität der gereinigten \acs{PPDK} zu bestimmten, wurde ein Aktivitätsassay \citep{Salahas1990} durchgeführt. Hierbei wurde \ac{PEP}-Bildung
|
||||
in einem gekoppelten Enzymassay über den \acs{NADH}"=Verbrauch verfolgt. Der geschwindigkeitsbestimmende Schritt ist in diesem Fall die Umsetzung
|
||||
Um die Aktivität der gereinigten \acs{PPDK} zu bestimmten, wurde ein Aktivitätstest \citep{Salahas1990} durchgeführt. Hierbei wurde die \ac{PEP}-Bildung
|
||||
in einem gekoppelten Enzymtest über den \acs{NADH}"=Verbrauch verfolgt. Der geschwindigkeitsbestimmende Schritt ist in diesem Fall die Umsetzung
|
||||
von Pyruvat, anorganischem Phosphat und \acs{ATP} zu \acl{PEP}, \acs{AMP} und Pyrophosphat \eqref{eq:aktivitaet_1}. Nachfolgend wird \acl{PEP} durch
|
||||
die \acl{PEPCase} über eine \textbeta-Carboxylierung mit Hydrogencarbonat zu Oxalacetat umgesetzt \eqref{eq:aktivitaet_2}. Letzteres wird durch eine
|
||||
NAD-abhängige Malatdehydrogenase zu Malat reduziert \eqref{eq:aktivitaet_3}.
|
||||
NAD-abhängige Malatdehydrogenase zu Malat reduziert \eqref{eq:aktivitaet_3}. Die Reaktionsabfolge entspricht somit einem Teil des Reaktionszyklus zur \ce{CO2}"=Fixierung in \ce{C_4}"=Pflanzen (vgl. \ref{sec:c4_ppdk}).
|
||||
%
|
||||
\begin{align}
|
||||
\cee{
|
||||
|
|
@ -828,11 +826,11 @@ NAD-abhängige Malatdehydrogenase zu Malat reduziert \eqref{eq:aktivitaet_3}.
|
|||
\end{align}
|
||||
%
|
||||
Der \acs{NADH}-Verbrauch kann photometrisch über die Abnahme der \acs{NADH}"=spezifischen Extinktion bei \SI{340}{\nano\meter} verfolgt werden. Da der
|
||||
Verbrauch eines \acs{NADH}-Moleküls gleichbedeutend ist mit der Bildung eines \acl{PEP}-Moleküls durch die \acs{PPDK}, kann aus dem Verbrauch an
|
||||
\acs{NADH} direkt auf die Bildungsrate von \acl{PEP} und somit auf die Aktivität der \acs{PPDK} geschlossen werden.
|
||||
Verbrauch eines \acs{NADH}"=Moleküls gleichbedeutend ist mit der Bildung eines \ac{PEP}-Moleküls durch die \acs{PPDK}, kann aus dem Verbrauch an
|
||||
\acs{NADH} direkt auf die Bildungsrate von \ac{PEP} und somit auf die Aktivität der \acs{PPDK} geschlossen werden.
|
||||
|
||||
Der Reaktionsansatz nach \citet{Salahas1990} (vgl.~\ref{sec:puffer_aktivitaetsassay}) wurde mit \SI{0,5}{\micro\liter} gereinigtem und entsalztem
|
||||
\acs{PPDK}-Konzentrat versetzt. Die \acs{PPDK}-Lösung wurde zuvor für \SI{30}{\minute} bei \SI{30}{\celsius} inkubiert, um eine möglichst vollständige
|
||||
Der Reaktionsansatz nach \citet{Salahas1990} wurde mit \SI{0,5}{\micro\liter} gereinigtem und entsalztem
|
||||
\acs{PPDK}-Konzentrat versetzt (vgl.~\ref{sec:puffer_aktivitaetsassay}). Die \acs{PPDK}-Lösung wurde zuvor für \SI{30}{\minute} bei \SI{30}{\celsius} inkubiert, um eine möglichst vollständige
|
||||
Aktivierung zu erreichen \citep{Ashton1990}. Die Reaktion wurde durch Zugabe von \SI{2,5}{\milli\liter} einer \SI{100}{\milli\Molar} \acs{ATP}-Lösung
|
||||
(Endkonzentration: \SI{1,25}{\milli\Molar}) gestartet und die Extinktion bei \SI{340}{\nano\meter} über einen Zeitraum von \SI{3}{\minute} bei \SI{30}{\celsius}
|
||||
aufgezeichnet.
|
||||
|
|
@ -874,6 +872,6 @@ Extremkonformationen des putativen \textit{Domain-swiveling}-Mechanismus.
|
|||
Jeweils fünf Homologiemodelle wurden mit dem Programm \textit{Modeller} \citep{Sali1993a} aus den jeweiligen Templaten und der Primärstruktur der
|
||||
\acs{PPDK} aus \acs{F. trinervia} \citep{Rosche1990} generiert. Im Falle des von \textit{Zea mays} abgeleiteten Modells wurde als Vorlage die Pyruvat gebundene Struktur
|
||||
verwendet (PDB: 1VBH). Lücken in der dreidimensionalen Struktur wurden anhand der ungebundenen Struktur (PDB: 1VBG) ergänzt. Um die Substratbindetasche möglichst
|
||||
exakt zu nachzubilden, wurde das in der Kristallstruktur 1VBH vorhandene \acs{PEP}-Molekül, sowie das \ce{Mg2+}-Ion beim Modellieren berücksichtigt.
|
||||
exakt zu nachzubilden, wurde das in der Kristallstruktur 1VBH vorhandene \acs{PEP}-Molekül, sowie das \ce{Mg^{2+}}-Ion beim Modellieren berücksichtigt.
|
||||
|
||||
Die Evaluation der erstellten Modelle erfolgte mit dem Programmpaket \textit{PROCHECK} \citep{Laskowski1993,Laskowski1996}.
|
||||
|
|
|
|||
|
|
@ -1 +1,13 @@
|
|||
\addchap{Zusammenfassung}
|
||||
\acresetall
|
||||
Ziel dieser Arbeit war es, die heterologe Expression der \ac{PPDK} aus \ac{F. trinervia} in \ac{E. coli}, sowie ein Reinigungsprotokoll zu etablieren und die Funktionalität über einen Aktivitätstest nachzuweisen.
|
||||
|
||||
Hierfür wurde Codon optimierte \acs{DNA} des für die \acs{PPDK} kodierenden Genabschnitts in einen aus pET-16b abgeleiteten Expressionsvektor kloniert. Mit diesem wurde der \ac{E. coli}"=Stamm BL21 (DE3) transformiert und die \acs{PPDK} in diesem exprimiert. Die heterolog exprimierte \acs{PPDK} wurde im Anschluss über einen Histidin-Tag affinitätschromatographisch
|
||||
gereinigt. Es wurden hierbei hohe Ausbeuten von bis zu \SI{118}{\milli\gram\per\liter} Kulturmedium erzielt.
|
||||
|
||||
Die Funktionalität des gereinigten Proteins wurde mittels einer \ac{CD}-Spektroskopie in Kombination mit einem Aktivitätstest überprüft, beim dem Pyruvat, \acs{ATP} und anorganisches Phosphat zu \ac{PEP}, \acs{AMP} und Pyrophosphat umgesetzt werden.
|
||||
Auf diese Weise wurden für die heterolog exprimierte \acs{PPDK} aus \acs{F. trinervia} ein \ce{K_m} von \SI[seperr]{50(9)}{\micro\Molar} (ATP) bzw. \SI[seperr]{270(44)}{\micro\Molar} (Pyruvat), sowie eine spezifische Aktivität von \SI[seperr]{0,99(9)}{\Unit\per\milli\gram} bestimmt.
|
||||
|
||||
Durch eine Größenausschlusschromatographie konnte gezeigt werden, dass bestimmte Fraktionen der der gereinigten \acs{PPDK} monodispers vorliegen und sich somit für Kristallisationsexperimente eignen.
|
||||
|
||||
Zusammenfassend konnte die \ac{PPDK} aus \ac{F. trinervia} erfolgreich in \ac{E. coli} exprimiert und zu einem hohen Grad gereinigt werden. Die gereinigte \ac{PPDK} zeigte eine Aktivität, was auf eine funktionelle und somit wahrscheinlich native Faltung hindeutet.
|
||||
|
|
|
|||
4943
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4943
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|
|
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|
|||
img_extensions=.eps .jpg .jpeg .png .pdf .ps .fig .gif
|
||||
kileprversion=2
|
||||
kileversion=2.1.2
|
||||
lastDocument=inc/einleitung.tex
|
||||
lastDocument=masterarbeit.tex
|
||||
masterDocument=
|
||||
name=Masterarbeit
|
||||
pkg_extIsRegExp=false
|
||||
|
|
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|
|||
|
||||
[item:inc/abkuerzungen.tex]
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
[item:inc/diskussion.tex]
|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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||||
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|
||||
|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
|
||||
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|
||||
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|
||||
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|
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||||
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||||
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||||
mode=LaTeX
|
||||
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|
||||
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||||
|
||||
[item:inc/material.tex]
|
||||
archive=true
|
||||
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|
||||
column=1
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||||
encoding=UTF-8
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
order=1
|
||||
|
||||
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||||
archive=true
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
|
||||
[item:library.bib]
|
||||
archive=true
|
||||
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|
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|
|||
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||||
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||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
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||||
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|
|||
BIN
masterarbeit.pdf
BIN
masterarbeit.pdf
Binary file not shown.
|
|
@ -29,7 +29,7 @@
|
|||
\usepackage{fontspec}
|
||||
%\newfontfeature{Microtype}{protrusion=default;expansion=default;}
|
||||
%\directlua{fonts.protrusions.setups.default.factor=.5}
|
||||
\defaultfontfeatures{Ligatures=TeX} %,Numbers=OldStyle}% ,Scale=MatchLowercase}
|
||||
\defaultfontfeatures{Ligatures=TeX, RawFeature={+itlc}} %,Numbers=OldStyle}% ,Scale=MatchLowercase}
|
||||
\usepackage{libertineotf}
|
||||
\setmonofont[Scale=1]{Inconsolata}
|
||||
%\setmonofont[Scale=0.9]{LinMonoO}
|
||||
|
|
@ -152,13 +152,15 @@
|
|||
\textsf{\textbf{Masterarbeit}}
|
||||
|
||||
\normalsize
|
||||
\textsf{\textbf{Heterologe Expression und Reinigung der \acl{PPDK} aus der C4 Pflanze \acl{F. trinervia}}}
|
||||
\sffamily
|
||||
\textbf{Heterologe Expression und Reinigung der Pyruvat"=Phosphat Dikinase (PPDK) aus der C4 Pflanze \textsl{Flaveria trinervia}}
|
||||
\rmfamily
|
||||
\vfill
|
||||
Zur Erlangung des akademischen Grades\\ Master of Science (M. Sc.) - Biochemistry
|
||||
\vfill
|
||||
vorgelegt von \\ \textbf{B. Sc. Alexander Ralph Michael Minges \\ (1804535)}
|
||||
\vfill
|
||||
im August 2011
|
||||
im September 2012
|
||||
\vfill \begin{description}
|
||||
\item[Erstprüfer:]{Univ. Prof. Dr. G. Groth\\ Institut für Biochemische Pflanzenphysiologie \\ Heinrich-Heine-Universität Düsseldorf}
|
||||
\item[Zweitprüfer:]{Univ. Prof. Dr. H. Gohlke\\ Institut für Pharmazeutische und Medizinische Chemie \\ Heinrich-Heine-Universität Düsseldorf}
|
||||
|
|
@ -170,7 +172,7 @@
|
|||
\thispagestyle{empty}
|
||||
\vspace*{\fill}
|
||||
\begin{center}
|
||||
\Large <Widmung>
|
||||
\Large Meinen Eltern
|
||||
\end{center}
|
||||
\vspace*{\fill}
|
||||
\clearpage
|
||||
|
|
|
|||
892
misc/1vbh.txt
Normal file
892
misc/1vbh.txt
Normal file
|
|
@ -0,0 +1,892 @@
|
|||
==== Secondary Structure Definition by the program DSSP, CMBI version by M.L. Hekkelman/2010-10-21 ==== DATE=2012-03-20 .
|
||||
REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 .
|
||||
HEADER TRANSFERASE 26-FEB-04 1VBH .
|
||||
COMPND 2 MOLECULE: PYRUVATE,ORTHOPHOSPHATE DIKINASE; .
|
||||
SOURCE 2 ORGANISM_SCIENTIFIC: ZEA MAYS; .
|
||||
AUTHOR T.NAKANISHI,T.NAKATSU,M.MATSUOKA,K.SAKATA,H.KATO,RIKEN STRUCTURAL .
|
||||
862 3 0 0 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) .
|
||||
37344.8 ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) .
|
||||
629 73.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES .
|
||||
52 6.0 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .
|
||||
78 9.0 TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES .
|
||||
3 0.3 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES .
|
||||
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES .
|
||||
3 0.3 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES .
|
||||
1 0.1 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES .
|
||||
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES .
|
||||
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES .
|
||||
0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES .
|
||||
43 5.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES .
|
||||
86 10.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES .
|
||||
324 37.6 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES .
|
||||
19 2.2 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES .
|
||||
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** .
|
||||
0 0 0 4 1 4 0 0 6 2 2 4 1 0 3 1 0 2 2 0 1 0 0 0 1 0 0 0 0 0 RESIDUES PER ALPHA HELIX .
|
||||
1 2 4 4 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PARALLEL BRIDGES PER LADDER .
|
||||
2 5 0 5 1 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ANTIPARALLEL BRIDGES PER LADDER .
|
||||
1 1 0 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 LADDERS PER SHEET .
|
||||
# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA
|
||||
1 3 A K 0 0 114 0, 0.0 4,-0.1 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 109.0 13.4 7.1 48.9
|
||||
2 4 A K + 0 0 148 2,-0.1 3,-0.1 44,-0.0 0, 0.0 0.511 360.0 11.8-109.4 -8.2 10.3 7.3 46.7
|
||||
3 5 A R S S+ 0 0 19 1,-0.3 43,-2.6 45,-0.1 2,-0.4 0.489 124.7 50.2-140.5 -19.5 8.9 10.7 47.8
|
||||
4 6 A V E -A 45 0A 6 41,-0.2 2,-0.5 39,-0.0 -1,-0.3 -0.965 60.6-173.8-132.4 117.1 11.6 12.4 49.9
|
||||
5 7 A F E -A 44 0A 18 39,-2.1 39,-2.3 -2,-0.4 2,-0.1 -0.932 8.9-155.9-114.1 118.2 15.2 12.6 48.6
|
||||
6 8 A H E -A 43 0A 27 -2,-0.5 7,-1.2 37,-0.3 8,-0.4 -0.348 12.5-170.3 -84.6 168.4 18.0 14.0 50.8
|
||||
7 9 A F E +AB 42 12A 4 35,-3.0 35,-2.1 5,-0.2 2,-0.3 -0.987 14.9 148.1-160.3 150.7 21.2 15.6 49.5
|
||||
8 10 A G E > - B 0 11A 0 3,-3.7 3,-3.3 -2,-0.3 28,-0.2 -0.944 61.2 -32.5-165.1 179.2 24.6 16.8 50.7
|
||||
9 11 A K T 3 S- 0 0 64 30,-0.5 29,-0.1 1,-0.3 24,-0.1 -0.243 132.9 -11.5 -48.4 111.6 28.2 17.2 49.6
|
||||
10 12 A G T 3 S+ 0 0 48 23,-1.4 2,-0.4 27,-0.3 -1,-0.3 0.683 122.6 96.5 67.6 20.0 28.7 14.3 47.3
|
||||
11 13 A K E < +B 8 0A 114 -3,-3.3 -3,-3.7 22,-0.1 2,-0.2 -0.989 35.0 133.0-145.4 132.8 25.4 12.6 48.4
|
||||
12 14 A S E -B 7 0A 30 -2,-0.4 -5,-0.2 -5,-0.3 31,-0.1 -0.752 39.3-149.6-178.0 128.7 21.9 12.6 46.9
|
||||
13 15 A E S S+ 0 0 43 -7,-1.2 -6,-0.1 -2,-0.2 -1,-0.1 0.847 87.4 59.8 -71.5 -34.7 19.3 10.0 46.1
|
||||
14 16 A G S S- 0 0 5 -8,-0.4 2,-0.3 12,-0.1 20,-0.0 -0.250 73.8-150.5 -85.4 179.6 18.0 12.0 43.1
|
||||
15 17 A N > - 0 0 60 -2,-0.1 3,-2.2 18,-0.0 16,-0.2 -0.955 35.0 -87.8-147.6 165.6 19.9 13.1 40.0
|
||||
16 18 A K T 3 S+ 0 0 124 -2,-0.3 3,-0.1 1,-0.3 11,-0.1 0.558 118.3 61.9 -50.7 -13.1 20.0 15.8 37.4
|
||||
17 19 A T T 3 S+ 0 0 99 1,-0.2 2,-1.7 10,-0.1 3,-0.4 0.680 77.9 87.8 -91.0 -18.2 17.5 14.0 35.2
|
||||
18 20 A M <> + 0 0 38 -3,-2.2 4,-2.0 1,-0.2 5,-0.2 -0.327 39.2 135.5 -82.0 58.7 14.5 14.0 37.6
|
||||
19 21 A K T 4 S+ 0 0 39 -2,-1.7 4,-0.4 3,-0.2 -1,-0.2 0.747 73.0 55.1 -74.0 -23.7 13.0 17.4 36.7
|
||||
20 22 A E T 4 S+ 0 0 55 -3,-0.4 27,-0.2 2,-0.1 -1,-0.2 0.959 120.0 25.8 -73.3 -53.6 9.6 15.7 36.8
|
||||
21 23 A L T 4 S+ 0 0 44 1,-0.2 26,-1.8 25,-0.1 27,-0.2 0.911 132.8 34.8 -77.6 -48.1 9.7 14.3 40.3
|
||||
22 24 A L S X S- 0 0 2 -4,-2.0 4,-1.1 24,-0.2 -3,-0.2 0.465 105.9-128.8 -88.7 -2.5 12.2 16.7 42.0
|
||||
23 25 A G H > - 0 0 0 -4,-0.4 4,-2.6 -5,-0.2 76,-0.3 0.081 38.9 -68.7 71.6 164.7 11.1 19.8 40.1
|
||||
24 26 A G H > S+ 0 0 33 74,-3.3 4,-1.5 1,-0.2 -1,-0.2 0.913 137.2 43.4 -56.6 -45.3 13.6 22.0 38.3
|
||||
25 27 A K H > S+ 0 0 89 73,-0.5 4,-2.3 2,-0.2 -1,-0.2 0.871 113.1 51.4 -70.0 -38.6 15.1 23.2 41.5
|
||||
26 28 A G H X S+ 0 0 1 -4,-1.1 4,-2.5 1,-0.2 -3,-0.2 0.945 109.1 49.9 -63.9 -48.3 15.2 19.8 43.2
|
||||
27 29 A A H X S+ 0 0 6 -4,-2.6 4,-2.0 1,-0.2 -1,-0.2 0.861 112.2 49.0 -58.4 -37.9 16.9 18.2 40.2
|
||||
28 30 A N H X S+ 0 0 61 -4,-1.5 4,-3.0 -5,-0.2 -1,-0.2 0.904 109.3 50.6 -69.6 -42.8 19.6 21.0 40.2
|
||||
29 31 A L H X S+ 0 0 23 -4,-2.3 4,-1.9 1,-0.2 -2,-0.2 0.918 112.0 49.1 -59.8 -42.7 20.2 20.7 43.9
|
||||
30 32 A A H X S+ 0 0 4 -4,-2.5 4,-2.9 2,-0.2 -1,-0.2 0.901 112.3 47.6 -62.9 -42.1 20.7 17.0 43.5
|
||||
31 33 A E H X S+ 0 0 34 -4,-2.0 4,-1.0 2,-0.2 -2,-0.2 0.929 109.9 51.9 -65.5 -46.0 23.0 17.5 40.6
|
||||
32 34 A M H <>S+ 0 0 10 -4,-3.0 5,-1.7 1,-0.2 3,-0.2 0.872 116.3 41.8 -57.3 -38.2 25.1 20.1 42.4
|
||||
33 35 A A H ><5S+ 0 0 0 -4,-1.9 3,-2.0 -5,-0.2 -23,-1.4 0.883 106.0 62.6 -75.5 -42.2 25.4 17.7 45.3
|
||||
34 36 A S H 3<5S+ 0 0 74 -4,-2.9 -1,-0.2 1,-0.3 -2,-0.2 0.674 104.2 49.7 -59.1 -19.1 26.0 14.7 43.0
|
||||
35 37 A I T 3<5S- 0 0 42 -4,-1.0 -1,-0.3 -3,-0.2 -2,-0.2 0.300 124.6 -96.4-106.3 8.8 29.3 16.4 41.8
|
||||
36 38 A G T < 5 + 0 0 19 -3,-2.0 2,-0.3 1,-0.2 -3,-0.2 0.771 64.3 159.6 86.2 29.2 30.7 17.2 45.2
|
||||
37 39 A L < - 0 0 0 -5,-1.7 2,-2.6 -29,-0.1 -27,-0.3 -0.664 50.6-114.2 -85.0 140.4 29.7 20.8 45.7
|
||||
38 40 A S + 0 0 1 -2,-0.3 288,-4.0 259,-0.2 -1,-0.1 -0.396 57.0 157.6 -73.0 68.5 29.6 22.1 49.3
|
||||
39 41 A V - 0 0 3 -2,-2.6 -30,-0.5 286,-0.2 288,-0.1 -0.825 50.3-104.3-100.4 132.4 25.9 22.6 49.5
|
||||
40 42 A P - 0 0 0 0, 0.0 -1,-0.1 0, 0.0 204,-0.1 -0.241 50.3-101.2 -52.1 135.2 24.1 22.7 52.9
|
||||
41 43 A P + 0 0 0 0, 0.0 201,-1.8 0, 0.0 2,-0.3 -0.164 59.9 129.8 -61.2 152.4 22.3 19.3 53.3
|
||||
42 44 A G E -AC 7 241A 1 -35,-2.1 -35,-3.0 199,-0.2 2,-0.3 -0.955 39.9-114.6-176.8-170.0 18.5 18.9 52.8
|
||||
43 45 A F E -AC 6 240A 2 197,-1.4 197,-3.3 -37,-0.3 2,-0.4 -0.972 13.4-133.1-148.4 161.7 15.8 16.9 51.0
|
||||
44 46 A T E -AC 5 239A 3 -39,-2.3 -39,-2.1 -2,-0.3 2,-0.7 -0.971 9.2-143.4-125.1 128.5 13.1 17.2 48.4
|
||||
45 47 A V E -AC 4 238A 0 193,-2.7 193,-1.8 -2,-0.4 -41,-0.2 -0.787 34.3-121.9 -89.3 115.1 9.5 16.1 48.5
|
||||
46 48 A S > - 0 0 0 -43,-2.6 4,-0.6 -2,-0.7 3,-0.2 0.049 14.8-114.6 -53.7 160.4 8.5 14.8 45.0
|
||||
47 49 A T H > S+ 0 0 1 -26,-1.8 4,-1.5 1,-0.2 189,-0.1 0.678 114.9 67.0 -71.1 -17.9 5.7 16.3 42.9
|
||||
48 50 A E H >> S+ 0 0 65 1,-0.2 4,-3.2 2,-0.2 3,-0.5 0.948 94.3 56.5 -65.2 -47.2 3.9 12.9 43.3
|
||||
49 51 A A H 3> S+ 0 0 0 1,-0.3 4,-0.7 2,-0.2 -1,-0.2 0.781 107.9 49.5 -53.2 -28.3 3.5 13.7 47.0
|
||||
50 52 A C H 3X S+ 0 0 4 -4,-0.6 4,-2.0 2,-0.2 -1,-0.3 0.822 112.0 47.1 -80.8 -33.1 1.8 16.9 45.9
|
||||
51 53 A Q H <X S+ 0 0 26 -4,-1.5 4,-2.3 -3,-0.5 5,-0.2 0.953 111.5 48.5 -71.8 -51.7 -0.5 15.0 43.5
|
||||
52 54 A Q H X S+ 0 0 61 -4,-3.2 4,-2.8 1,-0.2 7,-0.3 0.818 110.6 57.7 -56.4 -31.1 -1.4 12.3 46.0
|
||||
53 55 A Y H < S+ 0 0 15 -4,-0.7 6,-1.4 -5,-0.4 5,-0.3 0.985 110.0 38.1 -62.5 -61.8 -2.1 15.2 48.3
|
||||
54 56 A Q H < S+ 0 0 52 -4,-2.0 4,-0.5 4,-0.3 3,-0.3 0.753 122.4 46.7 -63.3 -26.0 -4.7 17.0 46.2
|
||||
55 57 A D H < S+ 0 0 131 -4,-2.3 2,-1.9 1,-0.2 -2,-0.2 0.887 97.9 64.6 -85.2 -43.8 -6.2 13.6 45.1
|
||||
56 58 A A S < S- 0 0 68 -4,-2.8 -1,-0.2 -5,-0.2 3,-0.1 -0.103 143.3 -64.9 -74.1 42.5 -6.5 11.8 48.5
|
||||
57 59 A G S S- 0 0 54 -2,-1.9 -1,-0.2 -3,-0.3 -2,-0.2 0.856 82.4 -74.6 77.7 36.7 -9.0 14.5 49.5
|
||||
58 60 A C S S+ 0 0 83 -4,-0.5 2,-0.3 -5,-0.3 -4,-0.3 0.857 103.2 121.7 40.2 49.8 -6.4 17.3 49.3
|
||||
59 61 A A S S- 0 0 48 -6,-1.4 -3,-0.2 -7,-0.3 -1,-0.2 -0.934 76.0 -70.4-136.2 157.8 -4.9 16.1 52.6
|
||||
60 62 A L - 0 0 60 -2,-0.3 3,-0.1 -3,-0.1 -10,-0.1 -0.263 59.0-121.4 -52.8 117.6 -1.4 15.0 53.8
|
||||
61 63 A P > - 0 0 9 0, 0.0 4,-0.6 0, 0.0 3,-0.5 -0.084 31.0 -89.1 -59.6 158.7 -0.7 11.5 52.2
|
||||
62 64 A A T 4 S+ 0 0 93 1,-0.2 -2,-0.0 2,-0.1 0, 0.0 -0.559 106.2 7.0 -77.5 126.9 0.0 8.3 54.2
|
||||
63 65 A G T > S+ 0 0 43 -2,-0.4 4,-2.0 -3,-0.1 3,-0.2 0.056 98.4 104.6 94.2 -25.3 3.6 7.6 55.0
|
||||
64 66 A L H > S+ 0 0 0 -3,-0.5 4,-2.8 1,-0.2 5,-0.2 0.953 78.8 49.6 -52.8 -58.4 4.9 10.9 53.7
|
||||
65 67 A W H X S+ 0 0 66 -4,-0.6 4,-2.3 1,-0.2 -1,-0.2 0.828 107.9 57.4 -51.6 -33.7 5.4 12.5 57.1
|
||||
66 68 A A H > S+ 0 0 58 -3,-0.2 4,-1.9 2,-0.2 -1,-0.2 0.973 110.1 42.0 -60.7 -54.3 7.3 9.4 58.1
|
||||
67 69 A E H X S+ 0 0 42 -4,-2.0 4,-2.9 1,-0.2 -2,-0.2 0.874 110.7 56.9 -59.3 -42.9 9.8 9.8 55.2
|
||||
68 70 A I H X S+ 0 0 2 -4,-2.8 4,-2.5 1,-0.2 -1,-0.2 0.923 107.2 49.6 -55.8 -44.4 10.0 13.6 55.8
|
||||
69 71 A V H X S+ 0 0 41 -4,-2.3 4,-2.6 -5,-0.2 -1,-0.2 0.890 108.1 52.8 -63.0 -40.3 11.1 12.7 59.4
|
||||
70 72 A D H X S+ 0 0 115 -4,-1.9 4,-2.9 1,-0.2 -2,-0.2 0.966 109.8 50.6 -57.8 -51.6 13.7 10.3 58.1
|
||||
71 73 A G H X S+ 0 0 7 -4,-2.9 4,-2.3 1,-0.2 -2,-0.2 0.910 111.1 45.4 -51.6 -53.0 15.0 13.1 55.9
|
||||
72 74 A L H X S+ 0 0 6 -4,-2.5 4,-3.2 2,-0.2 5,-0.2 0.914 112.4 51.4 -59.8 -44.0 15.3 15.6 58.6
|
||||
73 75 A Q H X S+ 0 0 45 -4,-2.6 4,-2.9 1,-0.2 5,-0.3 0.944 109.8 51.1 -58.2 -45.6 17.0 13.1 60.9
|
||||
74 76 A W H X S+ 0 0 69 -4,-2.9 4,-1.5 -5,-0.2 -1,-0.2 0.904 113.1 45.0 -56.6 -45.1 19.4 12.4 58.1
|
||||
75 77 A V H X S+ 0 0 2 -4,-2.3 4,-3.2 2,-0.2 -2,-0.2 0.906 113.4 49.2 -66.9 -43.6 20.1 16.1 57.8
|
||||
76 78 A E H X>S+ 0 0 30 -4,-3.2 4,-2.3 2,-0.2 5,-1.5 0.942 112.6 46.7 -61.1 -50.5 20.5 16.7 61.5
|
||||
77 79 A E H <5S+ 0 0 88 -4,-2.9 -1,-0.2 -5,-0.2 -2,-0.2 0.857 115.0 50.8 -59.8 -34.3 22.8 13.8 62.0
|
||||
78 80 A Y H <5S+ 0 0 62 -4,-1.5 -2,-0.2 -5,-0.3 -1,-0.2 0.939 115.6 37.7 -70.0 -50.4 24.7 15.2 58.9
|
||||
79 81 A M H <5S- 0 0 39 -4,-3.2 -2,-0.2 2,-0.2 -1,-0.2 0.658 104.0-120.2 -78.8 -18.9 25.0 18.8 60.1
|
||||
80 82 A G T <5S+ 0 0 61 -4,-2.3 2,-0.3 1,-0.3 -3,-0.2 0.964 79.4 97.2 75.0 51.9 25.7 18.1 63.8
|
||||
81 83 A A < - 0 0 14 -5,-1.5 2,-0.4 -6,-0.1 -1,-0.3 -0.965 60.4-136.0-163.8 158.4 22.6 20.1 64.9
|
||||
82 84 A T B > -f 89 0B 67 6,-4.7 8,-0.9 -2,-0.3 3,-0.8 -0.952 26.1-104.7-131.4 149.2 19.0 19.4 66.0
|
||||
83 85 A L T 3 S+ 0 0 21 -2,-0.4 119,-0.1 1,-0.3 8,-0.1 -0.563 105.7 8.1 -72.0 112.1 15.7 21.0 65.2
|
||||
84 86 A G T 3 S+ 0 0 32 -2,-0.6 -1,-0.3 29,-0.4 30,-0.1 0.904 95.5 124.9 82.0 48.7 14.5 23.0 68.2
|
||||
85 87 A D < - 0 0 35 -3,-0.8 -3,-0.3 1,-0.1 -1,-0.2 -0.927 47.6-157.9-140.9 113.0 17.7 22.8 70.3
|
||||
86 88 A P S S+ 0 0 59 0, 0.0 38,-0.1 0, 0.0 -1,-0.1 0.827 94.2 48.0 -57.2 -37.7 19.5 26.0 71.6
|
||||
87 89 A Q S S+ 0 0 168 1,-0.3 -2,-0.0 37,-0.0 31,-0.0 0.979 130.2 17.8 -69.1 -60.8 22.8 24.2 72.1
|
||||
88 90 A R S S- 0 0 35 2,-0.0 -6,-4.7 -6,-0.0 -1,-0.3 -0.604 93.5-169.3-110.4 65.4 23.0 22.5 68.7
|
||||
89 91 A P B -f 82 0B 44 0, 0.0 2,-0.4 0, 0.0 -6,-0.2 -0.275 12.4-163.9 -62.1 143.0 20.4 24.6 66.7
|
||||
90 92 A L - 0 0 8 -8,-0.9 2,-0.4 23,-0.2 -6,-0.4 -0.948 6.8-176.4-133.6 108.7 19.1 23.6 63.3
|
||||
91 93 A L - 0 0 19 -2,-0.4 152,-2.9 152,-0.2 2,-0.3 -0.844 11.6-157.8-104.9 140.5 17.2 26.2 61.2
|
||||
92 94 A L E -DE 112 242A 4 20,-2.4 20,-3.8 -2,-0.4 2,-0.4 -0.766 12.8-143.6-120.3 165.2 15.7 25.4 57.8
|
||||
93 95 A S E - E 0 241A 4 148,-2.4 148,-1.6 -2,-0.3 2,-0.5 -0.950 12.7-156.9-124.9 137.7 14.5 27.0 54.6
|
||||
94 96 A V E +DE 109 240A 0 15,-2.3 15,-1.8 -2,-0.4 2,-0.3 -0.939 17.5 169.5-125.9 112.7 11.5 25.8 52.6
|
||||
95 97 A R E - E 0 239A 80 144,-2.6 144,-2.5 -2,-0.5 12,-0.1 -0.871 20.8-143.1-119.4 153.2 11.2 26.6 48.9
|
||||
96 98 A S + 0 0 15 10,-0.5 142,-0.2 -2,-0.3 2,-0.1 -0.224 23.1 165.2 -97.8-169.1 8.7 25.3 46.3
|
||||
97 99 A G - 0 0 12 140,-0.4 140,-2.0 -2,-0.1 -71,-0.2 -0.213 17.6-156.0 151.4 117.1 9.5 24.5 42.6
|
||||
98 100 A A - 0 0 8 2,-0.5 -74,-3.3 138,-0.2 -73,-0.5 -0.212 44.6 -92.1 -94.9-172.1 7.8 22.7 39.7
|
||||
99 101 A A S S+ 0 0 46 136,-0.4 2,-0.3 -76,-0.3 -79,-0.1 0.759 113.1 24.7 -73.9 -24.2 9.3 21.1 36.6
|
||||
100 102 A V S S- 0 0 75 -80,-0.1 -2,-0.5 1,-0.1 -76,-0.1 -0.788 108.8 -68.4-130.2 174.0 8.8 24.4 34.8
|
||||
101 103 A S + 0 0 93 -2,-0.3 -2,-0.1 -4,-0.1 -1,-0.1 -0.365 55.0 173.9 -64.6 145.1 8.5 28.0 35.8
|
||||
102 104 A M > - 0 0 19 -4,-0.1 3,-0.5 -3,-0.0 -4,-0.1 -0.820 17.1-153.8-160.2 113.5 5.3 28.7 37.8
|
||||
103 105 A P T 3 S+ 0 0 34 0, 0.0 3,-0.1 0, 0.0 121,-0.1 -0.274 74.3 49.6 -80.1 172.7 4.2 31.9 39.5
|
||||
104 106 A G T 3 S+ 0 0 17 1,-0.3 117,-0.3 116,-0.2 114,-0.2 0.506 78.4 134.5 76.9 3.0 1.8 32.1 42.5
|
||||
105 107 A M < - 0 0 22 -3,-0.5 -1,-0.3 1,-0.1 107,-0.1 -0.501 69.7 -73.4 -84.8 156.4 3.6 29.4 44.4
|
||||
106 108 A M - 0 0 14 106,-0.3 -10,-0.5 105,-0.2 -1,-0.1 -0.197 54.8-115.8 -50.7 128.5 4.4 29.7 48.1
|
||||
107 109 A D - 0 0 116 1,-0.1 -1,-0.1 -12,-0.1 -13,-0.1 -0.268 41.0 -83.1 -66.1 152.8 7.2 32.2 48.8
|
||||
108 110 A T - 0 0 61 1,-0.1 2,-0.5 -13,-0.1 -13,-0.2 -0.283 41.3-153.2 -59.0 136.4 10.5 31.1 50.3
|
||||
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||||
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140 142 A D H X5S+ 0 0 45 -4,-2.3 4,-2.6 -5,-0.2 5,-0.2 0.986 119.1 40.0 -60.7 -63.0 5.9 37.5 60.2
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
207 209 A L H X S+ 0 0 33 -4,-2.4 4,-2.7 1,-0.2 -1,-0.2 0.927 110.2 54.1 -56.7 -47.9 2.5 23.2 58.0
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
819 831 A L < - 0 0 1 -3,-2.3 2,-0.4 -6,-0.1 -64,-0.2 -0.337 46.1-133.4 -54.8 124.8 18.3 28.1 -7.8
|
||||
820 832 A K E -a 755 0H 53 -66,-1.8 -64,-3.3 -2,-0.1 2,-0.5 -0.709 26.2-166.4 -83.5 132.5 20.3 30.4 -5.5
|
||||
821 833 A V E +a 756 0H 0 -2,-0.4 22,-3.2 -66,-0.2 23,-1.2 -0.956 16.7 151.6-129.9 118.9 18.0 31.8 -2.8
|
||||
822 834 A G E -ab 757 844H 0 -66,-3.6 -64,-3.1 -2,-0.5 2,-0.4 -0.692 32.3-130.5-131.5-176.4 18.7 34.6 -0.4
|
||||
823 835 A I E +ab 758 845H 0 21,-0.7 23,-2.2 -66,-0.3 -64,-0.2 -0.997 18.1 173.8-141.3 133.8 17.1 37.3 1.6
|
||||
824 836 A C + 0 0 2 -66,-3.0 -65,-0.2 -2,-0.4 -1,-0.1 0.300 46.6 111.0-121.5 5.1 18.0 41.0 1.7
|
||||
825 837 A G S > S- 0 0 1 -67,-1.1 3,-1.7 1,-0.1 21,-0.2 -0.208 89.8 -93.5 -69.0 174.3 15.2 42.5 3.8
|
||||
826 838 A E G > S+ 0 0 63 1,-0.3 3,-1.6 2,-0.2 -1,-0.1 0.675 120.3 75.7 -67.4 -17.3 16.3 43.7 7.3
|
||||
827 839 A H G > S+ 0 0 0 1,-0.3 3,-1.7 2,-0.2 -1,-0.3 0.693 75.2 85.1 -65.8 -13.4 15.4 40.3 8.9
|
||||
828 840 A G G < S+ 0 0 0 -3,-1.7 -1,-0.3 1,-0.3 -2,-0.2 0.601 95.8 37.5 -64.5 -12.0 18.7 39.2 7.3
|
||||
829 841 A G G < S+ 0 0 4 -3,-1.6 -1,-0.3 17,-0.1 -2,-0.2 0.239 92.2 102.9-122.9 12.9 20.6 40.5 10.3
|
||||
830 842 A E X> - 0 0 38 -3,-1.7 4,-3.0 1,-0.1 3,-1.1 -0.876 68.3-137.4-103.7 115.5 18.2 39.5 13.0
|
||||
831 843 A P H 3> S+ 0 0 42 0, 0.0 4,-2.3 0, 0.0 5,-0.1 0.782 100.8 42.5 -34.8 -58.9 19.2 36.4 15.0
|
||||
832 844 A S H 3> S+ 0 0 48 1,-0.2 4,-1.4 2,-0.2 5,-0.1 0.845 118.4 47.7 -65.4 -30.1 15.8 34.6 15.2
|
||||
833 845 A S H <> S+ 0 0 0 -3,-1.1 4,-2.5 2,-0.2 -1,-0.2 0.910 109.8 51.2 -74.5 -44.4 15.1 35.5 11.6
|
||||
834 846 A V H X S+ 0 0 0 -4,-3.0 4,-2.2 1,-0.2 -2,-0.2 0.911 108.2 54.3 -57.9 -40.7 18.5 34.3 10.4
|
||||
835 847 A A H X S+ 0 0 24 -4,-2.3 4,-2.1 -5,-0.3 -1,-0.2 0.892 108.2 48.4 -60.3 -42.8 17.8 31.0 12.3
|
||||
836 848 A F H X S+ 0 0 7 -4,-1.4 4,-1.4 1,-0.2 -1,-0.2 0.912 110.3 51.1 -64.3 -44.2 14.5 30.5 10.4
|
||||
837 849 A F H X>S+ 0 0 0 -4,-2.5 5,-2.1 2,-0.2 4,-0.5 0.880 108.0 53.6 -61.9 -37.4 16.2 31.2 7.0
|
||||
838 850 A A H ><5S+ 0 0 21 -4,-2.2 3,-1.4 1,-0.2 -2,-0.2 0.969 112.6 42.1 -63.1 -49.9 18.9 28.7 7.8
|
||||
839 851 A K H 3<5S+ 0 0 160 -4,-2.1 -1,-0.2 1,-0.3 -2,-0.2 0.698 105.9 64.1 -72.2 -14.3 16.4 25.9 8.5
|
||||
840 852 A A H 3<5S- 0 0 25 -4,-1.4 -1,-0.3 -5,-0.2 -2,-0.2 0.586 116.9-113.6 -81.3 -10.5 14.2 27.0 5.6
|
||||
841 853 A G T <<5 + 0 0 34 -3,-1.4 -3,-0.2 -4,-0.5 -2,-0.1 0.711 57.3 161.3 87.7 22.8 17.2 26.0 3.4
|
||||
842 854 A L < - 0 0 10 -5,-2.1 -1,-0.2 1,-0.1 -20,-0.2 -0.323 40.5-135.8 -69.1 162.9 18.1 29.4 2.0
|
||||
843 855 A D S S- 0 0 65 -22,-3.2 -317,-2.4 1,-0.3 2,-0.3 0.726 72.6 -17.4 -93.0 -24.9 21.6 29.8 0.6
|
||||
844 856 A Y E -ub 526 822H 4 -23,-1.2 -21,-0.7 -319,-0.3 2,-0.3 -0.992 49.0-132.0-171.5 168.4 22.4 33.1 2.2
|
||||
845 857 A V E -ub 527 823H 0 -319,-2.0 -317,-3.2 -2,-0.3 2,-0.4 -0.932 16.5-156.4-129.7 149.4 21.4 36.3 4.0
|
||||
846 858 A S E +u 528 0H 0 -23,-2.2 -317,-0.3 -2,-0.3 -18,-0.3 -0.997 22.4 154.6-134.9 127.7 22.4 39.8 3.3
|
||||
847 859 A C E -u 529 0H 0 -319,-1.7 -317,-2.9 -2,-0.4 -298,-0.2 -0.759 49.1 -56.7-138.3-177.8 22.4 42.7 5.8
|
||||
848 860 A S >> - 0 0 15 -319,-0.2 3,-1.2 -2,-0.2 4,-0.8 -0.153 60.9-101.9 -58.7 161.0 24.1 46.0 6.5
|
||||
849 861 A P G >4 S+ 0 0 12 0, 0.0 3,-1.0 0, 0.0 -395,-0.1 0.916 118.6 45.2 -54.3 -50.0 27.9 46.0 6.8
|
||||
850 862 A F G 34 S+ 0 0 44 -397,-0.9 4,-0.3 1,-0.2 -396,-0.1 0.471 108.3 58.0 -80.0 0.4 28.2 46.1 10.6
|
||||
851 863 A R G <> S+ 0 0 63 -3,-1.2 4,-2.4 -398,-0.1 3,-0.4 0.621 81.7 90.1 -99.1 -15.1 25.5 43.5 11.1
|
||||
852 864 A V H <X S+ 0 0 0 -3,-1.0 4,-2.5 -4,-0.8 5,-0.2 0.900 84.7 49.2 -48.0 -54.5 27.4 40.9 9.0
|
||||
853 865 A P H > S+ 0 0 2 0, 0.0 4,-2.7 0, 0.0 -1,-0.2 0.897 111.6 51.2 -57.6 -36.1 29.3 39.4 12.0
|
||||
854 866 A I H > S+ 0 0 18 -3,-0.4 4,-2.6 -4,-0.3 -2,-0.2 0.909 109.7 49.4 -65.3 -41.7 26.0 39.1 13.9
|
||||
855 867 A A H X S+ 0 0 0 -4,-2.4 4,-2.7 2,-0.2 -1,-0.2 0.915 110.6 50.6 -60.9 -45.7 24.4 37.3 11.0
|
||||
856 868 A R H X S+ 0 0 24 -4,-2.5 4,-1.2 1,-0.2 -2,-0.2 0.952 110.9 48.8 -59.2 -47.6 27.4 35.0 10.8
|
||||
857 869 A L H X S+ 0 0 0 -4,-2.7 4,-2.6 1,-0.2 3,-0.5 0.910 113.3 47.0 -59.1 -45.7 27.2 34.2 14.5
|
||||
858 870 A A H X S+ 0 0 5 -4,-2.6 4,-1.6 1,-0.2 -1,-0.2 0.863 106.3 57.2 -66.0 -38.0 23.4 33.5 14.2
|
||||
859 871 A A H < S+ 0 0 1 -4,-2.7 -335,-0.5 1,-0.2 -334,-0.2 0.764 113.7 41.7 -65.5 -23.1 23.8 31.3 11.2
|
||||
860 872 A A H >X S+ 0 0 0 -4,-1.2 3,-1.3 -3,-0.5 4,-0.6 0.883 108.9 56.4 -88.3 -45.4 26.2 29.1 13.3
|
||||
861 873 A Q H >< S+ 0 0 49 -4,-2.6 3,-0.7 1,-0.3 -2,-0.2 0.797 99.8 59.4 -58.4 -32.8 24.3 29.1 16.5
|
||||
862 874 A V T 3< S+ 0 0 39 -4,-1.6 -1,-0.3 1,-0.2 -2,-0.1 0.772 104.5 52.9 -68.5 -23.8 21.1 27.7 15.0
|
||||
863 875 A L T <4 0 0 67 -3,-1.3 -1,-0.2 -4,-0.2 -2,-0.2 0.561 360.0 360.0 -89.3 -10.4 23.1 24.7 13.8
|
||||
864 876 A V << 0 0 93 -3,-0.7 -1,-0.2 -4,-0.6 -2,-0.2 0.184 360.0 360.0-120.2 360.0 24.6 23.6 17.2
|
||||
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Add table
Reference in a new issue