Team:KAIST-Korea/Project/Modeling

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(→Structural alignment results of single chain antibodies with FGF binding domain)
 
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__NOTOC__
__NOTOC__
{{:Team:KAIST/header}}
{{:Team:KAIST/header}}
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== Single chain antibody structural alignment ==
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<table width="100%" border="0" cellpadding="20px">
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=== Protocol ===
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<tr>
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==== Data source ====
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<td valign="top" width="75%">
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==== Single chain antibody synthesis ====
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<span style=font-size:30px><font face="Maiandra GD"><b> Modeling </b></font></span>
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==== Structure Prediction ====
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<br>
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==== Structure Alignment ====
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----
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=== Result===
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<br>
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====Structural alignment results of single chain antibodies with FGF binding domain ====
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&nbsp;&nbsp;Leaving cell transmit signal through chemical modifications of signal-related molecules like phosphorylation, methylation, acetylation or ubiquitination. And these chemical modifications are basically chemical reactions. Therefore, we can assume signal transduction pathway as sequential chemical reactions. We applied this assumption to signal transduction initiated by modified FGFR-antigen binding. Signal transduction follows these steps.
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{| class="sortable wikitable" border="0" align="center" style="border: 1px solid #999; background-color:#FFFFFF"
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<br>
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|-align="left" bgcolor="#CCCCCC"
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<br>
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! Name
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# Antigen binds to the single chain antibody of modified FGFR and form FGFR-complex(FGFRC).
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!Core Residues||Core RMSD||Raw Score||P-value
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# Two FGFR-complexes bind each other and form FGFR-complex-dimer(FGFRCD).
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|-
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# FGFRCD phosphorylate each other and form FGFR-complex-dimer-phosphorylate (FGFRCDnP)
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| 2VXT
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# FGFRCDnP phosphorylate STAT1 to for STAT1P.
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| 95
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# Two STAT1Ps bind each other and form STAT1P-dimer.
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| 2.676
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# STAT1P-dimer near cell surface diffuse to inside of nucleus of yeast.
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| 84.306
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# STAT1P-dimer in nucleus binds to GAS element and activate GFP gene.
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| 0.000222
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<br>
-
|-
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<br>
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| 2VXU
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&nbsp;&nbsp;And these steps may be formulated as these reactions.
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| 98
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<br>
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| 2.563
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<html>
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| 92.118
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<img src = "https://static.igem.org/mediawiki/2010/b/bd/Modeling1.png" width = 400>
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| 0.0000823
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</html>
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|-
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<br>
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| 2VXV
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<br>
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| 77
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&nbsp;&nbsp;And we can expect that the concentration of FGFRCDnP is constant at equilibrium state. The concentration of FGFRCDnP is<br>
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| 2.64
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<html>
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| 52.269
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<img src = "https://static.igem.org/mediawiki/2010/a/a6/KAISTModeling2.png" width = 200>
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| 0.0644
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</html>
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|-
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<br>
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| 2ZKH
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<br>
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| 96
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&nbsp;&nbsp;And the concentration of FGFRCD is
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| 2.855
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<br>
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| 93.411
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<html>
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| 0.001
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<img src = "https://static.igem.org/mediawiki/2010/5/5e/KAISTModeling3.png" width = 150>
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|-
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</html>
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| 3AAZ
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<br>
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| 84
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<br>
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| 4.197
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&nbsp;&nbsp;And the concentration of FGFRC is
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| 68.078
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<br>
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| 0.0642
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<html>
-
|-
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<img src = "https://static.igem.org/mediawiki/2010/c/c0/KAISTModeling4.png" width = 200>
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| 3D69
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</html>
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| 137
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<br>
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| 12.224
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<br>
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| 98.134
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&nbsp;&nbsp;Therefore, the concentration of FGFRCDnP as the function of concentration of FGFR [FGFR], that of antigen [antigen] and phosphorylation number n is<br>
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| 0.00541
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<html>
-
|-
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<img src = "https://static.igem.org/mediawiki/2010/0/02/KAISTModeling5.png" width = 500>
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| 3EO9
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</html>
-
| 80
+
<br>
-
| 2.282
+
<br>
-
| 84.665
+
-
| 0.00295
+
-
|-
+
-
| 3EOA
+
-
| 116
+
-
| 10.402
+
-
| 98.544
+
-
| 0.0547
+
-
|-
+
-
| 3EOB
+
-
| 68
+
-
| 4.685
+
-
| 56.357
+
-
| 0.3753
+
-
|-
+
-
| 3EYV
+
-
| 85
+
-
| 4.704
+
-
| 66.669
+
-
| 0.1653
+
-
|-
+
-
| 3FMG
+
-
| 81
+
-
| 2.629
+
-
| 73.298
+
-
| 0.0129
+
-
|-
+
-
| 3FOG
+
-
| 90
+
-
| 7.243
+
-
| 74.031
+
-
| 0.0785
+
-
|-
+
-
| 3G6D
+
-
| 72
+
-
| 4.403
+
-
| 69.774
+
-
| 0.1281
+
-
|-
+
-
| 3GBM
+
-
| 119
+
-
| 10.331
+
-
| 115.929
+
-
| 0.0314
+
-
|-
+
-
| 3GBN
+
-
| 77
+
-
| 2.788
+
-
| 57.204
+
-
| 0.0592
+
-
|-
+
-
| 3GHB
+
-
| 101
+
-
| 12.861
+
-
| 81.189
+
-
| 0.3984
+
-
|-
+
-
| 3GHE
+
-
| 96
+
-
| 3.302
+
-
| 109.208
+
-
| 0.00117
+
-
|-
+
-
| 3GI8
+
-
| 127
+
-
| 6.837
+
-
| 113.467
+
-
| 0.00038
+
-
|-
+
-
| 3GI9
+
-
| 52
+
-
| 3.534
+
-
| 43.56
+
-
| 0.166
+
-
|-
+
-
| 3GIZ
+
-
| 89
+
-
| 8.217
+
-
| 68.702
+
-
| 0.3172
+
-
|-
+
-
| 3GK8
+
-
| 91
+
-
| 6.84
+
-
| 84.048
+
-
| 0.00811
+
-
|-
+
-
| 3GKW
+
-
| 74
+
-
| 3.205
+
-
| 47.096
+
-
| 0.1215
+
-
|-
+
-
| 3GNM
+
-
| 135
+
-
| 4.739
+
-
| 103.812
+
-
| 0.00000297
+
-
|-
+
-
| 3GO1
+
-
| 103
+
-
| 8.842
+
-
| 77.631
+
-
| 0.2587
+
-
|-
+
-
| 3GRW
+
-
| 107
+
-
| 9.819
+
-
| 108.405
+
-
| 0.0449
+
-
|-
+
-
| 3H42
+
-
| 69
+
-
| 4.389
+
-
| 59.165
+
-
| 0.3421
+
-
|-
+
-
| 3HC0
+
-
| 67
+
-
| 3.065
+
-
| 40.982
+
-
| 0.1028
+
-
|-
+
-
| 3HC3
+
-
| 67
+
-
| 3.173
+
-
| 49.109
+
-
| 0.0944
+
-
|-
+
-
| 3HC4
+
-
| 36
+
-
| 1.998
+
-
| 42.538
+
-
| 0.206
+
-
|-
+
-
| 3HI5
+
-
| 77
+
-
| 3.222
+
-
| 58.096
+
-
| 0.1832
+
-
|-
+
-
| 3HI6
+
-
| 81
+
-
| 3.646
+
-
| 63.526
+
-
| 0.0394
+
-
|-
+
-
| 3HMW
+
-
| 83
+
-
| 4.159
+
-
| 62.598
+
-
| 0.1976
+
-
|-
+
-
| 3HMX
+
-
| 70
+
-
| 5.215
+
-
| 62.814
+
-
| 0.2228
+
-
|-
+
-
| 3HNT
+
-
| 84
+
-
| 2.62
+
-
| 74.666
+
-
| 0.00118
+
-
|-
+
-
| 3HNV
+
-
| 84
+
-
| 2.998
+
-
| 77.17
+
-
| 0.00374
+
-
|-
+
-
| 3HR5
+
-
| 78
+
-
| 4.158
+
-
| 58.026
+
-
| 0.2978
+
-
|-
+
-
| 3I50
+
-
| 65
+
-
| 2.206
+
-
| 52.252
+
-
| 0.1156
+
-
|-
+
-
| 3I9G
+
-
| 84
+
-
| 5.026
+
-
| 64.155
+
-
| 0.1506
+
-
|-
+
-
| 3IU3
+
-
| 75
+
-
| 3.192
+
-
| 56.006
+
-
| 0.2552
+
-
|-
+
-
| 3IXT
+
-
| 78
+
-
| 2.951
+
-
| 68.627
+
-
| 0.0378
+
-
|-
+
-
| 3KDM
+
-
| 87
+
-
| 4.273
+
-
| 65.722
+
-
| 0.1683
+
-
|-
+
-
| 3KS0
+
-
| 81
+
-
| 3.039
+
-
| 55.562
+
-
| 0.0192
+
-
|-
+
-
| 3KYK
+
-
| 88
+
-
| 4.728
+
-
| 68.681
+
-
| 0.1016
+
-
|-
+
-
| 3KYM
+
-
| 85
+
-
| 6.52
+
-
| 66.102
+
-
| 0.5135
+
-
|-
+
-
| 3L1O
+
-
| 93
+
-
| 2.545
+
-
| 85.909
+
-
| 0.0014
+
-
|-
+
-
| 3L5W
+
-
| 89
+
-
| 4.925
+
-
| 72.178
+
-
| 0.0637
+
-
|-
+
-
| 3L5X
+
-
| 88
+
-
| 4.796
+
-
| 65.262
+
-
| 0.1111
+
-
|-
+
-
| 3L5Y
+
-
| 64
+
-
| 4.689
+
-
| 65.227
+
-
| 0.2007
+
-
|-
+
-
| 3L95
+
-
| 73
+
-
| 5.105
+
-
| 70.312
+
-
| 0.0515
+
-
|-
+
-
| 3LMJ
+
-
| 76
+
-
| 2.699
+
-
| 56.627
+
-
| 0.0237
+
-
|-
+
-
| 3LQA
+
-
| 75
+
-
| 8.371
+
-
| 58.374
+
-
| 0.8315
+
-
|-
+
-
| 3LS4
+
-
| 79
+
-
| 2.458
+
-
| 72.68
+
-
| 0.00694
+
-
|-
+
-
| 3LS5
+
-
| 81
+
-
| 2.443
+
-
| 73.043
+
-
| 0.0014
+
-
|-
+
-
| 3LZF
+
-
| 96
+
-
| 2.468
+
-
| 93.292
+
-
| 0.00155
+
-
|-
+
-
| 3MLR
+
-
| 71
+
-
| 2.574
+
-
| 64.979
+
-
| 0.0165
+
-
|-
+
-
| 3MLS
+
-
| 75
+
-
| 2.534
+
-
| 57.386
+
-
| 0.0202
+
-
|-
+
-
| 3MLU
+
-
| 127
+
-
| 10.025
+
-
| 73.766
+
-
| 0.0305
+
-
|-
+
-
| 3MLV
+
-
| 75
+
-
| 2.454
+
-
| 62.321
+
-
| 0.0218
+
-
|-
+
-
| 3MLW
+
-
| 83
+
-
| 8.94
+
-
| 59.029
+
-
| 0.4846
+
-
|-
+
-
| 3MLX
+
-
| 118
+
-
| 11.485
+
-
| 105.391
+
-
| 0.0961
+
-
|-
+
-
| 3MLY
+
-
| 84
+
-
| 4.704
+
-
| 63.962
+
-
| 0.1023
+
-
|-
+
-
| 3MLZ
+
-
| 82
+
-
| 3.995
+
-
| 64.563
+
-
| 0.123
+
-
|-
+
-
| 3MUG
+
-
| 79
+
-
| 2.827
+
-
| 68.72
+
-
| 0.0223
+
-
|-
+
-
| 3MXV
+
-
| 125
+
-
| 10.857
+
-
| 121.911
+
-
| 0.01
+
-
|-
+
-
| 3MXW
+
-
| 102
+
-
| 11.262
+
-
| 78.348
+
-
| 0.4213
+
-
|--bgcolor="#C3C4D8"
+
-
| AntiTB
+
-
| 86
+
-
| 2.139
+
-
| 89.893
+
-
| 0.00443
+
-
|-
+
-
|}
+
-
====Structural alignment results of random short proteins with FGF binding domain ====
+

Latest revision as of 05:22, 16 August 2010

 

Modeling


  Leaving cell transmit signal through chemical modifications of signal-related molecules like phosphorylation, methylation, acetylation or ubiquitination. And these chemical modifications are basically chemical reactions. Therefore, we can assume signal transduction pathway as sequential chemical reactions. We applied this assumption to signal transduction initiated by modified FGFR-antigen binding. Signal transduction follows these steps.

  1. Antigen binds to the single chain antibody of modified FGFR and form FGFR-complex(FGFRC).
  2. Two FGFR-complexes bind each other and form FGFR-complex-dimer(FGFRCD).
  3. FGFRCD phosphorylate each other and form FGFR-complex-dimer-phosphorylate (FGFRCDnP)
  4. FGFRCDnP phosphorylate STAT1 to for STAT1P.
  5. Two STAT1Ps bind each other and form STAT1P-dimer.
  6. STAT1P-dimer near cell surface diffuse to inside of nucleus of yeast.
  7. STAT1P-dimer in nucleus binds to GAS element and activate GFP gene.



  And these steps may be formulated as these reactions.


  And we can expect that the concentration of FGFRCDnP is constant at equilibrium state. The concentration of FGFRCDnP is


  And the concentration of FGFRCD is


  And the concentration of FGFRC is


  Therefore, the concentration of FGFRCDnP as the function of concentration of FGFR [FGFR], that of antigen [antigen] and phosphorylation number n is
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