Difference between revisions of "Structure-based mutation analysis GLA"

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m (Energy Comparison)
(Energy Comparison)
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|colspan="4"| WT||-||-20.93 ||- ||-20481.23 ||-
 
|colspan="4"| WT||-||-20.93 ||- ||-20481.23 ||-
 
|-
 
|-
| 1 || 42 || ATG-ACG || Met -> Thr ||343.25||157.29 ||−178.22 ||-20324.41 ||−156.82
+
| 1 || 42 || ATG-ACG || Met -> Thr ||343.25||157.29 ||-178.22 ||-20324.41 ||-156.82
 
|-
 
|-
| 2 || 65 || AGT-ACG || Ser -> Thr ||327.798||152.87 ||−173.8 ||-20339.34 ||−141.89
+
| 2 || 65 || AGT-ACG || Ser -> Thr ||327.798||152.87 ||-173.8 ||-20339.34 ||-141.89
 
|-
 
|-
| 3 || 117 || ATT-AGT || Ile -> Ser ||333.027||157.97 ||−178.9 ||-20353.47 ||−127.76
+
| 3 || 117 || ATT-AGT || Ile -> Ser ||333.027||157.97 ||-178.9 ||-20353.47 ||-127.76
 
|-
 
|-
| 4 || 143 ||cGCA-ACA || Ala -> Thr ||333.944||154.40 || −175.33||-20339.32 ||−141.91
+
| 4 || 143 ||cGCA-ACA || Ala -> Thr ||333.944||154.40 || -175.33||-20339.32 ||-141.91
 
|-
 
|-
| 5 || 186 || CAC-CGC || His -> Arg ||323.717||154.57 ||−175.5 ||-20321.32 ||−159.91
+
| 5 || 186 || CAC-CGC || His -> Arg ||323.717||154.57 ||-175.5 ||-20321.32 ||-159.91
 
|-
 
|-
| 6 || 205 || gCCT-ACT || Pro -> Thr ||340.619||155.96 ||−176.89 ||-20345.87 ||−135.36
+
| 6 || 205 || gCCT-ACT || Pro -> Thr ||340.619||155.96 ||-176.89 ||-20345.87 ||-135.36
 
|-
 
|-
| 7 || 244 || gGAC-CAC || Asp -> His ||333.594||152.08 ||−173.01 ||-20393.12 ||−88.11
+
| 7 || 244 || gGAC-CAC || Asp -> His ||333.594||152.08 ||-173.01 ||-20393.12 ||-88.11
 
|-
 
|-
| 8 || 283 || CAG-CCG || Gln -> Pro ||332.631||159.91 ||−180.84 ||-8027.71 ||−12453.52
+
| 8 || 283 || CAG-CCG || Gln -> Pro ||332.631||159.91 ||-180.84 ||-8027.71 ||-12453.52
 
|-
 
|-
| 9 || 321 || tCAG-TAG || Gln -> Glu ||332.853||160.95 ||−181.88 ||-20246.98 ||−234.25
+
|8.2||-||-||-||-||-||-||-19134.48||-1346,95
 
|-
 
|-
| 10 || 363 || TATa-TAA || Arg -> Cys ||330.56||150.50 ||−171.43 ||-20295.77 ||−185.46
+
| 9 || 321 || tCAG-TAG || Gln -> Glu ||332.853||160.95 ||-181.88 ||-20246.98 ||-234.25
  +
|-
  +
| 10 || 363 || TATa-TAA || Arg -> Cys ||330.56||150.50 ||-171.43 ||-20295.77 ||-185.46
 
|-
 
|-
 
|}
 
|}

Revision as of 20:28, 1 July 2011

by Benjamin Drexler and Fabian Grandke

Introduction

In this task we analyse the structure of our protein to find out what effects the point mutations have. Therefor we created mutated structures and compared them to the wild-type protein. Several tools based on different methods have been used to achieve that aim. We used the mutations that we have chosen in the previous task.

Structure Selection

There are several structure files available for our protein:

PDB ID Resolution [Å] ph-Value R-Factor Coverage [%] Missing Residues
1R46 3.25 8.0 0.262 99.7 422-429
1R47 3.45 8.0 0.285 99.5 422-429
3GXN 3.01 NULL 0.239 88.08 422-429
3GXP 2.20 NULL 0.204 81.9 422-429
3GXT 2.70 NULL 0.245 97.29 422-429
3HG2 2.30 4.6 0.178 97.32 422-429
3HG3 1.90 6.5 0.167 98.64 427-435
3HG4 2.30 4.6 0.166 99.86 422-429
3HG5 2.30 4.6 0.192 100 422-429
3LX9 2.04 6.5 0.178 98.92 423-435
3LXA 3.04 6.5 0.216 99.52 427-435
3LXB 2.85 6.5 0.227 99.3 427-435
3LXC 2.35 6.5 0.186 98.31 423-435

We set two cutoffs to decide which structures are excluded:

  • ph-value: < 6.5
  • resolution: > 2.7

After we applied the cutoffs to our set of structures three were left (exclusion factors are colored red in the table). One of them was slightly better than the other ones so we decided to use 3HG3 (worse values are colored gray in the table). Additionally 3GH3 has the best overall resolution and R-factor (colored green). As the missing residues are very similar for all structures they are not further taken into account.

Mutation Mapping

Energy Comparison

Number AA-Position Codon change Amino acid change SCWRL4 FoldX FoldX - Diff Minimise Minimise - Diff
WT - -20.93 - -20481.23 -
1 42 ATG-ACG Met -> Thr 343.25 157.29 -178.22 -20324.41 -156.82
2 65 AGT-ACG Ser -> Thr 327.798 152.87 -173.8 -20339.34 -141.89
3 117 ATT-AGT Ile -> Ser 333.027 157.97 -178.9 -20353.47 -127.76
4 143 cGCA-ACA Ala -> Thr 333.944 154.40 -175.33 -20339.32 -141.91
5 186 CAC-CGC His -> Arg 323.717 154.57 -175.5 -20321.32 -159.91
6 205 gCCT-ACT Pro -> Thr 340.619 155.96 -176.89 -20345.87 -135.36
7 244 gGAC-CAC Asp -> His 333.594 152.08 -173.01 -20393.12 -88.11
8 283 CAG-CCG Gln -> Pro 332.631 159.91 -180.84 -8027.71 -12453.52
8.2 - - - - - - -19134.48 -1346,95
9 321 tCAG-TAG Gln -> Glu 332.853 160.95 -181.88 -20246.98 -234.25
10 363 TATa-TAA Arg -> Cys 330.56 150.50 -171.43 -20295.77 -185.46

Gromacs

References

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