Structure-based mutation analysis GLA

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Revision as of 18:53, 29 June 2011 by Grandke (talk | contribs) (Structure Selection)

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 create a mutated structure and compare it to the wild-type protein.

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 certain 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 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

Gromacs

References

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