Analysis of the impact of solvent on contacts prediction in proteins.
BACKGROUND
The correlated mutations concept is based on the assumption that interacting protein residues coevolve, so that a mutation in one of the interacting counterparts is compensated by a mutation in the other. Approaches based on this concept have been widely used for protein contacts prediction since the 90s. Previously, we have shown that water-mediated interactions play an important role in protein interfaces. We have observed that current "dry" correlated mutations approaches might not properly predict certain interactions in protein interfaces due to the fact that they are water-mediated.


RESULTS
The goal of this study has been to analyze the impact of including solvent into the concept of correlated mutations. For this purpose we use linear combinations of the predictions obtained by the application of two different similarity matrices: a standard "dry" similarity matrix (DRY) and a "wet" similarity matrix (WET) derived from all water-mediated protein interfacial interactions in the PDB. We analyze two datasets containing 50 domains and 10 domain pairs from PFAM and compare the results obtained by using a combination of both matrices. We find that for both intra- and interdomain contacts predictions the introduction of a combination of a "wet" and a "dry" similarity matrix improves the predictions in comparison to the "dry" one alone.


CONCLUSIONS
Our analysis, despite the complexity of its possible general applicability, opens up that the consideration of water may have an impact on the improvement of the contact predictions obtained by correlated mutations approaches.
Samsonov
Sergey A
SA
Structural Bioinformatics, BIOTEC TU Dresden, Tatzberg, Germany. sergey.samsonov@biotec.tu-dresden.de
Teyra
Joan
J
Anders
Gerd
G
Pisabarro
M Teresa
MT
D030562:Databases, Protein; D009154:Mutation; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry; D018909:src Homology Domains
D011506:Proteins; D012997:Solvents; D014867:Water