Analysis of the impact of solvent on contacts prediction in proteins

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.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.The correlated mutations concept was introduced in the 90s [1-4] and has been widely used for protein contacts prediction [5]. The method is based on the assumption that interacting protein residues co-evolve, so that a mutation in one of the interacting counterparts is compensated by a mutation in the other. Therefore, it is possible to introduce an exchange matrix or other measures of similarity for each sequence position in a multiple sequence alignment and to use covariance (correlation coefficient) between two positions to predict if the residues at these positions may establish physical contact in 3D space, and develop contact maps. Several different similarity measures and algorithms have been implemented in the concept of correlated mutations [5-7]. Most exchange matrices are based either on physico-chemical properties of amino acids or on statistical data on the substitutions obtained from multiple sequence alignments [8]. Statistically it is clear that the distribution of distances between the re