Implementation of visualCMAT in the laboratory practice

The correlated mutations/co-evolving residues are strongly associated with contact prediction and protein structure modeling, but the interest is growing to implement these positions in other areas of protein sciences. Key residues important for structural stability and involved in protein function and regulation can be predicted from co-evolution, however further experimental studies are usually needed to establish the structure-function relationship. The visualCMAT web-server has been developed to bridge the gap between theoretical bioinformatics and experimental studies by providing an intuitive and easy-to-implement interface to the analysis of correlated mutations/co-evolving residues for common use in a laboratory practice. Basic experience with the PyMol's GUI and command line is the sole requirement for using the visualCMAT web-server. An important step of preparing the multiple alignment of a diverse set of related proteins can be automatically performed by the sister web-server Mustguseal that is capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The results of the visualCMAT are organized for convenient visual analysis and can be downloaded to a local computer or operated on-line. In addition to the graphical output, a text file with amino acid co-occurrence statistics in each pair of correlated positions is prepared. The visualCMAT web-server predicts correlated substitutions and classifies them into two classes: interacting co-evolving residues which either form direct physical contacts or interact with the same ligand (e.g., a substrate or a crystallographic water molecule), and the long-range correlations. These two classes of pairs are further processed and displayed separately in the visualCMAT output due to different possible interpretation of their structural, functional, and regulatory significance. In addition, the binding sites are automatically predicted, mapped onto the protein structure, and discriminated by the presence of co-evolving positions, in particular, pockets enriched by the most statistically significant correlated residues are ranked first to facilitate their further analysis in particular proteins. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand's binding and allosteric communication between topologically independent sites in protein structures.

We hope that the visualCMAT will facilitate further studies of the correlated mutations/co-evolving residues and their implication to protein structure, function, and regulation, first of all experimentally.

Please see the visualCMAT publication for a discussion of the server features and guidelines to implemented them for common use in the laboratory practice.

You should also see the following publication for more information on studying co-evolving/correlated positions and their role in proteins:

Suplatov, D., Kirilin, E., & Švedas, V. (2016). Bioinformatic Analysis of Protein Families to Select Function-Related Variable Positions. In Understanding Enzymes: Function, Design, Engineering, and Analysis (pp. 351-385) Ed. Allan Svendsen. Pan Stanford.

Suplatov, D., Voevodin, V., & Švedas, V. (2015). Robust enzyme design: Bioinformatic tools for improved protein stability. Biotechnology journal, 10(3), 344-355.

Suplatov, D., & Švedas, V. (2015). Study of functional and allosteric sites in protein superfamilies. Acta Naturae, 7(4), 27, 34-45.