Amino acid properties conserved in molecular evolution

PLoS One. 2014 Jun 26;9(6):e98983. doi: 10.1371/journal.pone.0098983. eCollection 2014.

Abstract

That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts - one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / chemistry*
  • Amino Acids / genetics
  • Evolution, Molecular*
  • Models, Genetic*
  • Protein Conformation

Substances

  • Amino Acids

Grants and funding

This research was partially funded within project No. 503-07-04-03. The project is subsidized by the Polish Ministry of Science and Higher Education as part of the statutory research of the Faculty of Applied IT, University of Information Technology and Management. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.