title: Sequence and structure space model of protein divergence driven by point mutations.
abstract: New folds of protein structures emerge in evolution as a result of insertions, deletions or shuffling of fragments of underlying gene sequences, and from aggregated effects of point mutations. The result of these evolutionary processes is a rich and complex universe of protein sequences and structures, with characteristic features such as heavy-tailed distribution of fold occurrences, and a distinct shape of relationship between sequence identity and structure similarity. Better understanding of how the protein universe evolved to its present form can be achieved by creating models of protein structure evolution. Here we introduce a stochastic model of evolution that involves residue substitutions as the sole source of structure innovation, and is nonetheless able to reproduce the diversity of the protein domains repertoire, its cluster structure with heavy-tailed distribution of family sizes, and presence of the twilight zone populated with remote homologs.
authors.affiliation: Department of Computer Science, School of Engineering, Virginia Commonwealth University, 401 W. Main St., Richmond, Virginia 23284, USA. tarodz@vcu.edu
authors.forename: Tomasz
authors.initials: T
authors.lastname: Arodź
authors.forename: Przemysław M
authors.initials: PM
authors.lastname: Płonka
mesh_terms: D019143:Evolution, Molecular; D008958:Models, Molecular; D017354:Point Mutation; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000235:genetics
chemical_list: D011506:Proteins