dorsal/arxiv
View SchemaPrediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences
| Authors | Markus Porto, H. Eduardo Roman, Michele Vendruscolo, Ugo Bastolla |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0410021 |
| URL | https://arxiv.org/abs/q-bio/0410021 |
| Journal | Mol. Biol. Evol. 22, 630-638 (2005) (see also Editor's Erratum, Mol. Biol. Evol. 22, 1156 (2005)) |
Abstract
We derive an analytic expression for site-specific stationary distributions of amino acids from the Structurally Constrained Neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that we obtain have a Boltzmann-like shape, and their effective temperature parameter, measuring the limit of divergent evolutionary changes at a given site, can be predicted from a site-specific topological property, the principal eigenvector of the contact matrix of the native conformation of the protein. These analytic results, obtained without free parameters, are compared with simulations of the SCN model and with the site-specific amino acid distributions obtained from the Protein Data Bank. These results also provide new insights into how the topology of a protein fold influences its designability, i.e. the number of sequences compatible with that fold. The dependence of the effective temperature on the principal eigenvector decreases for longer proteins, a possible consequence of the fact that selection for thermodynamic stability becomes weaker in this case.
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"abstract": "We derive an analytic expression for site-specific stationary distributions\nof amino acids from the Structurally Constrained Neutral (SCN) model of protein\nevolution with conservation of folding stability. The stationary distributions\nthat we obtain have a Boltzmann-like shape, and their effective temperature\nparameter, measuring the limit of divergent evolutionary changes at a given\nsite, can be predicted from a site-specific topological property, the principal\neigenvector of the contact matrix of the native conformation of the protein.\nThese analytic results, obtained without free parameters, are compared with\nsimulations of the SCN model and with the site-specific amino acid\ndistributions obtained from the Protein Data Bank. These results also provide\nnew insights into how the topology of a protein fold influences its\ndesignability, i.e. the number of sequences compatible with that fold. The\ndependence of the effective temperature on the principal eigenvector decreases\nfor longer proteins, a possible consequence of the fact that selection for\nthermodynamic stability becomes weaker in this case.",
"arxiv_id": "q-bio/0410021",
"authors": [
"Markus Porto",
"H. Eduardo Roman",
"Michele Vendruscolo",
"Ugo Bastolla"
],
"categories": [
"q-bio.BM",
"q-bio.PE"
],
"journal_ref": "Mol. Biol. Evol. 22, 630-638 (2005) (see also Editor\u0027s Erratum,\n Mol. Biol. Evol. 22, 1156 (2005))",
"title": "Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences",
"url": "https://arxiv.org/abs/q-bio/0410021"
},
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