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Artículo

Too packed to change: Side-chain packing and site-specific substitution rates in protein evolution

Marcos, María LauraIcon ; Echave, JuliánIcon
Fecha de publicación: 04/2015
Editorial: PeerJ Inc
Revista: PeerJ
ISSN: 2167-8359
Idioma: Inglés
Tipo de recurso: Artículo publicado
Clasificación temática:
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Resumen

In protein evolution, due to functional and biophysical constraints, the rates of amino acid substitution differ from site to site. Among the best predictors of site-specific rates are solvent accessibility and packing density. The packing density measure that best correlates with rates is the weighted contact number (WCN), the sum of inverse square distances between a site's Ca and the Ca of the other sites. According to a mechanistic stress model proposed recently, rates are determined by packing because mutating packed sites stresses and destabilizes the protein's active conformation. While WCN is a measure of Ca packing, mutations replace side chains. Here, we consider whether a site's evolutionary divergence is constrained by main-chain packing or side-chain packing. To address this issue, we extended the stress theory to model side chains explicitly. The theory predicts that rates should depend solely on side-chain contact density. We tested this prediction on a data set of structurally and functionally diverse monomeric enzymes. We compared side-chain contact density with main-chain contact density measures and with relative solvent accessibility (RSA). We found that side-chain contact density is the best predictor of rate variation among sites (it explains 39.2% of the variation). Moreover, the independent contribution of main-chain contact density measures and RSA are negligible. Thus, as predicted by the stress theory, site-specific evolutionary rates are determined by side-chain packing.
Palabras clave: Contact Density , Packing , Protein Evolution , Rate Variation Among Sites , Side Chain , Structural Constraints
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info:eu-repo/semantics/openAccess Excepto donde se diga explícitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
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URI: http://hdl.handle.net/11336/51783
DOI: https://dx.doi.org/10.7717/peerj.911
URL: https://peerj.com/articles/911/
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Citación
Marcos, María Laura; Echave, Julián; Too packed to change: Side-chain packing and site-specific substitution rates in protein evolution; PeerJ Inc; PeerJ; 2015; 3; 4-2015; 1-12
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