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Open Access Research article

A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility

Tsun-Tsao Huang12, María Laura del Valle Marcos3, Jenn-Kang Hwang12 and Julian Echave3*

Author Affiliations

1 Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30050, Taiwan

2 Center for Bioinformatics Research, National Chiao Tung University, HsinChu 30050, Taiwan

3 Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, Martín de Irigoyen 3100, 1650 San Martín, Buenos Aires Argentina

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BMC Evolutionary Biology 2014, 14:78  doi:10.1186/1471-2148-14-78

Published: 9 April 2014

Abstract

Background

Protein sites evolve at different rates due to functional and biophysical constraints. It is usually considered that the main structural determinant of a site’s rate of evolution is its Relative Solvent Accessibility (RSA). However, a recent comparative study has shown that the main structural determinant is the site’s Local Packing Density (LPD). LPD is related with dynamical flexibility, which has also been shown to correlate with sequence variability. Our purpose is to investigate the mechanism that connects a site’s LPD with its rate of evolution.

Results

We consider two models: an empirical Flexibility Model and a mechanistic Stress Model. The Flexibility Model postulates a linear increase of site-specific rate of evolution with dynamical flexibility. The Stress Model, introduced here, models mutations as random perturbations of the protein’s potential energy landscape, for which we use simple Elastic Network Models (ENMs). To account for natural selection we assume a single active conformation and use basic statistical physics to derive a linear relationship between site-specific evolutionary rates and the local stress of the mutant’s active conformation.

We compare both models on a large and diverse dataset of enzymes. In a protein-by-protein study we found that the Stress Model outperforms the Flexibility Model for most proteins. Pooling all proteins together we show that the Stress Model is strongly supported by the total weight of evidence. Moreover, it accounts for the observed nonlinear dependence of sequence variability on flexibility. Finally, when mutational stress is controlled for, there is very little remaining correlation between sequence variability and dynamical flexibility.

Conclusions

We developed a mechanistic Stress Model of evolution according to which the rate of evolution of a site is predicted to depend linearly on the local mutational stress of the active conformation. Such local stress is proportional to LPD, so that this model explains the relationship between LPD and evolutionary rate. Moreover, the model also accounts for the nonlinear dependence between evolutionary rate and dynamical flexibility.

Keywords:
Protein evolution; Site-specific substitution rate; Local packing density; Elastic network model; Flexibility; Stress; Mean square fluctuation; Mean local mutational stress