標題: Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure
作者: Yeh, So-Wei
Liu, Jen-Wei
Yu, Sung-Huan
Shih, Chien-Hua
Hwang, Jenn-Kang
Echave, Julian
生物資訊及系統生物研究所
Institude of Bioinformatics and Systems Biology
關鍵字: protein evolution;site-specific evolutionary rate;protein structure;local packing density;contact number;weighted contact number;relative solvent accessibility
公開日期: 1-Jan-2014
摘要: Protein sequences evolve under selection pressures imposed by functional and biophysical requirements, resulting in site-dependent rates of amino acid substitution. Relative solvent accessibility (RSA) and local packing density (LPD) have emerged as the best candidates to quantify structural constraint. Recent research assumes that RSA is the main determinant of sequence divergence. However, it is not yet clear which is the best predictor of substitution rates. To address this issue, we compared RSA and LPD with site-specific rates of evolution for a diverse data set of enzymes. In contrast with recent studies, we found that LPD measures correlate better than RSA with evolutionary rate. Moreover, the independent contribution of RSA is minor. Taking into account that LPD is related to backbone flexibility, we put forward the possibility that the rate of evolution of a site is determined by the ease with which the backbone deforms to accommodate mutations.
URI: http://dx.doi.org/10.1093/molbev/mst178
http://hdl.handle.net/11536/23381
ISSN: 0737-4038
DOI: 10.1093/molbev/mst178
期刊: MOLECULAR BIOLOGY AND EVOLUTION
Volume: 31
Issue: 1
起始頁: 135
結束頁: 139
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