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Three Independent Determinants of Protein Evolutionary Rate

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Abstract

One of the most widely accepted ideas related to the evolutionary rates of proteins is that functionally important residues or regions evolve slower than other regions, a reasonable outcome of which should be a slower evolutionary rate of the proteins with a higher density of functionally important sites. Oddly, the role of functional importance, mainly measured by essentiality, in determining evolutionary rate has been challenged in recent studies. Several variables other than protein essentiality, such as expression level, gene compactness, protein–protein interactions, etc., have been suggested to affect protein evolutionary rate. In the present review, we try to refine the concept of functional importance of a gene, and consider three factors—functional importance, expression level, and gene compactness, as independent determinants of evolutionary rate of a protein, based not only on their known correlation with evolutionary rate but also on a reasonable mechanistic model. We suggest a framework based on these mechanistic models to correctly interpret the correlations between evolutionary rates and the various variables as well as the interrelationships among the variables.

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Acknowledgments

This research was supported by Kangwon National University and Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (NRF-2011-0010679). SH is funded by NIH R01GM085226. Authors would like to thank the anonymous reviewers for their very generous comments, and Dr. Leonid Sukharnikov and Justin Malin for additional comments on the revised version.

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  1. Department of Medical Biotechnology, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, 200-701, South Korea

    Sun Shim Choi

  2. Department of Cell Biology and Molecular Genetics, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA

    Sridhar Hannenhalli

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  1. Sun Shim Choi
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Correspondence to Sun Shim Choi.

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Choi, S.S., Hannenhalli, S. Three Independent Determinants of Protein Evolutionary Rate. J Mol Evol 76, 98–111 (2013). https://doi.org/10.1007/s00239-013-9543-6

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