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Evol Appl. 2013 Apr;6(3):423-33. doi: 10.1111/eva.12052. Epub 2013 Feb 13.

Structural dynamics flexibility informs function and evolution at a proteome scale.

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1
Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University Tempe, AZ, USA ; Department of Physics, Center for Biological Physics, Bateman Physical Sciences F-Wing, Arizona State University Tempe, AZ, USA.

Abstract

Protein structures are dynamic entities with a myriad of atomic fluctuations, side-chain rotations, and collective domain movements. Although the importance of these dynamics to proper functioning of proteins is emerging in the studies of many protein families, there is a lack of broad evidence for the critical role of protein dynamics in shaping the biological functions of a substantial fraction of residues for a large number of proteins in the human proteome. Here, we propose a novel dynamic flexibility index (dfi) to quantify the dynamic properties of individual residues in any protein and use it to assess the importance of protein dynamics in 100 human proteins. Our analyses involving functionally critical positions, disease-associated and putatively neutral population variations, and the rate of interspecific substitutions per residue produce concordant patterns at a proteome scale. They establish that the preservation of dynamic properties of residues in a protein structure is critical for maintaining the protein/biological function. Therefore, structural dynamics needs to become a major component of the analysis of protein function and evolution. Such analyses will be facilitated by the dfi, which will also enable the integrative use of structural dynamics with evolutionary conservation in genomic medicine as well as functional genomics investigations.

KEYWORDS:

elastic network models; functional genomics; single nucleotide variants; structural dynamics

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