Open AccessStructural dynamics flexibility informs function and evolution at a proteome scale
Author(s) -
Nevin Gerek Zeynep,
Kumar Sudhir,
Banu Ozkan Sefika
Publication year - 2013
Publication title -
evolutionary applications
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.776
H-Index - 68
ISSN - 1752-4571
DOI - 10.1111/eva.12052
Subject(s) - biology , proteome , computational biology , evolutionary dynamics , protein domain , flexibility (engineering) , function (biology) , human proteome project , protein dynamics , protein function , proteomics , protein structure , evolutionary biology , population , genetics , gene , biochemistry , statistics , demography , mathematics , sociology
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.