Structural dynamics flexibility informs function and evolution at a proteome scale

Zeynep Nevin Gerek, Sudhir Kumar, Sefika Ozkan

Research output: Contribution to journalArticle

44 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)423-433
Number of pages11
JournalEvolutionary Applications
Volume6
Issue number3
DOIs
StatePublished - Apr 2013

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Proteome
proteome
protein
Proteins
proteins
dynamic property
protein structure
genomics
Genomics
medicine
substitution
Medicine

Keywords

  • Elastic network models
  • Functional genomics
  • Single nucleotide variants
  • Structural dynamics

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

Structural dynamics flexibility informs function and evolution at a proteome scale. / Nevin Gerek, Zeynep; Kumar, Sudhir; Ozkan, Sefika.

In: Evolutionary Applications, Vol. 6, No. 3, 04.2013, p. 423-433.

Research output: Contribution to journalArticle

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