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Coevolution in defining the functional specificity.

Saikat Chakrabarti1, Anna R Panchenko

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA. chakraba@ncbi.nlm.nih.gov

Proteins
|October 3, 2008
PubMed
Summary
This summary is machine-generated.

Protein site covariation is driven by evolutionary history, protein structure, and function. Specificity determinants coevolve more frequently, influencing functional diversification and evolutionary rates.

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Area of Science:

  • Evolutionary biology
  • Molecular biology
  • Biochemistry

Background:

  • Covariation between protein sites can stem from shared evolutionary history.
  • Protein structure and function also influence site evolvability, independent of ancestry.
  • The precise forces driving residue coevolution and its link to functional diversification in protein families remain unclear.

Purpose of the Study:

  • To investigate the functional and structural factors contributing to covariation among specificity determinants.
  • To understand the relationship between coevolutionary processes and functional diversification within protein families.

Main Methods:

  • Analysis of functional and structural factors influencing site covariation.
  • Comparison of coevolutionary relationships among specificity determinants versus other functional and non-functional sites.

Main Results:

  • Specificity determinants coevolve more frequently with each other and other sites than non-specificity or less constrained sites.
  • Protein sites with numerous coevolutionary connections exhibit slower evolutionary rates.
  • Coevolutionary links were observed between spatially distant specificity sites sharing similar functional constraints.

Conclusions:

  • Functional and structural constraints significantly shape coevolutionary patterns in proteins.
  • Coevolutionary processes, including those between distant sites under similar constraints, contribute to functional diversification.
  • Stepwise coevolutionary processes offer insights into the mechanisms driving protein functional diversification.