Estimation of evolutionary distances from protein spatial structures

Research output: Contribution to journalArticle

34 Citations (Scopus)

Abstract

New equations are derived to estimate the number of amino acid substitutions per site between two homologous proteins from the root mean square (RMS) deviation between two spatial structures and from the fraction of identical residues between two sequences. The equations are based on evolutionary models, analyzing predominantly structural changes and not sequence changes. Evolution of spatial structure is treated as a diffusion in an elastic force field. Diffusion accounts for structural changes caused by amino acid substitutions, and elastic force reflects selection, which preserves protein fold. Obtained equations are supported by analysis of protein spatial structures.

Original languageEnglish (US)
Pages (from-to)359-369
Number of pages11
JournalJournal of Molecular Evolution
Volume45
Issue number4
DOIs
StatePublished - Oct 1997

Fingerprint

amino acid substitution
Amino Acid Substitution
structural change
protein
substitution
Substitution reactions
amino acid
Amino Acids
Proteins
Spatial Analysis
proteins
preserves
fold
analysis
preserve

Keywords

  • Evolutionary distance
  • Molecular evolution
  • Protein structure
  • RMS deviation
  • Substitution rates

ASJC Scopus subject areas

  • Genetics(clinical)
  • Molecular Biology
  • Genetics
  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Ecology, Evolution, Behavior and Systematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Agricultural and Biological Sciences(all)

Cite this

Estimation of evolutionary distances from protein spatial structures. / Grishin, Nick V.

In: Journal of Molecular Evolution, Vol. 45, No. 4, 10.1997, p. 359-369.

Research output: Contribution to journalArticle

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