Compactness determines protein folding type

Oxana V. Galzitskaya, Natalyya S. Bogatyreva, Dmitry N. Ivankov

Research output: Contribution to journalArticlepeer-review

22 Citations (Scopus)

Abstract

We have demonstrated here that protein compactness, which we define as the ratio of the accessible surface area of a protein to that of the ideal sphere of the same volume, is one of the factors determining the mechanism of protein folding. Proteins with multi-state kinetics, on average, are more compact (compactness is 1.49 ± 0.02 for proteins within the size range of 101-151 amino acid residues) than proteins with two-state kinetics (compactness is 1.59 ± 0.03 for proteins within the same size range of 101-151 amino acid residues). We have shown that compactness for homologous proteins can explain both the difference in folding rates and the difference in folding mechanisms.

Original languageEnglish
Pages (from-to)667-680
Number of pages14
JournalJournal of Bioinformatics and Computational Biology
Volume6
Issue number4
DOIs
Publication statusPublished - 2008
Externally publishedYes

Keywords

  • Compactness
  • Multi-state kinetics
  • Protein packing
  • Sphericity
  • Structural class
  • Two-state kinetics

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