Molecular Biology

, Volume 42, Issue 4, pp 623–628

Radius of gyration as an indicator of protein structure compactness

Authors

  • M. Yu. Lobanov
    • Institute of Protein ResearchRussian Academy of Sciences, Pushchino
  • N. S. Bogatyreva
    • Institute of Protein ResearchRussian Academy of Sciences, Pushchino
    • Institute of Protein ResearchRussian Academy of Sciences, Pushchino
Structural-Functional Analysis of Biopolymers and Their Complexes

DOI: 10.1134/S0026893308040195

Cite this article as:
Lobanov, M.Y., Bogatyreva, N.S. & Galzitskaya, O.V. Mol Biol (2008) 42: 623. doi:10.1134/S0026893308040195

Abstract

Identification and study of the main principles underlying the kinetics and thermodynamics of protein folding generate a new insight into the factors that control this process. Statistical analysis of the radius of gyration for 3769 protein domains of four major classes (α, β, α/β, and α + β) showed that each class has a characteristic radius of gyration that determines the protein structure compactness. For instance, α proteins have the highest radius of gyration throughout the protein size range considered, suggesting a less tight packing as compared with β-and (α + β)-proteins. The lowest radius of gyration and, accordingly, the tightest packing are characteristic of α/β-proteins. The protein radius of gyration normalized by the radius of gyration of a ball with the same volume is independent of the protein size, in contrast to compactness and the number of contacts per residue.

Key words

structural class of proteinscontact densitycompactnessall-or-none simple folding mechanismcomplex folding mechanism with accumulation of intermediate state

Copyright information

© MAIK Nauka 2008