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Molecular Biology

, Volume 42, Issue 4, pp 623–628 | Cite as

Radius of gyration as an indicator of protein structure compactness

  • M. Yu. Lobanov
  • N. S. Bogatyreva
  • O. V. GalzitskayaEmail author
Structural-Functional Analysis of Biopolymers and Their Complexes

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 proteins contact density compactness all-or-none simple folding mechanism complex folding mechanism with accumulation of intermediate state 

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Copyright information

© MAIK Nauka 2008

Authors and Affiliations

  • M. Yu. Lobanov
    • 1
  • N. S. Bogatyreva
    • 1
  • O. V. Galzitskaya
    • 1
    Email author
  1. 1.Institute of Protein ResearchRussian Academy of Sciences, PushchinoMoscow regionRussia

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