, Volume 42, Issue 4, pp 623-628
Date: 10 Aug 2008

Radius of gyration as an indicator of protein structure compactness

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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.

Original Russian Text © M.Yu. Lobanov, N.S. Bogatyreva, O.V. Galzitskaya, 2008, published in Molekulyarnaya Biologiya, 2008, Vol. 42, No. 4, pp. 701–706.