Radius of gyration as an indicator of protein structure compactness

Abstract

Identification and study of the main principles underlying the kinetics and thermodynamics of pro- tein 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. DOI: 10.1134/S0026893308040195