Radius of gyration as an indicator of protein structure compactness

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 (alpha, beta, alpha/beta, and alpha + beta) showed that each class has a characteristic radius of gyration that determines the protein structure compactness. For instance, alpha proteins have the highest radius of gyration throughout the protein size range considered, suggesting a less tight packing as compared with beta-and (alpha + beta)-proteins. The lowest radius of gyration and, accordingly, the tightest packing are characteristic of alpha/beta-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.