Cavities and atomic packing in protein structures and interfaces.

ABSTRACT: A comparative analysis of cavities enclosed in a tertiary structure of proteins and interfaces formed by the interaction of two protein subunits in obligate and non-obligate categories (represented by homodimeric molecules and heterocomplexes, respectively) is presented. The total volume of cavities increases with the size of the protein (or the interface), though the exact relationship may vary in different cases. Likewise, for individual cavities also there is quantitative dependence of the volume on the number of atoms (or residues) lining the cavity. The larger cavities tend to be less spherical, solvated, and the interfaces are enriched in these. On average 15 A(3) of cavity volume is found to accommodate single water, with another 40-45 A(3) needed for each additional solvent molecul

SUBMITTER: Sonavane S 

PROVIDER: S-EPMC2582456 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature