title: Cavities in protein-DNA and protein-RNA interfaces.
abstract: An analysis of cavities present in protein-DNA and protein-RNA complexes is presented. In terms of the number of cavities and their total volume, the interfaces formed in these complexes are akin to those in transient protein-protein heterocomplexes. With homodimeric proteins protein-DNA interfaces may contain cavities involving both the protein subunits and DNA, and these are more than twice as large as cavities involving a single protein subunit and DNA. A parameter, cavity index, measuring the degree of surface complementarity, indicates that the packing of atoms in protein-protein/DNA/RNA is very similar, but it is about two times less efficient in the permanent interfaces formed between subunits in homodimers. As within the tertiary structure and protein-protein interfaces, protein-DNA interfaces have a higher inclination to be lined by beta-sheet residues; from the DNA side, base atoms, in particular those in minor grooves, have a higher tendency to be located in cavities. The larger cavities tend to be less spherical and solvated. A small fraction of water molecules are found to mediate hydrogen-bond interactions with both the components, suggesting their primary role is to fill in the void left due to the local non-complementary nature of the surface patches.
authors.affiliation: Department of Biochemistry and Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054, India.
authors.forename: Shrihari
authors.initials: S
authors.lastname: Sonavane
authors.forename: Pinak
authors.initials: P
authors.lastname: Chakrabarti
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry; D017433:Protein Structure, Secondary; D012313:RNA / Q000737:chemistry; D016601:RNA-Binding Proteins / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D000596:Amino Acids; D004268:DNA-Binding Proteins; D009711:Nucleotides; D016601:RNA-Binding Proteins; D014867:Water; D012313:RNA; D004247:DNA