Structural segments and residue propensities in protein-RNA interfaces: comparison with protein-protein and protein-DNA complexes.

TitleStructural segments and residue propensities in protein-RNA interfaces: comparison with protein-protein and protein-DNA complexes.
Publication TypeJournal Article
Year of Publication2008
AuthorsBiswas, S., M. Guharoy, and P. Chakrabarti
JournalBioinformation
Volume2
Issue10
Pagination422-7
Date Published2008
ISSN0973-2063
Abstract

The interface of a protein molecule that is involved in binding another protein, DNA or RNA has been characterized in terms of the number of unique secondary structural segments (SSSs), made up of stretches of helix, strand and non-regular (NR) regions. On average 10-11 segments define the protein interface in protein-protein (PP) and protein-DNA (PD) complexes, while the number is higher (14) for protein-RNA (PR) complexes. While the length of helical segments in PP interaction increases with the interface area, this is not the case in PD and PR complexes. The propensities of residues to occur in the three types of secondary structural elements (SSEs) in the interface relative to the corresponding elements in the protein tertiary structures have been calculated. Arg, Lys, Asn, Tyr, His and Gln are preferred residues in PR complexes; in addition, Ser and Thr are also favoured in PD interfaces.

Alternate JournalBioinformation
PubMed ID18841236
PubMed Central IDPMC2561160
Research group: