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

Biswas, Sumit ; Guharoy, Mainak ; Chakrabarti, Pinak (2008) Structural segments and residue propensities in protein-RNA interfaces: comparison with protein-protein and protein-DNA complexes Bioinformation, 2 (10). pp. 422-427. ISSN 0973-2063

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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.

Item Type:Article
Source:Copyright of this article belongs to Biomedical Informatics.
Keywords:Protein-protein Interactions; Protein-DNA Interactions; Protein-RNA Interactions; Binding Interface; Protein Secondary Structure
ID Code:89214
Deposited On:24 Apr 2012 12:38
Last Modified:19 May 2016 03:48

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