Dissection, residue conservation, and structural classification of protein-DNA interfaces.

TitleDissection, residue conservation, and structural classification of protein-DNA interfaces.
Publication TypeJournal Article
Year of Publication2009
AuthorsBiswas, S., M. Guharoy, and P. Chakrabarti
JournalProteins
Volume74
Issue3
Pagination643-54
Date Published2009 Feb 15
ISSN1097-0134
KeywordsBinding Sites, Databases, Protein, DNA, DNA-Binding Proteins, Entropy, Models, Molecular, Protein Conformation, Protein Structure, Secondary, Water
Abstract

The basic DNA-binding modules of 128 protein-DNA interfaces have been analyzed. Although these are less planar, like the protein-protein interfaces, the protein-DNA interfaces can also be dissected into core regions in which all the fully-buried atoms are located, and rim regions having atoms with residual accessibilities. The sequence entropy of the core residues is smaller than those in the rim, indicating that the former are better conserved and possibly contribute more towards the binding free energy, as has been implicated in protein-protein interactions. On the protein side, 1014 A(2) of the surface is buried of which 63% belong to the core. There are some differences in the propensities of residues to occur in the core and the rim. In the DNA strands, the nucleotide(s) containing fully-buried atoms in all three components usually occupy central positions of the binding region. A new classification scheme for the interfaces has been introduced based on the composition of secondary structural elements of residues and the results compared with the conventional classification of DNA-binding proteins, as well as the protein class of the molecule. It appears that a common framework may be developed to understand both protein-protein and protein-DNA interactions.

DOI10.1002/prot.22180
Alternate JournalProteins
PubMed ID18704949
Research group: