From face to interface recognition: a differential geometric approach to distinguish DNA from RNA binding surfaces.

ABSTRACT: Protein nucleic acid interactions play a critical role in all steps of the gene expression pathway. Nucleic acid (NA) binding proteins interact with their partners, DNA or RNA, via distinct regions on their surface that are characterized by an ensemble of chemical, physical and geometrical properties. In this study, we introduce a novel methodology based on differential geometry, commonly used in face recognition, to characterize and predict NA binding surfaces on proteins. Applying the method on experimentally solved three-dimensional structures of proteins we successfully classify double-stranded DNA (dsDNA) from single-stranded RNA (ssRNA) binding proteins, with 83% accuracy. We show that the method is insensitive to conformational changes that occur upon binding and can be applicable f

SUBMITTER: Shazman S 

PROVIDER: S-EPMC3177183 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature