Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity.

ABSTRACT: Nucleotides are involved in several cellular processes, ranging from the transmission of genetic information, to energy transfer and storage. Both sequence and structure based methods have been developed to predict the location of nucleotide-binding sites in proteins. Here we propose a novel methodology that leverages the observation that nucleotide-binding sites have a modular structure. Nucleotides are composed of identifiable fragments, i.e. the phosphate, the nucleobase and the carbohydrate moieties. These fragments are bound by specific structural motifs that recur in proteins of different fold. Moreover these motifs behave as modules and are found in different combinations across fold space. Our method predicts binding sites for each nucleotide fragment by comparing a query protein w

SUBMITTER: Parca L 

PROVIDER: S-EPMC3507729 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature