An Evolutionary View on Disulfide Bond Connectivities Prediction Using Phylogenetic Trees and a Simple Cysteine Mutation Model.

ABSTRACT: Disulfide bonds are crucial for many structural and functional aspects of proteins. They have a stabilizing role during folding, can regulate enzymatic activity and can trigger allosteric changes in the protein structure. Moreover, knowledge of the topology of the disulfide connectivity can be relevant in genomic annotation tasks and can provide long range constraints for ab-initio protein structure predictors. In this paper we describe PhyloCys, a novel unsupervised predictor of disulfide bond connectivity from known cysteine oxidation states. For each query protein, PhyloCys retrieves and aligns homologs with HHblits and builds a phylogenetic tree using ClustalW. A simplified model of cysteine co-evolution is then applied to the tree in order to hypothesize the presence of oxidized cyste

SUBMITTER: Raimondi D 

PROVIDER: S-EPMC4498770 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature