Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening.

ABSTRACT: The binding of short disordered peptide stretches to globular protein domains is important for a wide range of cellular processes, including signal transduction, protein transport, and immune response. The often promiscuous nature of these interactions and the conformational flexibility of the peptide chain, sometimes even when bound, make the binding specificity of this type of protein interaction a challenge to understand. Here we develop and test a Monte Carlo-based procedure for calculating protein-peptide binding thermodynamics for many sequences in a single run. The method explores both peptide sequence and conformational space simultaneously by simulating a joint probability distribution which, in particular, makes searching through peptide sequence space computationally efficient.

SUBMITTER: Bhattacherjee A 

PROVIDER: S-EPMC3812049 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature