Dokholyan lab has a cover story in the December 7, 2011 issue of Structure. Dagliyan et al. present a rapid molecular dynamics-based approach to reveal the mechanism of protein-peptide recognition. The authors find that the peptide, rather than the protein, undergoes an induced fit, and that electrostatic interactions guide the peptide toward the binding region.
Onur Dagliyan is a graduate student in the laboratory of Dr. Nikolay Dokholyan, Professor of Biochemistry and Biophysics. He is the first-author on a paper in the journal Structure which was featured on the cover of their December 7, 2011 issue. The paper titled “Structural and Dynamic Determinants of Protein-peptide Recognition” presents a rapid molecular dynamics-based approach to reveal the mechanism of protein-peptide recognition.
Authors: Onur Dagliyan, Elizabeth A. Proctor, Kevin M. D’Auria, Feng Ding, Nikolay V. Dokholyan
Abstract: Protein-peptide interactions play important roles in many cellular processes, including signal transduction, trafficking, and immune recognition. Protein conformational changes upon binding, an ill-defined peptide binding surface, and the large number of peptide degrees of freedom make the prediction of protein-peptide interactions particularly challenging. To address these challenges, we perform rapid molecular dynamics simulations in order to examine the energetic and dynamic aspects of protein-peptide binding. We find that, in most cases, we recapitulate the native binding sites and native-like poses of protein-peptide complexes. Inclusion of electrostatic interactions in simulations significantly improves the prediction accuracy. Our results also highlight the importance of protein conformational flexibility, especially side-chain movement, which allows the peptide to optimize its conformation. Our findings not only demonstrate the importance of sufficient sampling of the protein and peptide conformations, but also reveal the possible effects of electrostatics and conformational flexibility on peptide recognition.