Recognition-induced Conformational Changes in Protein-Protein Docking

M.   F.   Lensink; R.      Mendez

Abstract

The ability to predict the three-dimensional structure of a protein complex starting from the isolated binding partners is becoming increasingly relevant. As our understanding of the molecular mechanisms behind protein-protein binding improves, so do the docking methods, however, it remains a challenge to adequately predict the unbound to bound transition. Side-chain flexibility is routinely handled and most docking methods allow for a certain degree of backbone flexibility, but systems undergoing moderate to large conformational changes can at present not correctly be modeled. The docking community is therefore putting an increased effort in the treatment of protein flexibility. Here we present a survey of the existing computational techniques to model protein flexibility in the context of protein-protein docking.

Keywords: Conformational Change, Protein-Protein Interaction, Protein Docking, Receptor-Ligand Binding, Conformational Selection, CAPRI, Protein Flexibility, Induced Fit