A molecular dynamics simulation study of glutamine-binding protein

Abstract

Glutamine-binding protein (GlnBP) is one of the periplastic binding proteins from Gram-negative bacteria, whose crystal structure has been solved in both open and closed forms. GlnBP shares the common architecture with the other periplastic binding proteins composed of two domains linked by a hinge region. Molecular dynamics (MD) simulations were performed with the gromos96 program package to study the characters of GlnBP in both ligand-free and ligand-binding states. We also expected to provide some useful hints for understanding the mechanisms of inter-domain motions and ligand binding by analyzing the flexibility of the GlnBP. MD simulations reproduced most of the key hydrogen bonds observed in crystal structure. Binding of the ligand induced the formation of some stable hydrogen bonds, which made the hinge strands more rigid and further stabilized the complex. The analysis of MD trajectories of 2 ns showed that the open–close motion was coupled with inter-domain twisting motion in the ligand-free state, and some loop regions in the small domain contributed primarily to the flexibility of this protein while the main secondary structures maintained the fairly stable conformation. These motions seemed to shed some light on the mechanisms of ligand binding and releasing. All the results kept in good consistence with experimental data.