Watching Conformational Changes in Proteins by Molecular Dynamics Simulations

Abstract

Proteins are dynamical molecules and their ability to adopt alternative conformations is central to their biological function. Examples include motions that underlie allosteric regulation or ligand binding, or protein dynamics in enzymes that can modulate the overall catalytic efficiency. Protein motions can often be described as an exchange between a dominant, ground state structure and one or more minor states. The structural and biophysical properties of these transiently and sparsely populated states are, however, difficult to study, and an atomic-level description of those states is challenging. In an attempt to determine how well molecular dynamics simulations can capture slow, conformational changes in protein molecules we have studied two protein systems which are known to undergo conformational exchange on the millisecond timescale, and for which structural information is available for both major and minor states. Using enhanced-sampling all-atom, explicit-solvent molecular simulations, guided by structural information from X-ray crystallography and NMR, we show that current force fields and sampling methods allow us to sample experimentally-determined alternative conformations with surprisingly high accuracy. In particular, we find that we can reversible sample both the ground state and minor state, at that the simulations capture the structure of the minor states also. Our simulations enable us to calculate the conformational free energy between the two states, and comparison with experiments demonstrates a high accuracy. Our simulations provide insight into the structural and biophysical properties of transiently populated minor states, and help reinterpret previous experimental measurements. Further, our results demonstrate that, at least in the two cases we have studied, modern simulation methods enable us to examine these otherwise “invisible” states of proteins and describe their structural, functional and thermodynamic properties.