Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results

Abstract

We present a method to incorporate structural results from neutron reflectometry, a technique that determines interfacial structures such as protein-membrane complexes at a solid surface, into molecular dynamics simulations. By analyzing component volume occupancy profiles, which describe the one-dimensional distribution of a particular molecular component within an interfacial architecture, we construct a real-space constraint in the form of a biasing potential for the simulation that vanishes when the simulated and experimental profiles agree. This approach improves the correspondence between simulation and experiment, as shown for an earlier investigation where an NR-derived structure was well captured by an independent MD simulation, and may lead to faster equilibration of ensemble structures. We further show that time averaging of the observable when biasing with this approach permits fluctuations about the average, which are necessary for conformational exploration of the protein. The method described here also provides insights into systems that are characterized by NR and MD when the two show slight differences in their profiles. This is particularly valuable for studies of proteins at interfaces that contain disordered regions since the conformation of such regions is difficult to judge from the analysis of one-dimensional experimental profiles and take prohibitively long to equilibrate in simulations.