Enhancing Protein Adsorption Simulations by Using Accelerated Molecular Dynamics

Abstract

The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation (≪1 μs) and experiment (up to hours), and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces. © 2013 Mücksch, Urbassek.