Towards Molecular Dynamics Simulations of Large Protein Complexes

Abstract

The structure and dynamics of large (membrane)protein complexes is an important challenge for biophysical sciences. The formation of such complexes plays a major role in many biological pathways. Despite of their importance, until recently molecular dynamics simulations of protein complexes were impossible because of their large size.Coarse grained molecular dynamic force fields, like the Martini force field [Monticelli, 2008], are potentially powerful tools to investigate protein complex formation. Therefor it is important to probe there performance. To assess the performance of the Martini force field on protein interactions, we calculated the binding free energies of pairs of amino acid side chains in different solvents. The binding free energies were calculated from both equilibrium and PMF-simulations. The results were compared to results for united-atom (Gromos53) and all-atom (OPLS-AA) force fields.View Large Image | View Hi-Res Image | Download PowerPoint Slide