Estimating the accuracy of the MARTINI model towards the investigation of peripheral protein–membrane interactions
Sriraksha Srinivasan, Valeria Zoni, Stefano Vanni
Abstract
experimental validation. In this article, we investigate the ability of the MARTINI CG force field, specifically the 3 open-beta version, to reproduce known experimental observations regarding the membrane binding behavior of 12 peripheral membrane proteins and peptides. Based on observations of multiple binding and unbinding events in several independent replicas, we found that, despite the presence of false positives and false negatives, this model is mostly able to correctly characterize the membrane binding behavior of peripheral proteins, and to identify key residues found to disrupt membrane binding in mutagenesis experiments. While preliminary, our investigations suggest that transferable chemical-specific CG force fields have enormous potential in the characterization of the membrane binding process by peripheral proteins, and that the identification of negative results could help drive future force field development efforts.