title: Adaptive resolution simulation of an atomistic protein in MARTINI water.
abstract: We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.
authors: Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.
authors: Julija
authors: J
authors: Zavadlav
authors: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors: Manuel Nuno
authors: MN
authors: Melo
authors: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
authors: Siewert J
authors: SJ
authors: Marrink
authors: Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.
authors: Matej
authors: M
authors: Praprotnik
mesh_terms: D003198:Computer Simulation; D020962:Heterotrimeric GTP-Binding Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water; D020962:Heterotrimeric GTP-Binding Proteins