Adaptive resolution simulation of an atomistic protein in MARTINI water

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 coa...

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Bibliographic Details
Published in:The Journal of chemical physics 2014-02, Vol.140 (5), p.054114-054114
Main Authors: Zavadlav, Julija, Melo, Manuel Nuno, Marrink, Siewert J, Praprotnik, Matej
Format: Article
Language:English
Subjects:
Atomic radius
Computer Simulation
Coupling (molecular)
FLUCTUATIONS
Fluid dynamics
Heterotrimeric GTP-Binding Proteins - chemistry
INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY
Molecular dynamics
MOLECULAR DYNAMICS METHOD
Molecular Dynamics Simulation
MOLECULES
Physical simulation
Physics
PROTEINS
RESOLUTION
SIMULATION
SOLVENTS
STABILITY
SURFACE AREA
Variation
WATER
Water - chemistry
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Summary: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.
ISSN:0021-9606
1089-7690
DOI:10.1063/1.4863329