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Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm

Zavadlav, J., Marrink, S. J. & Praprotnik, M., Mar-2018, In : Journal of Chemical Theory and Computation. 14, 3, p. 1754-1761 8 p.

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  • Multiscale Simulation of Protein Hydration Using the SWINGERDynamical Clustering Algorithm

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DOI

To perform computationally efficient concurrent multiscale simulations of biological macromolecules in solution, where the all-atom (AT) models are coupled to supramolecular coarse-grained (SCG) solvent models, previous studies resorted to modified AT water models, such as the bundled-simple point charge (SPC) models, that use semiharmonic springs to restrict the relative movement of water molecules within a cluster. Those models can have a significant impact on the simulated biomolecules and can lead, for example, to a partial unfolding of a protein. In this work, we employ the recently developed alternative approach with a dynamical clustering algorithm, SWINGER, which enables a direct coupling of original unmodified AT and SCG water models. We perform an adaptive resolution molecular dynamics simulation of a Trp-Cage miniprotein in multiscale water, where the standard SPC water model is interfaced with the widely used MARTINI SCG model, and demonstrate that, compared to the corresponding full-blown AT simulations, the structural and dynamic properties of the solvated protein and surrounding solvent are well reproduced by our approach.

Original languageEnglish
Pages (from-to)1754-1761
Number of pages8
JournalJournal of Chemical Theory and Computation
Volume14
Issue number3
Publication statusPublished - Mar-2018

    Keywords

  • ADAPTIVE RESOLUTION SIMULATION, COARSE-GRAINED WATER, POLARIZABLE FORCE-FIELD, TRP-CAGE MINIPROTEIN, MOLECULAR-DYNAMICS, BIOMOLECULAR SIMULATIONS, LIQUID WATER, SOFT MATTER, EWALD SUMMATION, SOLVENT MODEL

ID: 78530545