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- W2018326682 abstract "Here we present a multiscale simulation approach to study aggregation of small peptides. We develop a protocol that uses atomistic trajectories and the Iterative Boltzmann method to construct a mixed representation of the peptide/solvent system, in which the peptide is described with the united atom GROMOS forcefield and the solvent is described with effective potentials derived from atomistic radial distribution functions. For a test system composed of di-alanine peptide and octane as solvent, we show that the peptide structural properties (see figure) as well as solvation free energy obtained in the hybrid approach matches results obtained from reference atomistic simulations. Next, the model is used to calculate the potential of mean force between two peptides to evaluate how the reduced representation of the solvent influences solute aggregation properties. We show that accurate reproduction of the octane and di-alanine solvation free energy as well as careful choice of the degree of coarse-graining of the peptide-solvent interactions are important to obtain a realistic potential of mean force. Finally aggregation of many peptides is studied with this multiscale protocol. The future applications include aggregation and folding of atomistic peptides and proteins in coarse grained bilayers." @default.
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- W2018326682 date "2010-01-01" @default.
- W2018326682 modified "2023-09-28" @default.
- W2018326682 title "Hybrid Simulations: Atomistic Peptides in Coarse Grained Solvent" @default.
- W2018326682 doi "https://doi.org/10.1016/j.bpj.2009.12.3092" @default.
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