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- W1998015700 abstract "Discrete molecular dynamics (DMD) has been applied in many areas of protein folding and aggregation because relatively long time scales can be simulated. Coarse-graining and implicit solvent models have been implemented to maximize its efficiency. However, there has been no rigorous evaluation with DMD on experimentally known structures. Here, we ran DMD with four-bead peptide model on X-ray structure of a human serum retinol-binding protein and NMR structure of a regulator of G-Protein signaling, and compared the results to those of simulations by NAMD (all atom molecular dynamics with explicit water). DMD showed larger root mean squared deviation (RMSD) from the starting conformation compared to NAMD though tertiary structures were mostly maintained. We developed a new implicit solvent model for DMD based on Miyazawa-Jernigan interaction pair potential that has advantage of unambiguous implementation to address dependencies in implicit solvent models. Results obtained with the Miyazawa-Jernigan implicit solvent model were comparable to those obtained with a previously used implicit solvent model based on Kyte-Doolittle hydropathy scale. We ran DMD and NAMD on incorrectly folded models. Structures of the incorrectly folded models were very poorly preserved during the DMD simulations. Both methods were able to distinguish between the correct and incorrect structures based on differences in the magnitudes of the RMSD from the starting conformation. Hence, we suggest that DMD may be useful as a tool to test soluble protein models." @default.
- W1998015700 created "2016-06-24" @default.
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- W1998015700 date "2010-01-01" @default.
- W1998015700 modified "2023-09-26" @default.
- W1998015700 title "Discrete Molecular Dynamics as a Tool to Test Soluble Protein Models" @default.
- W1998015700 doi "https://doi.org/10.1016/j.bpj.2009.12.3093" @default.
- W1998015700 hasPublicationYear "2010" @default.
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