Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins

TitleDiscrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins
Publication TypeJournal Article
Year of Publication2017
AuthorsEmperador, Agustí, and Orozco Modesto
JournalJournal of Chemical Theory and Computation
Volume13
Issue3
Pagination1454 - 1461
Date Published03/2017
ISBN Number1549-9618
Abstract

We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.

URLhttp://dx.doi.org/10.1021/acs.jctc.6b01153
Short TitleJ. Chem. Theory Comput.
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