Journal of Computational Chemistry
Journal of Computational Chemistry
5 years ago

Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins

Temperature-shuffled parallel cascade selection molecular dynamics accelerates the structural transitions of proteins
Yasuteru Shigeta, Ryuhei Harada
Parallel cascade selection molecular dynamics (PaCS-MD) is an enhanced conformational sampling method for searching structural transition pathways from a given reactant to a product. Recently, a temperature-aided PaCS-MD (Vinod et al., Eur. Biophys. J. 2016, 45, 463) has been proposed as its extension, in which the temperatures were introduced as additional parameters in conformational resampling, whereas the temperature is fixed in the original PaCS-MD. In the present study, temperature-shuffled PaCS-MD is proposed as a further extension of temperature-aided PaCS-MD in which the temperatures are shuffled among different replicas at the beginning of each cycle of conformational resampling. To evaluate their conformational sampling efficiencies, the original, temperature-aided, and temperature-shuffled PaCS-MD were applied to a protein-folding process of Trp-cage, and their minimum computational costs to identify the native state were addressed. Through the evaluation, it was confirmed that temperature-shuffled PaCS-MD remarkably accelerated the protein-folding process of Trp-cage compared with the other methods. © 2017 Wiley Periodicals, Inc. Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is an enhanced conformational sampling method for searching structural transition pathways from a given reactant to a product. In the present study, Temperature-Shuffled PaCS-MD (TSF-PaCS-MD) is proposed as a further extension of PaCS-MD in which the temperatures are shuffled among different replicas at the beginning of each cycle of conformational resampling. Through evaluations, it was confirmed that TSF-PaCS-MD remarkably accelerated structural transitions of proteins than the original PaCS-MD.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/jcc.25060

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