Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction

Biophysics Reviews
Jinzen IkebeJunichi Higo

Abstract

Molecular dynamics (MD) simulations using all-atom and explicit solvent models provide valuable information on the detailed behavior of protein-partner substrate binding at the atomic level. As the power of computational resources increase, MD simulations are being used more widely and easily. However, it is still difficult to investigate the thermodynamic properties of protein-partner substrate binding and protein folding with conventional MD simulations. Enhanced sampling methods have been developed to sample conformations that reflect equilibrium conditions in a more efficient manner than conventional MD simulations, thereby allowing the construction of accurate free-energy landscapes. In this review, we discuss these enhanced sampling methods using a series of case-by-case examples. In particular, we review enhanced sampling methods conforming to trivial trajectory parallelization, virtual-system coupled multicanonical MD, and adaptive lambda square dynamics. These methods have been recently developed based on the existing method of multicanonical MD simulation. Their applications are reviewed with an emphasis on describing their practical implementation. In our concluding remarks we explore extensions of the enhanced sampl...Continue Reading

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Citations

Apr 16, 2017·Physics of Life Reviews·J Rydzewski, W Nowak
Feb 22, 2018·Journal of Computational Chemistry·Tomonori HayamiJunichi Higo
Aug 4, 2019·International Journal of Molecular Sciences·Nidhi Singh, Wenjin Li
May 17, 2017·Biophysics Reviews·Cris Dos Remedios
May 24, 2017·Scientific Reports·Zilvinas Rimas, Sergei N Taraskin
Jan 12, 2021·Frontiers in Chemistry·Christopher Sutton, Sergey V Levchenko
Sep 25, 2021·Journal of Chemical Information and Modeling·Cristina González-FernándezInmaculada Ortiz

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