Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes.

Biophysics Reviews
Junichi HigoHaruki Nakamura

Abstract

Protein folding and protein-ligand docking have long persisted as important subjects in biophysics. Using multicanonical molecular dynamics (McMD) simulations with realistic expressions, i.e., all-atom protein models and an explicit solvent, free-energy landscapes have been computed for several systems, such as the folding of peptides/proteins composed of a few amino acids up to nearly 60 amino-acid residues, protein-ligand interactions, and coupled folding and binding of intrinsically disordered proteins. Recent progress in conformational sampling and its applications to biophysical systems are reviewed in this report, including descriptions of several outstanding studies. In addition, an algorithm and detailed procedures used for multicanonical sampling are presented along with the methodology of adaptive umbrella sampling. Both methods control the simulation so that low-probability regions along a reaction coordinate are sampled frequently. The reaction coordinate is the potential energy for multicanonical sampling and is a structural identifier for adaptive umbrella sampling. One might imagine that this probability control invariably enhances conformational transitions among distinct stable states, but this study examines t...Continue Reading

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Citations

Oct 10, 2014·The Journal of Chemical Physics·Rikhia GhoshBiman Bagchi
Apr 29, 2016·Proteins·Koji UmezawaMitsunori Takano
Aug 16, 2016·Protein Engineering, Design & Selection : PEDS·Hiroshi NishigamiHaruki Nakamura
Oct 25, 2016·Journal of Chemical Information and Modeling·Noriko ShimbaHaruki Nakamura
Feb 22, 2018·Journal of Computational Chemistry·Tomonori HayamiJunichi Higo
Aug 4, 2015·Journal of Computational Chemistry·Timothy J HughesPaul L A Popelier
Sep 26, 2014·Europhysics Letters·Fatih YaşarUlrich H E Hansmann
Mar 26, 2013·Journal of Computational Chemistry·Jose Antonio Garate, Chris Oostenbrink
Oct 30, 2013·Journal of Computational Chemistry·Jinzen IkebeHidetoshi Kono
Jun 6, 2015·Journal of Computational Chemistry·Junichi HigoHaruki Nakamura
Feb 6, 2017·The Journal of Chemical Physics·Junichi HigoHaruki Nakamura
Oct 11, 2017·The Journal of Chemical Physics·Junichi HigoHaruki Nakamura
Nov 27, 2020·Biophysics and Physicobiology·Kota KasaharaJunichi Higo
Jul 8, 2014·Journal of Chemical Theory and Computation·Niels Hansen, Wilfred F van Gunsteren
Nov 8, 2013·Journal of Chemical Theory and Computation·Ping JiangUlrich H E Hansmann
Feb 28, 2019·The Journal of Physical Chemistry. B·Gert-Jan BekkerNarutoshi Kamiya
Dec 23, 2021·Physical Chemistry Chemical Physics : PCCP·Anna S KamenikSereina Riniker

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Methods Mentioned

BETA
protein folding
PCA
NMR
nuclear magnetic resonance

Software Mentioned

NRSF
GROMACS
MDGRAPE
REST
TTP
McMD
REM

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