Molecular Simulations by Generalized-ensemble Algorithms in Isothermal-isobaric Ensemble

Overview

Journal Biophys Rev

Publisher Springer

Specialty Biophysics

Date 2019 May 23

PMID 31115865

Citations 10

Authors

Masataka Yamauchi

Yoshiharu Mori

Hisashi Okumura

Affiliations

Soon will be listed here.

Abstract

Generalized-ensemble algorithms are powerful techniques for investigating biomolecules such as protein, DNA, lipid membrane, and glycan. The generalized-ensemble algorithms were originally developed in the canonical ensemble. On the other hand, not only temperature but also pressure is controlled in experiments. Additionally, pressure is used as perturbation to study relationship between function and structure of biomolecules. For this reason, it is important to perform efficient conformation sampling based on the isothermal-isobaric ensemble. In this article, we review a series of the generalized-ensemble algorithms in the isothermal-isobaric ensemble: multibaric-multithermal, pressure- and temperature-simulated tempering, replica-exchange, and replica-permutation methods. These methods achieve more efficient simulation than the conventional isothermal-isobaric simulation. Furthermore, the isothermal-isobaric generalized-ensemble simulation samples conformations of biomolecules from wider range of temperature and pressure. Thus, we can estimate physical quantities more accurately at any temperature and pressure values. The applications to the biomolecular system are also presented.

Citing Articles

Inhibition of amyloid-β(16-22) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation.

Fukuhara D, Itoh S, Okumura H Biophys Physicobiol. 2024; 20(4):e200045.

PMID: 38344035 PMC: 10850463. DOI: 10.2142/biophysico.bppb-v20.0045.

Dissociation process of polyalanine aggregates by free electron laser irradiation.

Okumura H, Itoh S, Zen H, Nakamura K PLoS One. 2023; 18(9):e0291093.

PMID: 37683014 PMC: 10491298. DOI: 10.1371/journal.pone.0291093.

Structural evolution of Delta lineage of SARS-CoV-2.

Gomari M, Tarighi P, Choupani E, Abkhiz S, Mohamadzadeh M, Rostami N Int J Biol Macromol. 2022; 226:1116-1140.

PMID: 36435470 PMC: 9683856. DOI: 10.1016/j.ijbiomac.2022.11.227.

Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency.

Fukuhara D, Yamauchi M, Itoh S, Okumura H J Comput Chem. 2022; 44(4):534-545.

PMID: 36346137 PMC: 10099539. DOI: 10.1002/jcc.27020.

Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments.

Tachi Y, Itoh S, Okumura H Biophys Physicobiol. 2022; 19:1-18.

PMID: 35666692 PMC: 9135617. DOI: 10.2142/biophysico.bppb-v19.0010.

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