Theoretical approaches for dynamical ordering of biomolecular systems

Hisashi Okumura, Masahiro Higashi, Yuichiro Yoshida, Hirofumi Sato, Ryo Akiyama

Research output: Contribution to journalReview article

2 Citations (Scopus)

Abstract

Background Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. Scope of review We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. Major conclusions The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. General significance These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled “Biophysical Exploration of Dynamical Ordering of Biomolecular Systems” edited by Dr. Koichi Kato.

Original languageEnglish
Pages (from-to)212-228
Number of pages17
JournalBiochimica et Biophysica Acta - General Subjects
Volume1862
Issue number2
DOIs
Publication statusPublished - Feb 1 2018

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Molecular Dynamics Simulation
Biomolecules
Atoms
Integral equations
Molecular dynamics
Liquids
Computer simulation
Electrons
Costs and Cost Analysis
Self assembly
Distribution functions
Chemical reactions
Molecules
Costs

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Biochemistry
  • Molecular Biology

Cite this

Theoretical approaches for dynamical ordering of biomolecular systems. / Okumura, Hisashi; Higashi, Masahiro; Yoshida, Yuichiro; Sato, Hirofumi; Akiyama, Ryo.

In: Biochimica et Biophysica Acta - General Subjects, Vol. 1862, No. 2, 01.02.2018, p. 212-228.

Research output: Contribution to journalReview article

Okumura, Hisashi ; Higashi, Masahiro ; Yoshida, Yuichiro ; Sato, Hirofumi ; Akiyama, Ryo. / Theoretical approaches for dynamical ordering of biomolecular systems. In: Biochimica et Biophysica Acta - General Subjects. 2018 ; Vol. 1862, No. 2. pp. 212-228.
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