Theoretical approaches for dynamical ordering of biomolecular systems

• Published in: Biochimica et biophysica acta Vol. 1862; no. 2; pp. 212 - 228
• Main Authors: Okumura, Hisashi, Higashi, Masahiro, Yoshida, Yuichiro, Sato, Hirofumi, Akiyama, Ryo
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.02.2018
• Subjects: All-atom model; biochemical compounds; chemical reactions; Coarse-grained model; electrons; equations; Integral equation theory; liquids; Molecular dynamics; QM/MM method; quantum mechanics; Molecular dynamics; Integral equation theory; QM/MM method; All-atom model; Coarse-grained model
• ISSN: 0304-4165; 0006-3002; 1872-8006
• DOI: 10.1016/j.bbagen.2017.10.001

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. 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. 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. 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. [Display omitted] •Four theoretical approaches to understand ordering phenomena are reviewed.•QM/MM calculation enables to study chemical reactions in large systems.•All-atom molecular dynamics simulations can follow longer time-scale phenomena.•Besides computational efficiency, CG model offers abstraction of the target system.•Integral equation theories elucidate the stability of biomolecular association.