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Cited by 32Protein Structure and DynamicsAdvanced Physical and Chemical Molecular InteractionsSpectroscopy and Quantum Chemical Studies

Structural fluctuation of protein in water around its native state: A new statistical mechanics formulation

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Kim, Bongsoo, Hirata, Fumio·2013·The Journal of Chemical Physics
DOI 10.1063/1.4776655
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Abstract

A new statistical mechanics formulation of characterizing the structural fluctuation of protein correlated with that of water is presented based on the generalized Langevin equation and the 3D-reference interaction site model (RISM)/RISM theory of molecular liquids. The displacement vector of atom positions, and their conjugated momentum, are chosen for the dynamic variables for protein, while the density fields of atoms and their momentum fields are chosen for water. Projection of other degrees of freedom onto those dynamic variables using the standard projection operator method produces essentially two equations, which describe the time evolution of fluctuation concerning the density field of solvent and the conformation of protein around an equilibrium state, which are coupled with each other. The equation concerning the protein dynamics is formally akin to that of the coupled Langevin oscillators, and is a generalization of the latter, to atomic level. The most intriguing feature of the new equation is that it contains the variance-covariance matrix as the “Hessian” term describing the “force” restoring an equilibrium conformation, which is the second moment of the fluctuation of atom positions. The “Hessian” matrix is naturally identified as the second derivative of the free energy surface around the equilibrium. A method to evaluate the Hessian matrix based on the 3D-RISM/RISM theory is proposed. Proposed also is an application of the present formulation to the molecular recognition, in which the conformational fluctuation of protein around its native state becomes an important factor as exemplified by so called “induced fitting.”

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  1. [6]M. Feig (ed), Modeling Solvent Environment: Applications to Simulations of Biomolecules , Wiley-VCH Verlag, 2010, and references therein.
  2. [14]R. Zwanzig, Phys. Rev. 124 , 983 (1961); R. Zwanzig, Nonequilibrium Statistical Mechanics , Oxford University Press, 2001.
  3. [15]U. Balucani and M. Zoppi, Dynamics of the Liquid State , Oxford University Press, 1994.
  4. [16]G. F. Mazenko, Nonequilibrium Statistical Mechanics , Wiley-VCH Verlag, 2006.
  5. [31]M. Doi and S. F. Edwards, The Theory of Polymer Dynamics , Oxford University Press, 1986.

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Authors
Kim, B., & Hirata, F.
Affiliations
  • Changwon National University (KR)
  • Ritsumeikan University (JP)
ORCID
Hirata, Fumio
Venue
The Journal of Chemical Physics
Publisher
AIP Publishing
Published
2013-02-04
Volume
138
Issue
5
Pages
054108-054108
ISSN
  • 0021-9606 (ISSN-L)
  • 1089-7690
DOI
10.1063/1.4776655
OpenAlex
W2000808698
Cited by
32
References
38
Citations by year
2025: 5 · 2024: 1 · 2023: 4 · 2022: 1 · 2021: 2 · 2019: 1 · 2018: 2 · 2017: 4 · 2016: 5 · 2015: 6 · 2014: 1
FWCI
1.79
Type
journal article
Language
en
Open access
Locations
  • The Journal of Chemical Physics (publishedVersion)
  • PubMed (publishedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • arXiv (Cornell University)
Funders
Japan Society for the Promotion of Science (22245002)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Spectroscopy and Quantum Chemical Studies
Keywords
protein structural fluctuations, generalized Langevin equation, projection operator method, Hessian matrix, free energy landscape, protein conformational dynamics, molecular recognition, induced fit
MeSH terms
Protein Conformation, Proteins, Quantum Theory, Water, Models, Statistical

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