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PreprintCited by 5Force Microscopy Techniques and Applicationsstochastic dynamics and bifurcationAdvanced Fluorescence Microscopy Techniques

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Chemical-state-dependent free energy profile from single-molecule trajectories of biomolecular motor: Application to processive chitinase

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Okazaki, Kei-ichi, Nakamura, Akihiko, Iino, Ryota·2019·The Journal of Physical Chemistry B
DOI 10.1101/655878

Preprint — published as 10.1021/acs.jpcb.0c02698

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Abstract

The mechanism of biomolecular motors has been elucidated using single-molecule experiments for visualizing motor motion. However, it remains elusive that how changes in the chemical state during the catalytic cycle of motors lead to unidirectional motions. In this study, we use singlemolecule trajectories to estimate an underlying diffusion model with chemical-state-dependent free energy profile. To consider nonequilibrium trajectories driven by the chemical energy consumed by biomolecular motors, we develop a novel framework based on a hidden Markov model, wherein switching among multiple energy profiles occurs reflecting the chemical state changes in motors. The method is tested using simulation trajectories and applied to singlemolecule trajectories of processive chitinase, a linear motor that is driven by the hydrolysis energy of a single chitin chain. The chemical-state-dependent free energy profile underlying the burnt- bridge Brownian ratchet mechanism of processive chitinase is determined. The novel framework allows us to connect the chemical state changes to the unidirectional motion of biomolecular motors.

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Metadata

Authors
Okazaki, K.-I., Nakamura, A., & Iino, R.
Affiliations
  • National Institutes of Natural Sciences (JP)
  • Shizuoka University (JP)
Corresponding author
Okazaki, Kei-ichi
ORCID
Venue
The Journal of Physical Chemistry B
Publisher
openRxiv
Published
2019-05-30
Volume
124
Issue
30
Pages
6475-6487
ISSN
1520-5207 (ISSN-L)
DOI
10.1101/655878
OpenAlex
W3039422301
Cited by
5
References
1
Citations by year
2026: 1 · 2023: 1 · 2022: 1 · 2021: 1 · 2020: 1
FWCI
0.41
Type
journal article
Language
en
Open access
Locations
  • The Journal of Physical Chemistry B (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
Funders
  • Ministry of Education, Culture, Sports, Science and Technology (JP18H02418, JP18H02415, J281002, JP18H05424)
  • Japan Society for the Promotion of Science (18H02418, JP18H05424, 18H02415)
  • National Institutes of Natural Sciences (J281002)
Topics
  • Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Force Microscopy Techniques and Applications
  • Physical Sciences › Physics and Astronomy › Statistical and Nonlinear Physics › stochastic dynamics and bifurcation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
Keywords
molecular motors, single-molecule trajectories, hidden Markov models, unidirectional motion, chitin hydrolysis
MeSH terms
Chitinases, Diffusion, Kinetics, Motion, Molecular Motor Proteins

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CoChat. (2026). Citation check: Chemical-state-dependent free energy profile from single-molecule trajectories of biomolecular motor: Application to processive chitinase. https://app.cochat.ai/papers/10.1101/655878
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Okazaki, K.-I., Nakamura, A., & Iino, R. (2019). Chemical-state-dependent free energy profile from single-molecule trajectories of biomolecular motor: Application to processive chitinase. The Journal of Physical Chemistry B. https://doi.org/10.1101/655878