Understanding a molecular motor walking along a microtubule: an asymmetric Brownian motor driven by bubble formation with a focus on binding affinity

Masakazu Hojo, Noriyoshi Arai, Toshikazu Ebisuzaki

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

In recent years, many studies on a molecular motor have been conducted in the fields of biorheology and nanoengineering. The molecular motor is a molecule that converts the chemical energy obtained by ATP hydrolysis into mechanical energy. Explaining this mechanism is important for nanoengineering. A kinesin, which is a type of molecular motor, has the characteristics to move on a microtubule with hand-over-hand steps. The kinesin walking behaviour is explained by the ‘asymmetric Brownian ratchet model’. Previously, we had suggested that the walking mechanism was achieved by the bubble formation in a nanosized channel surrounded by hydrophobic atoms with the transition between the two states–bubble state and liquid state. However, the walking behaviour of the model motor was different from that of a single molecule measurement of a kinesin. In this study, we constructed a new motor system focused on the asymmetric binding affinity of a motor protein and performed a model simulation using the dissipative particle dynamics method. As a result, it was observed that hand-over-hand walking depends on the transition position ratio and the transition frequency coefficient. Moreover, the efficiency of the new motor system is higher than that of the previous motor systems. The new motor model can provide a simulation guide for the design of biomimetic nanomachines.

Original languageEnglish
Pages (from-to)523-529
Number of pages7
JournalMolecular Simulation
Volume44
Issue number7
DOIs
Publication statusPublished - 2018 May 3
Externally publishedYes

Fingerprint

Brownian Motors
Molecular Motor
Bubble formation
Microtubules
walking
Bubble
Affine transformation
affinity
bubbles
efferent nervous systems
Kinesin
Handover
Brownian Ratchet
Dissipative Particle Dynamics
chemical energy
adenosine triphosphate
biomimetics
Energy
Convert
hydrolysis

Keywords

  • Brownian ratchet
  • bubble formation
  • dissipative particle dynamics
  • molecular motor
  • walking mechanism

ASJC Scopus subject areas

  • Chemistry(all)
  • Information Systems
  • Modelling and Simulation
  • Chemical Engineering(all)
  • Materials Science(all)
  • Condensed Matter Physics

Cite this

Understanding a molecular motor walking along a microtubule : an asymmetric Brownian motor driven by bubble formation with a focus on binding affinity. / Hojo, Masakazu; Arai, Noriyoshi; Ebisuzaki, Toshikazu.

In: Molecular Simulation, Vol. 44, No. 7, 03.05.2018, p. 523-529.

Research output: Contribution to journalArticle

@article{83b2b73a33864425ab301398db8f5d1e,
title = "Understanding a molecular motor walking along a microtubule: an asymmetric Brownian motor driven by bubble formation with a focus on binding affinity",
abstract = "In recent years, many studies on a molecular motor have been conducted in the fields of biorheology and nanoengineering. The molecular motor is a molecule that converts the chemical energy obtained by ATP hydrolysis into mechanical energy. Explaining this mechanism is important for nanoengineering. A kinesin, which is a type of molecular motor, has the characteristics to move on a microtubule with hand-over-hand steps. The kinesin walking behaviour is explained by the ‘asymmetric Brownian ratchet model’. Previously, we had suggested that the walking mechanism was achieved by the bubble formation in a nanosized channel surrounded by hydrophobic atoms with the transition between the two states–bubble state and liquid state. However, the walking behaviour of the model motor was different from that of a single molecule measurement of a kinesin. In this study, we constructed a new motor system focused on the asymmetric binding affinity of a motor protein and performed a model simulation using the dissipative particle dynamics method. As a result, it was observed that hand-over-hand walking depends on the transition position ratio and the transition frequency coefficient. Moreover, the efficiency of the new motor system is higher than that of the previous motor systems. The new motor model can provide a simulation guide for the design of biomimetic nanomachines.",
keywords = "Brownian ratchet, bubble formation, dissipative particle dynamics, molecular motor, walking mechanism",
author = "Masakazu Hojo and Noriyoshi Arai and Toshikazu Ebisuzaki",
year = "2018",
month = "5",
day = "3",
doi = "10.1080/08927022.2017.1393812",
language = "English",
volume = "44",
pages = "523--529",
journal = "Molecular Simulation",
issn = "0892-7022",
publisher = "Taylor and Francis Ltd.",
number = "7",

}

TY - JOUR

T1 - Understanding a molecular motor walking along a microtubule

T2 - an asymmetric Brownian motor driven by bubble formation with a focus on binding affinity

AU - Hojo, Masakazu

AU - Arai, Noriyoshi

AU - Ebisuzaki, Toshikazu

PY - 2018/5/3

Y1 - 2018/5/3

N2 - In recent years, many studies on a molecular motor have been conducted in the fields of biorheology and nanoengineering. The molecular motor is a molecule that converts the chemical energy obtained by ATP hydrolysis into mechanical energy. Explaining this mechanism is important for nanoengineering. A kinesin, which is a type of molecular motor, has the characteristics to move on a microtubule with hand-over-hand steps. The kinesin walking behaviour is explained by the ‘asymmetric Brownian ratchet model’. Previously, we had suggested that the walking mechanism was achieved by the bubble formation in a nanosized channel surrounded by hydrophobic atoms with the transition between the two states–bubble state and liquid state. However, the walking behaviour of the model motor was different from that of a single molecule measurement of a kinesin. In this study, we constructed a new motor system focused on the asymmetric binding affinity of a motor protein and performed a model simulation using the dissipative particle dynamics method. As a result, it was observed that hand-over-hand walking depends on the transition position ratio and the transition frequency coefficient. Moreover, the efficiency of the new motor system is higher than that of the previous motor systems. The new motor model can provide a simulation guide for the design of biomimetic nanomachines.

AB - In recent years, many studies on a molecular motor have been conducted in the fields of biorheology and nanoengineering. The molecular motor is a molecule that converts the chemical energy obtained by ATP hydrolysis into mechanical energy. Explaining this mechanism is important for nanoengineering. A kinesin, which is a type of molecular motor, has the characteristics to move on a microtubule with hand-over-hand steps. The kinesin walking behaviour is explained by the ‘asymmetric Brownian ratchet model’. Previously, we had suggested that the walking mechanism was achieved by the bubble formation in a nanosized channel surrounded by hydrophobic atoms with the transition between the two states–bubble state and liquid state. However, the walking behaviour of the model motor was different from that of a single molecule measurement of a kinesin. In this study, we constructed a new motor system focused on the asymmetric binding affinity of a motor protein and performed a model simulation using the dissipative particle dynamics method. As a result, it was observed that hand-over-hand walking depends on the transition position ratio and the transition frequency coefficient. Moreover, the efficiency of the new motor system is higher than that of the previous motor systems. The new motor model can provide a simulation guide for the design of biomimetic nanomachines.

KW - Brownian ratchet

KW - bubble formation

KW - dissipative particle dynamics

KW - molecular motor

KW - walking mechanism

UR - http://www.scopus.com/inward/record.url?scp=85032810933&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85032810933&partnerID=8YFLogxK

U2 - 10.1080/08927022.2017.1393812

DO - 10.1080/08927022.2017.1393812

M3 - Article

AN - SCOPUS:85032810933

VL - 44

SP - 523

EP - 529

JO - Molecular Simulation

JF - Molecular Simulation

SN - 0892-7022

IS - 7

ER -