A matrix computational approach to kinesin neck linker extension

John Hughes; William O. Hancock; John Fricks

doi:10.1016/j.jtbi.2010.10.005

A matrix computational approach to kinesin neck linker extension

John Hughes, William O. Hancock, John Fricks

Research output: Contribution to journal › Article › peer-review

13 Scopus citations

Abstract

Kinesin stepping requires both tethered diffusion of the free head and conformational changes driven by the chemical state of the motor. We present a numerical method using matrix representations of approximating Markov chains and renewal theory to compute important experimental quantities for models that include both tethered diffusion and chemical transitions. Explicitly modeling the tethered diffusion allows for exploration of the model under perturbation of the neck linker; comparisons are made between the computed models and in vitro assays.

Original language	English (US)
Pages (from-to)	181-194
Number of pages	14
Journal	Journal of Theoretical Biology
Volume	269
Issue number	1
DOIs	https://doi.org/10.1016/j.jtbi.2010.10.005
State	Published - Jan 21 2011
Externally published	Yes

Keywords

Chemical kinetics
Kinesin
Molecular motors
Renewal-reward process
Stochastic models

ASJC Scopus subject areas

Statistics and Probability
Modeling and Simulation
General Biochemistry, Genetics and Molecular Biology
General Immunology and Microbiology
General Agricultural and Biological Sciences
Applied Mathematics

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10.1016/j.jtbi.2010.10.005

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title = "A matrix computational approach to kinesin neck linker extension",

abstract = "Kinesin stepping requires both tethered diffusion of the free head and conformational changes driven by the chemical state of the motor. We present a numerical method using matrix representations of approximating Markov chains and renewal theory to compute important experimental quantities for models that include both tethered diffusion and chemical transitions. Explicitly modeling the tethered diffusion allows for exploration of the model under perturbation of the neck linker; comparisons are made between the computed models and in vitro assays.",

keywords = "Chemical kinetics, Kinesin, Molecular motors, Renewal-reward process, Stochastic models",

author = "John Hughes and Hancock, {William O.} and John Fricks",

note = "Funding Information: We gratefully acknowledge the NSF who supported the present work though the Joint DMS/NIGMS Initiative to Support Research in the Area of Mathematical Biology (DMS-0714939) and through a visiting position at Statistical and Applied Mathematical Sciences Institute for John Fricks. Appendix A ",

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doi = "10.1016/j.jtbi.2010.10.005",

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AU - Hughes, John

AU - Hancock, William O.

AU - Fricks, John

N1 - Funding Information: We gratefully acknowledge the NSF who supported the present work though the Joint DMS/NIGMS Initiative to Support Research in the Area of Mathematical Biology (DMS-0714939) and through a visiting position at Statistical and Applied Mathematical Sciences Institute for John Fricks. Appendix A

PY - 2011/1/21

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N2 - Kinesin stepping requires both tethered diffusion of the free head and conformational changes driven by the chemical state of the motor. We present a numerical method using matrix representations of approximating Markov chains and renewal theory to compute important experimental quantities for models that include both tethered diffusion and chemical transitions. Explicitly modeling the tethered diffusion allows for exploration of the model under perturbation of the neck linker; comparisons are made between the computed models and in vitro assays.

AB - Kinesin stepping requires both tethered diffusion of the free head and conformational changes driven by the chemical state of the motor. We present a numerical method using matrix representations of approximating Markov chains and renewal theory to compute important experimental quantities for models that include both tethered diffusion and chemical transitions. Explicitly modeling the tethered diffusion allows for exploration of the model under perturbation of the neck linker; comparisons are made between the computed models and in vitro assays.

KW - Chemical kinetics

KW - Kinesin

KW - Molecular motors

KW - Renewal-reward process

KW - Stochastic models

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A matrix computational approach to kinesin neck linker extension

Abstract

Keywords

ASJC Scopus subject areas

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