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Kinesin model for Brownian dynamics simulations of stepping efficiency

Murrow, Matthew Alan
http://rave.ohiolink.edu/etdc/view?acc_num=akron156441669721832

Abstract Details

2019, Master of Science, University of Akron, Physics.
Motor proteins are molecular motors capable of active movement within cells. The motor protein kinesin plays an integral role in cell function, transporting, for example, cargo from the center to the periphery of a cell. Kinesins are composed of two heads, two neck linkers, and a coil connecting these parts to the carried cargo. Kinesin molecules have been shown experimentally to walk along tubulin-based protein structures called microtubules in a hand-over-hand stepping motion, carrying their cargo eight nanometers per step. However, details of the stepping process, including the role of the neck-linkers, are still under investigation. They are difficult to study with atomistic simulations due to the size of the proteins and the long time-scales involved. In this work we develop a 3D model of kinesin stepping on a rigid microtubule substrate that can be simulated efficiently with Brownian dynamics simulations. The geometric parameters of our five-site kinesin model reflect the geometry of a kinesin motor protein. The interactions governing the motor protein conformations and the interactions between kinesin sites and the microtubule sites are designed to reproduce important aspects of the biological system. We perform simulations spanning many kinesin steps to investigate the stepping efficiency of the motor protein. To compare with experiments, we study kinesin motors with neck linkers of different lengths. We find that neck linkers close to the wild-type length have the highest stepping efficiency, about 90%, in agreement with experimental data. In addition, we find that increasing the neck-linker length leads to a decrease in efficiency, as has also been observed in experiments.
Jutta Luettmer-Strathmann, Ph.D. (Advisor)
Alper Buldum, Ph.D. (Committee Member)
Yu-Kuang Hu, Ph.D (Committee Chair)
69 p.
Biophysics; Molecular Biology; Physics; Theoretical Physics
kinesin; neck linker; molecular motor; Brownian dynamics; efficiency; coarse grained model; computer simulations

Recommended Citations

Citations

  • Murrow, M. A. (2019). Kinesin model for Brownian dynamics simulations of stepping efficiency [Master's thesis, University of Akron]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=akron156441669721832

    APA Style (7th edition)

  • Murrow, Matthew. Kinesin model for Brownian dynamics simulations of stepping efficiency. 2019. University of Akron, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=akron156441669721832.

    MLA Style (8th edition)

  • Murrow, Matthew. "Kinesin model for Brownian dynamics simulations of stepping efficiency." Master's thesis, University of Akron, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=akron156441669721832

    Chicago Manual of Style (17th edition)

akron156441669721832
464
© 2019, some rights reserved.Creative Commons License Kinesin model for Brownian dynamics simulations of stepping efficiency by Matthew Alan Murrow is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Based on a work at etd.ohiolink.edu.
This open access ETD is published by University of Akron and OhioLINK.