Kinesin model for Brownian dynamics simulations of stepping efficiency
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2019
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| Online Access: | http://rave.ohiolink.edu/etdc/view?acc_num=akron156441669721832 |
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ndltd-OhioLink-oai-etd.ohiolink.edu-akron1564416697218322021-08-03T07:12:14Z Kinesin model for Brownian dynamics simulations of stepping efficiency Murrow, Matthew Alan Biophysics Physics Theoretical Physics Molecular Biology kinesin neck linker molecular motor Brownian dynamics efficiency coarse grained model computer simulations 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. 2019-08-29 English text University of Akron / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=akron156441669721832 http://rave.ohiolink.edu/etdc/view?acc_num=akron156441669721832 unrestricted This thesis or dissertation is protected by copyright: some rights reserved. It is licensed for use under a Creative Commons license. Specific terms and permissions are available from this document's record in the OhioLINK ETD Center. |
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NDLTD |
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English |
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NDLTD |
| topic |
Biophysics Physics Theoretical Physics Molecular Biology kinesin neck linker molecular motor Brownian dynamics efficiency coarse grained model computer simulations |
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Biophysics Physics Theoretical Physics Molecular Biology kinesin neck linker molecular motor Brownian dynamics efficiency coarse grained model computer simulations Murrow, Matthew Alan Kinesin model for Brownian dynamics simulations of stepping efficiency |
| author |
Murrow, Matthew Alan |
| author_facet |
Murrow, Matthew Alan |
| author_sort |
Murrow, Matthew Alan |
| title |
Kinesin model for Brownian dynamics simulations of stepping efficiency |
| title_short |
Kinesin model for Brownian dynamics simulations of stepping efficiency |
| title_full |
Kinesin model for Brownian dynamics simulations of stepping efficiency |
| title_fullStr |
Kinesin model for Brownian dynamics simulations of stepping efficiency |
| title_full_unstemmed |
Kinesin model for Brownian dynamics simulations of stepping efficiency |
| title_sort |
kinesin model for brownian dynamics simulations of stepping efficiency |
| publisher |
University of Akron / OhioLINK |
| publishDate |
2019 |
| url |
http://rave.ohiolink.edu/etdc/view?acc_num=akron156441669721832 |
| work_keys_str_mv |
AT murrowmatthewalan kinesinmodelforbrowniandynamicssimulationsofsteppingefficiency |
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1719456002847277056 |