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    Role of Static and Dynamic Obstacles in the Protein Search for Targets on DNA

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    Author
    Shvets, Alexey; Kochugaeva, Maria; Kolomeisky, Anatoly B.
    Date
    2015
    Abstract
    Protein search for specific sequences on DNA marks the beginning of major biological processes. Experiments indicate that proteins find and recognize their targets quickly and efficiently. Because of the large number of experimental and theoretical investigations, there is a reasonable understanding of the protein search processes in purifiedᅠin vitroᅠsystems. However, the situation is much more complex in live cells where multiple biochemical and biophysical processes can interfere with the protein search dynamics. In this study, we develop a theoretical method that explores the effect of crowding on DNA chains during the protein search. More specifically, the role of static and dynamic obstacles is investigated. The method employs a discrete-state stochastic framework that accounts for most relevant physical and chemical processes in the system. Our approach also provides an analytical description for all dynamic properties. It is found that the presence of the obstacles can significantly modify the protein search dynamics. This effect depends on the size of the obstacles, on the spatial positions of the target and the obstacles, on the nature of the search regime, and on the dynamic nature of the obstacles. It is argued that the crowding on DNA can accelerate or slow down the protein search dynamics depending on these factors. A comparison with existing experimental and theoretical results is presented. Theoretical results are discussed using simple physical-chemical arguments, and they are also tested with extensive Monte Carlo computer simulations.
    Citation
    Shvets, Alexey, Kochugaeva, Maria and Kolomeisky, Anatoly B.. "Role of Static and Dynamic Obstacles in the Protein Search for Targets on DNA." The Journal of Physical Chemistry B, (2015) America Chemical Society: http://dx.doi.org/10.1021/acs.jpcb.5b09814.
    Published Version
    http://dx.doi.org/10.1021/acs.jpcb.5b09814
    Keyword
    protein-DNA interactions; crowding; discrete-state stochastic models; first-passage processes
    Type
    Journal article
    Publisher
    America Chemical Society
    Citable link to this page
    https://hdl.handle.net/1911/87816
    Rights
    This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Chemical Society.
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    • Chemistry Publications [636]
    • Faculty Publications [4990]

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    Home | FAQ | Contact Us | Privacy Notice | Accessibility Statement
    Managed by the Digital Scholarship Services at Fondren Library, Rice University
    Physical Address: 6100 Main Street, Houston, Texas 77005
    Mailing Address: MS-44, P.O.BOX 1892, Houston, Texas 77251-1892
    Site Map