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    Optimal Length of Conformational Transition Region in Protein Search for Targets on DNA

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    Author
    Kochugaeva, Maria P.; Berezhkovskii, Alexander M.; Kolomeisky, Anatoly B.
    Date
    2017
    Abstract
    The starting point of many fundamental biological processes is associated with protein molecules finding and recognizing specific sites on DNA. However, despite a large number of experimental and theoretical studies on protein search for targets on DNA, many molecular aspects of underlying mechanisms are still not well understood. Experiments show that proteins bound to DNA can switch between slow recognition and fast search conformations. However, from a theoretical point of view, such conformational transitions should slow down the protein search for specific sites on DNA, in contrast to available experimental observations. In addition, experiments indicate that the nucleotide composition near the target site is more symmetrically homogeneous, leading to stronger effective interactions between proteins and DNA at these locations. However, as has been shown theoretically, this should also make the search less efficient, which is not observed. We propose a possible resolution of these problems by suggesting that conformational transitions occur only within a segment around the target where stronger interactions between proteins and DNA are observed. Two theoretical methods, based on continuum and discrete-state stochastic calculations, are developed, allowing us to obtain a comprehensive dynamic description for the protein search process in this system. The existence of an optimal length of the conformational transition zone with the shortest mean search time is predicted.
    Citation
    Kochugaeva, Maria P., Berezhkovskii, Alexander M. and Kolomeisky, Anatoly B.. "Optimal Length of Conformational Transition Region in Protein Search for Targets on DNA." The Journal of Physical Chemistry Letters, 8, no. 17 (2017) American Chemical Society: 4049-4054. https://doi.org/10.1021/acs.jpclett.7b01750.
    Published Version
    https://doi.org/10.1021/acs.jpclett.7b01750
    Type
    Journal article
    Publisher
    American Chemical Society
    Citable link to this page
    https://hdl.handle.net/1911/98821
    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