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dc.contributor.authorShvets, Alexey
Kochugaeva, Maria
Kolomeisky, Anatoly B.
dc.date.accessioned 2016-01-14T20:01:03Z
dc.date.available 2016-01-14T20:01:03Z
dc.date.issued 2015
dc.identifier.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.
dc.identifier.urihttps://hdl.handle.net/1911/87816
dc.description.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.
dc.language.iso eng
dc.publisher America Chemical Society
dc.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.
dc.title Role of Static and Dynamic Obstacles in the Protein Search for Targets on DNA
dc.type Journal article
dc.contributor.funder Welch Foundation
dc.contributor.funder National Science Foundation
dc.citation.journalTitle The Journal of Physical Chemistry B
dc.contributor.org Center for Theoretical Biological Physics
dc.subject.keywordprotein-DNA interactions
crowding
discrete-state stochastic models
first-passage processes
dc.type.dcmi Text
dc.identifier.doihttp://dx.doi.org/10.1021/acs.jpcb.5b09814
dc.identifier.grantID C-1559 (Welch Foundation)
dc.identifier.grantID CHE-1360979 (National Science Foundation)
dc.identifier.grantID PHY-1427654 (National Science Foundation)
dc.type.publication post-print


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