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

dc.citation.journalTitleThe Journal of Physical Chemistry Ben_US
dc.contributor.authorShvets, Alexeyen_US
dc.contributor.authorKochugaeva, Mariaen_US
dc.contributor.authorKolomeisky, Anatoly B.en_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.description.abstractProtein 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.en_US
dc.identifier.citationShvets, Alexey, Kochugaeva, Maria and Kolomeisky, Anatoly B.. "Role of Static and Dynamic Obstacles in the Protein Search for Targets on DNA." <i>The Journal of Physical Chemistry B,</i> (2015) America Chemical Society:
dc.publisherAmerica Chemical Society
dc.rightsThis is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Chemical Society.en_US
dc.subject.keywordprotein-DNA interactionsen_US
dc.subject.keyworddiscrete-state stochastic modelsen_US
dc.subject.keywordfirst-passage processesen_US
dc.titleRole of Static and Dynamic Obstacles in the Protein Search for Targets on DNAen_US
dc.typeJournal articleen_US
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