Crowding on DNA in Protein Search for Targets

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dc.citation.firstpage2502en_US
dc.citation.issueNumber13en_US
dc.citation.journalTitleThe Journal of Physical Chemistry Lettersen_US
dc.citation.lastpage2506en_US
dc.citation.volumeNumber7en_US
dc.contributor.authorShvets, Alexey A.en_US
dc.contributor.authorKolomeisky, Anatoly B.en_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2016-09-19T21:20:39Zen_US
dc.date.available2016-09-19T21:20:39Zen_US
dc.date.issued2016en_US
dc.description.abstractProteins searching and recognizing specific sites on DNA is required for initiating all major biological processes. While the details of the protein search for targets on DNA in purified in vitro systems are reasonably well understood, the situation in real cells is much less clear. The presence of other types of molecules on DNA should prevent reaching the targets, but experiments show that, surprisingly, the molecular crowding on DNA influences the search dynamics much less than expected. We develop a theoretical method that allowed us to clarify the mechanisms of the protein search on DNA in the presence of crowding. It is found that the dimensionality of the search trajectories specifies whether the crowding will affect the target finding. For 3D search pathways it is minimal, while the strongest effect is for 1D search pathways when the crowding particle can block the search. In addition, for 1D search we determined that the critical parameter is a mobility of crowding agents: highly mobile molecules do not affect the search dynamics, while the slow particles can significantly slow down the process. Physical-chemical explanations of the observed phenomena are presented. Our theoretical predictions thus explain the experimental observations, and they are also supported by extensive numerical simulations.en_US
dc.identifier.citationShvets, Alexey A. and Kolomeisky, Anatoly B.. "Crowding on DNA in Protein Search for Targets." <i>The Journal of Physical Chemistry Letters,</i> 7, no. 13 (2016) American Chemical Society: 2502-2506. http://dx.doi.org/10.1021/acs.jpclett.6b00905.en_US
dc.identifier.doihttp://dx.doi.org/10.1021/acs.jpclett.6b00905en_US
dc.identifier.urihttps://hdl.handle.net/1911/91580en_US
dc.language.isoengen_US
dc.publisherAmerican Chemical Societyen_US
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.titleCrowding on DNA in Protein Search for Targetsen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpost-printen_US
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