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

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dc.citation.firstpage4049en_US
dc.citation.issueNumber17en_US
dc.citation.journalTitleThe Journal of Physical Chemistry Lettersen_US
dc.citation.lastpage4054en_US
dc.citation.volumeNumber8en_US
dc.contributor.authorKochugaeva, Maria P.en_US
dc.contributor.authorBerezhkovskii, Alexander M.en_US
dc.contributor.authorKolomeisky, Anatoly B.en_US
dc.date.accessioned2017-11-15T14:12:33Zen_US
dc.date.available2017-11-15T14:12:33Zen_US
dc.date.issued2017en_US
dc.description.abstractThe 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.en_US
dc.identifier.citationKochugaeva, Maria P., Berezhkovskii, Alexander M. and Kolomeisky, Anatoly B.. "Optimal Length of Conformational Transition Region in Protein Search for Targets on DNA." <i>The Journal of Physical Chemistry Letters,</i> 8, no. 17 (2017) American Chemical Society: 4049-4054. https://doi.org/10.1021/acs.jpclett.7b01750.en_US
dc.identifier.digitaloptimal-length-conformationalen_US
dc.identifier.doihttps://doi.org/10.1021/acs.jpclett.7b01750en_US
dc.identifier.urihttps://hdl.handle.net/1911/98821en_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.titleOptimal Length of Conformational Transition Region in Protein Search for Targets on DNAen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpost-printen_US
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