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dc.contributor.authorLange, Martin
Kochugaeva, Maria
Kolomeisky, Anatoly B.
dc.date.accessioned 2017-06-05T19:27:05Z
dc.date.available 2017-06-05T19:27:05Z
dc.date.issued 2015
dc.identifier.citation Lange, Martin, Kochugaeva, Maria and Kolomeisky, Anatoly B.. "Protein search for multiple targets on DNA." The Journal of Chemical Physics, 143, no. 10 (2015) AIP Publishing LLC.: http://dx.doi.org/10.1063/1.4930113.
dc.identifier.urihttps://hdl.handle.net/1911/94776
dc.description.abstract Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of experimental and theoretical investigations have been devoted to uncovering the molecular description of these phenomena, but many aspects of the mechanisms of protein search for the targets on DNA remain not well understood. One of the most intriguing problems is the role of multiple targets in protein search dynamics. Using a recently developed theoretical framework we analyze this question in detail. Our method is based on a discrete-state stochastic approach that takes into account most relevant physical-chemical processes and leads to fully analytical description of all dynamic properties. Specifically, systems with two and three targets have been explicitly investigated. It is found that multiple targets in most cases accelerate the search in comparison with a single target situation. However, the acceleration is not always proportional to the number of targets. Surprisingly, there are even situations when it takes longer to find one of the multiple targets in comparison with the single target. It depends on the spatial position of the targets, distances between them, average scanning lengths of protein molecules on DNA, and the total DNA lengths. Physical-chemical explanations of observed results are presented. Our predictions are compared with experimental observations as well as with results from a continuum theory for the protein search. Extensive Monte Carlo computer simulations fully support our theoretical calculations.
dc.language.iso eng
dc.publisher AIP Publishing LLC.
dc.rights Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use.
dc.title Protein search for multiple targets on DNA
dc.type Journal article
dc.citation.journalTitle The Journal of Chemical Physics
dc.contributor.org Center for Theoretical Biological Physics
dc.citation.volumeNumber 143
dc.citation.issueNumber 10
dc.type.dcmi Text
dc.identifier.doihttp://dx.doi.org/10.1063/1.4930113
dc.type.publication publisher version
dc.citation.articleNumber 105102


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