Dynamics of the Protein Search for Targets on DNA in the Presence of Traps

The Journal of Physical Chemistry. B
Martin LangeAnatoly B Kolomeisky

Abstract

Protein search for specific binding sites on DNA is a fundamental biological phenomenon associated with the beginning of most major biological processes. It is frequently found that proteins find and recognize their specific targets quickly and efficiently despite the complex nature of protein-DNA interactions in living cells. Although significant experimental and theoretical efforts were made in recent years, the mechanisms of these processes remain not well-clarified. We present a theoretical study of the protein target search dynamics in the presence of semispecific binding sites which are viewed as traps. Our theoretical approach employs a discrete-state stochastic method that accounts for the most important physical and chemical processes in the system. It also leads to a full analytical description for all dynamic properties of the protein search. It is found that the presence of traps can significantly modify the protein search dynamics. This effect depends on the spatial positions of the targets and traps, on distances between them, on the average sliding length of the protein along the DNA, and on the total length of DNA. Theoretical predictions are discussed using simple physical-chemical arguments, and they are also ...Continue Reading

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Citations

May 20, 2016·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Iris DrorYael Mandel-Gutfreund
Aug 23, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Alexey A ShvetsAnatoly B Kolomeisky
Jan 30, 2020·Nature Communications·Milagros CastellanosVictor Muñoz
Apr 10, 2020·The Journal of Physical Chemistry. B·Kinjal Mondal, Srabanti Chaudhury
Nov 11, 2021·Biophysical Journal·Anupam MondalArnab Bhattacherjee

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