Coarse-grained models for studying protein diffusion along DNA

Arnab Bhattacherjee; Dana Krepel; Yaakov Levy

doi:https://doi.org/10.1002/wcms.1262

Coarse-grained models for studying protein diffusion along DNA

Arnab Bhattacherjee, Dana Krepel, Yaakov Levy

Department of Chemical and Structural Biology

Weizmann Institute of Science

Research output: Contribution to journal › Review article › peer-review

Abstract

Understanding the molecular mechanism and the fast kinetics of DNA target site recognition by a protein is essential to decipher genetic activity in the cell. The speed of searching DNA may depend on the structural complexity of the proteins and the DNA molecules as well as the cellular environment. Coarse-grained (CG) molecular dynamics simulations are powerful means to investigate the molecular details of the search performed by protein to locate the target sites. Recent studies showed how different proteins scan DNA and how the search efficiency can be enhanced and regulated by the protein properties. In this review, we discuss computational approaches to study the physical chemistry of DNA search processes using CG molecular dynamics simulations and their advantage in covering long time-scale biomolecular processes. WIREs Comput Mol Sci 2016, 6:515–531. doi: 10.1002/wcms.1262. For further resources related to this article, please visit the WIREs website.

Original language	English
Pages (from-to)	515-531
Number of pages	17
Journal	Wiley Interdisciplinary Reviews-Computational Molecular Science
Volume	6
Issue number	5
DOIs	https://doi.org/10.1002/wcms.1262
State	Published - 1 Sep 2016

All Science Journal Classification (ASJC) codes

Computational Mathematics
Materials Chemistry
Biochemistry
Computer Science Applications
Physical and Theoretical Chemistry

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https://doi.org/10.1002/wcms.1262

Cite this

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title = "Coarse-grained models for studying protein diffusion along DNA",

abstract = "Understanding the molecular mechanism and the fast kinetics of DNA target site recognition by a protein is essential to decipher genetic activity in the cell. The speed of searching DNA may depend on the structural complexity of the proteins and the DNA molecules as well as the cellular environment. Coarse-grained (CG) molecular dynamics simulations are powerful means to investigate the molecular details of the search performed by protein to locate the target sites. Recent studies showed how different proteins scan DNA and how the search efficiency can be enhanced and regulated by the protein properties. In this review, we discuss computational approaches to study the physical chemistry of DNA search processes using CG molecular dynamics simulations and their advantage in covering long time-scale biomolecular processes. WIREs Comput Mol Sci 2016, 6:515–531. doi: 10.1002/wcms.1262. For further resources related to this article, please visit the WIREs website.",

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AB - Understanding the molecular mechanism and the fast kinetics of DNA target site recognition by a protein is essential to decipher genetic activity in the cell. The speed of searching DNA may depend on the structural complexity of the proteins and the DNA molecules as well as the cellular environment. Coarse-grained (CG) molecular dynamics simulations are powerful means to investigate the molecular details of the search performed by protein to locate the target sites. Recent studies showed how different proteins scan DNA and how the search efficiency can be enhanced and regulated by the protein properties. In this review, we discuss computational approaches to study the physical chemistry of DNA search processes using CG molecular dynamics simulations and their advantage in covering long time-scale biomolecular processes. WIREs Comput Mol Sci 2016, 6:515–531. doi: 10.1002/wcms.1262. For further resources related to this article, please visit the WIREs website.

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Coarse-grained models for studying protein diffusion along DNA

Abstract

All Science Journal Classification (ASJC) codes

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