Coarse-grained models for studying protein diffusion along DNA

被引：28

作者：

Bhattacherjee, Arnab ^{[1
]}

Krepel, Dana ^{[2
]}

Levy, Yaakov ^{[2
]}

机构：

[1] Jawaharlal Nehru Univ, Sch Computat & Integrat Sci, Ctr Computat Biol & Bioinformat, New Delhi, India

[2] Weizmann Inst Sci, Dept Biol Struct, Rehovot, Israel

来源：

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE | 2016年 / 6卷 / 05期

关键词：

TRANSCRIPTION-FACTOR-BINDING; FACILITATED DIFFUSION; MINIMAL MODELS; NUCLEIC-ACIDS; COGNATE SITES; DYNAMICS; SEARCH; TRANSLOCATION; SIMULATION; RNA;

D O I：

10.1002/wcms.1262

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

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. (C) 2016 John Wiley & Sons, Ltd

引用

页码：515 / 531

页数：17

共 97 条

[31] The lac Repressor Displays Facilitated Diffusion in Living Cells [J].