Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction

被引：50
作者：
Etheve, Loic [1 ]
Martin, Juliette [1 ]
Lavery, Richard [1 ]
机构：
[1] Univ Lyon 1, Inst Biol & Chim Prot, CNRS, BMSSI UMR 5086, 7 Passage Vercors, F-69367 Lyon, France
来源：
NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / 03期
关键词：
BINDING DOMAIN; NUCLEIC-ACIDS; FORCE-FIELD; SPECIFICITY; AMBER; ORGANIZATION; HOMEODOMAIN; SIMULATIONS; MECHANICS; MODEL;
D O I：
10.1093/nar/gkv1511
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Molecular dynamics simulations of the Caenorhab-ditis elegans transcription factor SKN-1 bound to its cognate DNA site show that the protein-DNA interface undergoes significant dynamics on the microsecond timescale. A detailed analysis of the simulation shows that movements of two key arginine side chains between the major groove and the backbone of DNA generate distinct conformational sub-states that each recognize only part of the consensus binding sequence of SKN-1, while the experimentally observed binding specificity results from a time-averaged view of the dynamic recognition occurring within this complex.
引用
收藏
页码：1440 / 1448
页数：9
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