最新《Nature》DNA识别机制

【字体: 时间:2009年11月02日 来源:生物通

编辑推荐:

  生物通报道,哥伦比亚大学计算机生物与生物信息学研究中心,生物化学与分子生物学中心,霍华休斯医学研究所的科学家在DNA复制成型的研究方面取得新的进展,相关成果文章The role of DNA shape in protein–DNA recognition发表在最新一期的Nature上。

  

生物通报道,哥伦比亚大学计算机生物与生物信息学研究中心,生物化学与分子生物学中心,霍华休斯医学研究所的科学家在DNA复制成型的研究方面取得新的进展,相关成果文章The role of DNA shape in protein–DNA recognition发表在最新一期的Nature上。

 

序列特异性DNA结合蛋白何以能在数量巨大的非特异性DNA中找到目标是一个长期未解之谜。

 

哥伦比亚大学的研究者得出一个比较被接受的解释是,序列是作为DNA螺旋的“大沟”中蛋白与碱基之间氢键的形成被读取的。对蛋白-DNA复合物三维结构所做的一项新的分析表明,DNA形状是识别的关键。DNA序列的前后部分通过让精氨酸优先与带负电的“口袋”结合改变DNA螺旋“小沟”的宽度。DNA在核小体核心颗粒中的定位是这一效应的一个例子。

(生物通 小茜)

生物通推荐原文摘要

Nature 461, 1248-1253 (29 October 2009) | doi:10.1038/nature08473; Received 24 July 2009; Accepted 2 September 2009

 

 

The role of DNA shape in protein–DNA recognition

Remo Rohs1,3, Sean M. West1,3, Alona Sosinsky1,4, Peng Liu1, Richard S. Mann2 & Barry Honig1

 

Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA

Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168th Street, HHSC 1104, New York, New York 10032, USA

These authors contributed equally to this work.

Present address: Institute of Structural and Molecular Biology, School of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK.

Correspondence to: Richard S. Mann2Barry Honig1 Correspondence and requests for materials should be addressed to B.H. (Email: bh6@columbia.edu) or R.S.M. (Email: rsm10@columbia.edu).

 

 

Abstract

The recognition of specific DNA sequences by proteins is thought to depend on two types of mechanism: one that involves the formation of hydrogen bonds with specific bases, primarily in the major groove, and one involving sequence-dependent deformations of the DNA helix. By comprehensively analysing the three-dimensional structures of protein–DNA complexes, here we show that the binding of arginine residues to narrow minor grooves is a widely used mode for protein–DNA recognition. This readout mechanism exploits the phenomenon that narrow minor grooves strongly enhance the negative electrostatic potential of the DNA. The nucleosome core particle offers a prominent example of this effect. Minor-groove narrowing is often associated with the presence of A-tracts, AT-rich sequences that exclude the flexible TpA step. These findings indicate that the ability to detect local variations in DNA shape and electrostatic potential is a general mechanism that enables proteins to use information in the minor groove, which otherwise offers few opportunities for the formation of base-specific hydrogen bonds, to achieve DNA-binding specificity.

 

 

 

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