Origins of specificity in protein-DNA recognition.
Origins of specificity in protein-DNA recognition.
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DOI：
10.1146/annurev-biochem-060408-091030
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发表时间：
2010
影响因子：
16.6
通讯作者：
Mann RS
中科院分区：
文献类型：
--
作者：
Rohs R;Jin X;West SM;Joshi R;Honig B;Mann RS
蛋白质和DNA之间的特异性相互作用是许多生物过程的基础。在这篇综述中，我们提供了一个修订后的蛋白质-DNA相互作用的观点，强调了这两个大分子的三维结构的重要性。我们将蛋白质-DNA相互作用分为两类：一类是蛋白质识别DNA碱基的独特化学特征（碱基读出），另一类是蛋白质识别序列依赖的DNA形状（形状读出）。我们进一步将碱基读出分为发生在大沟中的相互作用和发生在小沟中的相互作用。类似地，DNA形状的读出被细分为全局形状识别，例如当DNA螺旋呈现整体弯曲时，和局部形状识别，例如当碱基对台阶扭结或当小沟的区域窄时。基于蛋白质数据库中现有的>1500种蛋白质-DNA复合物的结构，我们认为单个DNA结合蛋白结合联合收割机多种读出机制以实现DNA结合特异性。区分家族的特异性通常涉及大沟中的碱基读出，而形状读出通常用于更高分辨率的特异性，以区分相同DNA结合蛋白家族内的成员。
Specific interactions between proteins and DNA are fundamental to many biological processes. In this review, we provide a revised view of protein-DNA interactions that emphasizes the importance of the three-dimensional structures of both macromolecules. We divide protein-DNA interactions into two categories: those where the protein recognizes the unique chemical signatures of the DNA bases (base readout) and those where the protein recognizes a sequence-dependent DNA shape (shape readout). We further divide base readout into those interactions that occur in the major groove from those that occur in the minor groove. Analogously, the readout of DNA shape is subdivided into global shape recognition, for example when the DNA helix exhibits an overall bend, and local shape recognition, for example when a base pair step is kinked or when a region of the minor groove is narrow. Based on the >1500 structures of protein-DNA complexes now available in the Protein Data Base, we argue that individual DNA binding proteins combine multiple readout mechanisms to achieve DNA binding specificity. Specificity that distinguishes between families frequently involves base readout in the major groove while shape readout is often exploited for higher resolution specificity, to distinguish between members within the same DNA-binding protein family.
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影响因子：
56.9
作者：
CHO, YJ;GORINA, S;PAVLETICH, NP
通讯作者：
PAVLETICH, NP
DOI：
10.1126/science.1162327
发表时间：
2009-06-26
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Badis G;Berger MF;Philippakis AA;Talukder S;Gehrke AR;Jaeger SA;Chan ET;Metzler G;Vedenko A;Chen X;Kuznetsov H;Wang CF;Coburn D;Newburger DE;Morris Q;Hughes TR;Bulyk ML
通讯作者：
Bulyk ML
影响因子：
16
作者：
Badis, Gwenael;Chan, Esther T.;van Bakel, Harm;Pena-Castillo, Lourdes;Tillo, Desiree;Tsui, Kyle;Carlson, Clayton D.;Gossett, Andrea J.;Hasinoff, Michael J.;Warren, Christopher L.;Gebbia, Marinella;Talukder, Shaheynoor;Yang, Ally;Mnaimneh, Sanie;Terterov, Dimitri;Coburn, David;Yeo, Ai Li;Yeo, Zhen Xuan;Clarke, Neil D.;Lieb, Jason D.;Ansari, Aseem Z.;Nislow, Corey;Hughes, Timothy R.
通讯作者：
Hughes, Timothy R.
影响因子：
56.9
作者：
AGGARWAL, AK;RODGERS, DW;HARRISON, SC
通讯作者：
HARRISON, SC
影响因子：
16.8
作者：
Daniels, DS;Woo, TT;Tainer, JA
通讯作者：
Tainer, JA