论DNA与蛋白质相互作用的特异性
On the specificity of DNA-protein interactions.
作者信息
von Hippel P H, Berg O G
出版信息
Proc Natl Acad Sci U S A. 1986 Mar;83(6):1608-12. doi: 10.1073/pnas.83.6.1608.
Abstract
In this paper we summarize the various factors that must be considered in establishing the operational specificity of the binding of a protein regulator of gene expression to a DNA target site. We consider informational (combinatorial) aspects of binding-site specification, actual recognition mechanisms, and the thermodynamics of target-site selection against a background of competing pseudospecific and non-(sequence)-specific DNA binding sites. The results provide insight into the design, specification, and possibly the evolution of regulatory proteins and their chromosomal binding targets, as well as into practical aspects of the design of regulatory-protein isolation schemes and physicochemical regulatory considerations in vivo.
摘要
在本文中，我们总结了在确定基因表达的蛋白质调节因子与DNA靶位点结合的操作特异性时必须考虑的各种因素。我们考虑了结合位点特异性的信息（组合）方面、实际识别机制，以及在竞争性假特异性和非（序列）特异性DNA结合位点背景下靶位点选择的热力学。这些结果为调节蛋白及其染色体结合靶标的设计、特异性以及可能的进化提供了见解，同时也为调节蛋白分离方案的设计以及体内物理化学调节考虑的实际方面提供了见解。
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本文引用的文献
1
Interactions of bacteriophage T4-coded gene 32 protein with nucleic acids. I. Characterization of the binding interactions.噬菌体T4编码的基因32蛋白与核酸的相互作用。I. 结合相互作用的特性
J Mol Biol. 1981 Jan 5;145(1):75-104. doi: 10.1016/0022-2836(81)90335-1.
2
Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor--operator interaction: kinetic measurements and conclusions.核酸上蛋白质转位的扩散驱动机制。3. 大肠杆菌乳糖阻遏物-操纵基因相互作用：动力学测量与结论。
Biochemistry. 1981 Nov 24;20(24):6961-77. doi: 10.1021/bi00527a030.
3
On the processivity of DNA replication.
J Biomol Struct Dyn. 1983 Dec;1(3):715-27. doi: 10.1080/07391102.1983.10507477.
4
Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor--operator interaction: equilibrium measurements.核酸上蛋白质转位的扩散驱动机制。2. 大肠杆菌阻遏蛋白-操纵基因相互作用：平衡测量
Biochemistry. 1981 Nov 24;20(24):6948-60. doi: 10.1021/bi00527a029.
5
Protein-DNA recognition.蛋白质-脱氧核糖核酸识别
Annu Rev Biochem. 1984;53:293-321. doi: 10.1146/annurev.bi.53.070184.001453.
6
The molecular basis of DNA-protein recognition inferred from the structure of cro repressor.从cro阻遏蛋白结构推断的DNA-蛋白质识别的分子基础。
Nature. 1982 Aug 19;298(5876):718-23. doi: 10.1038/298718a0.
7
Recognition of nucleotide sequences.核苷酸序列的识别
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8
Non-specific DNA binding of genome regulating proteins as a biological control mechanism: I. The lac operon: equilibrium aspects.作为一种生物控制机制的基因组调控蛋白的非特异性DNA结合：I. 乳糖操纵子：平衡方面
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9
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J Mol Biol. 1974 May 15;85(2):231-48. doi: 10.1016/0022-2836(74)90362-3.
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