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1
DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families.螺旋-转角-螺旋、探测螺旋、激素受体和锌指家族中转录因子的DNA识别密码。
Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12357-61. doi: 10.1073/pnas.91.26.12357.
2
Stereochemical basis of DNA recognition by Zn fingers.锌指对DNA识别的立体化学基础。
Nucleic Acids Res. 1994 Aug 25;22(16):3397-405. doi: 10.1093/nar/22.16.3397.
3
A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules.转录因子中探针螺旋DNA-蛋白质识别密码的框架：化学和立体化学规则
Structure. 1994 Apr 15;2(4):317-26. doi: 10.1016/s0969-2126(00)00033-2.
4
Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition.Zif268突变体中侧链的重排突出了锌指-DNA识别的复杂性。
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The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition.一种双锌指肽的晶体结构揭示了锌指/DNA识别规则的扩展。
Nature. 1993 Dec 2;366(6454):483-7. doi: 10.1038/366483a0.
6
Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity.与同源DNA序列结合的TFIIIA前三个锌指的溶液结构：亲和力和序列特异性的决定因素
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7
Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code.通过噬菌体展示优化的锌指分析：评估识别密码的效用。
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8
DNA-induced alpha-helix capping in conserved linker sequences is a determinant of binding affinity in Cys(2)-His(2) zinc fingers.保守连接序列中DNA诱导的α-螺旋封端是Cys(2)-His(2)锌指结合亲和力的决定因素。
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Repetitive use of a phosphate-binding module in DNA polymerase beta, Oct-1 POU domain and phage repressors.DNA聚合酶β、Oct-1 POU结构域和噬菌体阻遏物中磷酸结合模块的重复使用。
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Toward rules relating zinc finger protein sequences and DNA binding site preferences.关于锌指蛋白序列与DNA结合位点偏好性相关的规则。
Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7345-9. doi: 10.1073/pnas.89.16.7345.

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Dynamics simulations for engineering macromolecular interactions.工程大分子相互作用的动力学模拟。
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本文引用的文献

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Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain.Max通过二聚体b/HLH/Z结构域识别其同源DNA。
Nature. 1993 May 6;363(6424):38-45. doi: 10.1038/363038a0.
2
Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins.利用锌指共有序列框架和特异性规则设计特异性DNA结合蛋白。
Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2256-60. doi: 10.1073/pnas.90.6.2256.
3
Identification of three residues in the basic regions of the bZIP proteins GCN4, C/EBP and TAF-1 that are involved in specific DNA binding.鉴定碱性亮氨酸拉链蛋白GCN4、C/EBP和TAF-1的碱性区域中参与特异性DNA结合的三个残基。
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Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers.一种五指GLI-DNA复合物的晶体结构：锌指结构的新视角
Science. 1993 Sep 24;261(5129):1701-7. doi: 10.1126/science.8378770.
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The X-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility.与ATF/CREB位点DNA结合的GCN4-bZIP的X射线结构表明，该复合物依赖于DNA的灵活性。
J Mol Biol. 1993 Sep 5;233(1):139-54. doi: 10.1006/jmbi.1993.1490.
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Common features in DNA recognition helices of eukaryotic transcription factors.真核转录因子DNA识别螺旋中的共同特征。
EMBO J. 1993 Aug;12(8):3221-6. doi: 10.1002/j.1460-2075.1993.tb05991.x.
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NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1.GATA-1含锌DNA结合结构域特定DNA复合物的核磁共振结构
Science. 1993 Jul 23;261(5120):438-46. doi: 10.1126/science.8332909.
8
Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5.肝细胞核因子3/叉头DNA识别基序的共晶体结构类似于组蛋白H5。
Nature. 1993 Jul 29;364(6436):412-20. doi: 10.1038/364412a0.
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Structure and function of the b/HLH/Z domain of USF.上游刺激因子（USF）的b/HLH/Z结构域的结构与功能
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Hin recombinase bound to DNA: the origin of specificity in major and minor groove interactions.与DNA结合的Hin重组酶：主沟和副沟相互作用中特异性的起源。
Science. 1994 Jan 21;263(5145):348-55. doi: 10.1126/science.8278807.

螺旋-转角-螺旋、探测螺旋、激素受体和锌指家族中转录因子的DNA识别密码。

DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families.

作者信息

Suzuki M, Yagi N

机构信息

Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.

出版信息

Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12357-61. doi: 10.1073/pnas.91.26.12357.

DOI:10.1073/pnas.91.26.12357
PMID:7809040
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC45436/
Abstract

We have previously reported that in four transcription factor families the DNA-recognition rules can be described as (i) chemical rules, which list possible pairings between the 20 amino acid residues and the four DNA bases, and (ii) stereochemical rules, which describe the base and amino acid positions in contact. We have incorporated these rules into a computer program and examined the nature of the rules. Here we conclude that the DNA recognition rules are simple, logical, and consistent. The rules are specific enough to predict DNA-binding characteristics from a protein sequence.

摘要

我们之前报道过，在四个转录因子家族中，DNA识别规则可描述为：（i）化学规则，列出了20种氨基酸残基与四种DNA碱基之间可能的配对；（ii）立体化学规则，描述了相互接触的碱基和氨基酸位置。我们已将这些规则纳入一个计算机程序，并研究了这些规则的性质。在此我们得出结论，DNA识别规则简单、符合逻辑且一致。这些规则足够具体，能够从蛋白质序列预测DNA结合特性。