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酶、蛋白质和抗体如何识别扩展 DNA；一般规律。

How Enzymes, Proteins, and Antibodies Recognize Extended DNAs; General Regularities.

机构信息

Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 63009 Novosibirsk, Russia.

出版信息

Int J Mol Sci. 2021 Jan 29;22(3):1369. doi: 10.3390/ijms22031369.

DOI:10.3390/ijms22031369
PMID:33573045
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7866405/
Abstract

X-ray analysis cannot provide quantitative estimates of the relative contribution of non-specific, specific, strong, and weak contacts of extended DNA molecules to their total affinity for enzymes and proteins. The interaction of different enzymes and proteins with long DNA and RNA at the quantitative molecular level can be successfully analyzed using the method of the stepwise increase in ligand complexity (SILC). The present review summarizes the data on stepwise increase in ligand complexity (SILC) analysis of nucleic acid recognition by various enzymes-replication, restriction, integration, topoisomerization, six different repair enzymes (uracil DNA glycosylase, Fpg protein from , human 8-oxoguanine-DNA glycosylase, human apurinic/apyrimidinic endonuclease, RecA protein, and DNA-ligase), and five DNA-recognizing proteins (RNA helicase, human lactoferrin, alfa-lactalbumin, human blood albumin, and IgGs against DNA). The relative contributions of structural elements of DNA fragments "covered" by globules of enzymes and proteins to the total affinity of DNA have been evaluated. Thermodynamic and catalytic factors providing discrimination of unspecific and specific DNAs by these enzymes on the stages of primary complex formation following changes in enzymes and DNAs or RNAs conformations and direct processing of the catalysis of the reactions were found. General regularities of recognition of nucleic acid by DNA-dependent enzymes, proteins, and antibodies were established.

摘要

X 射线分析无法定量估计伸展 DNA 分子的非特异性、特异性、强相互作用和弱相互作用对其与酶和蛋白质总亲和力的相对贡献。使用逐步增加配体复杂性（SILC）的方法可以成功分析不同酶和蛋白质与长 DNA 和 RNA 的定量分子水平相互作用。本综述总结了关于逐步增加配体复杂性（SILC）分析各种酶（复制、限制、整合、拓扑异构酶、6 种不同的修复酶（尿嘧啶 DNA 糖基化酶、来自的 Fpg 蛋白、人 8-氧鸟嘌呤-DNA 糖基化酶、人无嘌呤/嘧啶内切核酸酶、RecA 蛋白和 DNA-连接酶）和 5 种 DNA 识别蛋白（RNA 解旋酶、人乳铁蛋白、α-乳白蛋白、人血白蛋白和针对 DNA 的 IgG）对核酸识别的研究数据。评估了“覆盖”在酶和蛋白质球蛋白中的 DNA 片段的结构元素对 DNA 总亲和力的相对贡献。发现了在酶和 DNA 或 RNA 构象改变以及反应的直接催化过程中，区分非特异性和特异性 DNA 的热力学和催化因素，这些因素为这些酶在初级复合物形成阶段提供了区分。建立了 DNA 依赖性酶、蛋白质和抗体识别核酸的一般规律。

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