Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Novosibirsk 63009, Russia.
J Mol Recognit. 2011 Jul-Aug;24(4):656-77. doi: 10.1002/jmr.1096.
X-ray structural analysis provides no quantitative estimate of the relative contribution of specific and nonspecific or strong and weak interactions to the total affinity of enzymes for nucleic acids. We have shown that the interaction between enzymes and long nucleic acids at the molecular level can be successfully analyzed by the method of stepwise increase in ligand complexity (SILC). In the present review we summarize our studies of human uracil DNA glycosylase and apurinic/apyrimidinic endonuclease, E. coli 8-oxoguanine DNA glycosylase and RecA protein using the SILC approach. The relative contribution of structural (X-ray analysis data), thermodynamic, and catalytic factors to the discrimination of specific and nonspecific DNA by these enzymes at the stages of complex formation, the following changes in DNA and enzyme conformations and especially the catalysis of the reactions is discussed.
X 射线结构分析无法定量估计特定和非特定、强和弱相互作用对酶与核酸亲和力的相对贡献。我们已经表明，通过逐步增加配体复杂性（SILC）的方法可以成功分析酶与长核酸在分子水平上的相互作用。在本综述中，我们总结了使用 SILC 方法研究人类尿嘧啶 DNA 糖基化酶和无嘌呤/无嘧啶内切核酸酶、大肠杆菌 8-氧鸟嘌呤 DNA 糖基化酶和 RecA 蛋白的研究结果。讨论了结构（X 射线分析数据）、热力学和催化因素相对贡献，这些因素在这些酶识别特定和非特定 DNA 的各个阶段，即复合物形成阶段、随后 DNA 和酶构象的变化，特别是反应的催化中发挥作用。
