Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
J Phys Chem B. 2010 Jun 10;114(22):7662-71. doi: 10.1021/jp1017289.
Cys(2)His(2) zinc finger proteins are one of the most frequently observed DNA-binding motifs in eukaryotes. They have been widely used as a framework for designing new DNA-binding proteins. In this work, the binding affinity and conformational change of the Zif268-DNA complex were successfully reproduced with MD simulations and MM-PBSA analysis. The following new discoveries on the zinc finger protein-DNA interactions were obtained by careful energy decomposition analysis. First, a dramatic increase in the binding affinity was observed when the third zinc finger is added, indicating a cooperative nature. This cooperativity is shown to be a consequence of the small but distinctive conformational change of DNA, which enables a tight fit of the protein into the major groove of DNA. Second, specificity of the amino acid-nucleotide recognitions observed in the crystal structure is explained as originating from the ability of specific side chains and bases to take the optimal geometries for favorable interactions between polar groups. The success of the current approach implies that similar methods could be further applied to the study of protein-DNA interactions involving longer polyfingers or different linkers between fingers to provide insights for design of novel zinc finger proteins.
Cys(2)His(2)锌指蛋白是真核生物中最常见的 DNA 结合基序之一。它们已被广泛用作设计新的 DNA 结合蛋白的框架。在这项工作中，通过 MD 模拟和 MM-PBSA 分析成功再现了 Zif268-DNA 复合物的结合亲和力和构象变化。通过仔细的能量分解分析，获得了关于锌指蛋白-DNA 相互作用的以下新发现。首先，当添加第三个锌指时，观察到结合亲和力显著增加，表明存在协同性。这种协同作用是 DNA 发生微小但独特的构象变化的结果，这使得蛋白质能够紧密地适配到 DNA 的大沟中。其次，晶体结构中观察到的氨基酸-核苷酸识别特异性解释为源于特定侧链和碱基具有的能力，这些侧链和碱基能够采取最佳的几何形状，以实现极性基团之间有利的相互作用。当前方法的成功意味着类似的方法可以进一步应用于研究涉及更长的多锌指或指之间不同连接物的蛋白质-DNA 相互作用，为设计新型锌指蛋白提供见解。
