Schlick Tamar, Arora Karunesh, Beard William A, Wilson Samuel H
Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA. Courant Institute of Mathematical Sciences, New York, University, 251 Mercer Street, New York, NY 10012, USA.
Theor Chem Acc. 2012 Nov 1;131:1287. doi: 10.1007/s00214-012-1287-7. Epub 2012 Nov 23.
In recent papers, there has been a lively exchange concerning theories for enzyme catalysis, especially the role of protein dynamics/pre-chemistry conformational changes in the catalytic cycle of enzymes. Of particular interest is the notion that substrate-induced conformational changes that assemble the polymerase active site prior to chemistry are required for DNA synthesis and impact fidelity (i.e., substrate specificity). High-resolution crystal structures of DNA polymerase representing intermediates of substrate complexes prior to the chemical step are available. These structures indicate that conformational adjustments in both the protein and substrates must occur to achieve the requisite geometry of the reactive participants for catalysis. We discuss computational and kinetic methods to examine possible conformational change pathways that lead from the observed crystal structure intermediates to the final structures poised for chemistry. The results, as well as kinetic data from site-directed mutagenesis studies, are consistent with models requiring pre-chemistry conformational adjustments in order to achieve high fidelity DNA synthesis. Thus, substrate-induced conformational changes that assemble the polymerase active site prior to chemistry contribute to DNA synthesis even when they do not represent actual rate-determining steps for chemistry.
在最近的论文中，围绕酶催化理论展开了热烈的讨论，尤其是蛋白质动力学/化学前构象变化在酶催化循环中的作用。特别令人感兴趣的是这样一种观点，即DNA合成和影响保真度（即底物特异性）需要在化学反应之前组装聚合酶活性位点的底物诱导构象变化。目前已有代表化学步骤之前底物复合物中间体的DNA聚合酶的高分辨率晶体结构。这些结构表明，蛋白质和底物都必须发生构象调整，以实现催化反应中反应物所需的几何结构。我们讨论了计算和动力学方法，以研究从观察到的晶体结构中间体到准备进行化学反应的最终结构的可能构象变化途径。这些结果以及定点诱变研究的动力学数据与需要化学前构象调整以实现高保真DNA合成的模型一致。因此，即使底物诱导的构象变化不代表化学反应的实际速率决定步骤，在化学反应之前组装聚合酶活性位点的这些变化也有助于DNA合成。
