Kuttner Yosef Y, Engel Stanislav
Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
Proteins. 2018 Feb;86(2):229-236. doi: 10.1002/prot.25430. Epub 2017 Dec 1.
A rational design of protein complexes with defined functionalities and of drugs aimed at disrupting protein-protein interactions requires fundamental understanding of the mechanisms underlying the formation of specific protein complexes. Efforts to develop efficient small-molecule or protein-based binders often exploit energetic hot spots on protein surfaces, namely, the interfacial residues that provide most of the binding free energy in the complex. The molecular basis underlying the unusually high energy contribution of the hot spots remains obscure, and its elucidation would facilitate the design of interface-targeted drugs. To study the nature of the energetic hot spots, we analyzed the backbone dynamic properties of contact surfaces in several protein complexes. We demonstrate that, in most complexes, the backbone dynamic landscapes of interacting surfaces form complementary "stability patches," in which static areas from the opposing surfaces superimpose, and that these areas are predominantly located near the geometric center of the interface. We propose that a diminished enthalpy-entropy compensation effect augments the degree to which residues positioned within the complementary stability patches contribute to complex affinity, thereby giving rise to the energetic hot spots. These findings offer new insights into the nature of energetic hot spots and the role that backbone dynamics play in facilitating intermolecular recognition. Mapping the interfacial stability patches may provide guidance for protein engineering approaches aimed at improving the stability of protein complexes and could facilitate the design of ligands that target complex interfaces.
合理设计具有特定功能的蛋白质复合物以及旨在破坏蛋白质 - 蛋白质相互作用的药物，需要对特定蛋白质复合物形成背后的机制有基本的了解。开发高效的小分子或基于蛋白质的结合剂的努力通常利用蛋白质表面的能量热点，即那些在复合物中提供大部分结合自由能的界面残基。热点异常高能量贡献背后的分子基础仍然不清楚，对其进行阐明将有助于设计针对界面的药物。为了研究能量热点的性质，我们分析了几种蛋白质复合物中接触表面的主链动力学特性。我们证明，在大多数复合物中，相互作用表面的主链动力学景观形成互补的“稳定性斑块”，其中相对表面的静态区域相互叠加，并且这些区域主要位于界面的几何中心附近。我们提出，焓 - 熵补偿效应的减弱增强了位于互补稳定性斑块内的残基对复合物亲和力的贡献程度，从而产生了能量热点。这些发现为能量热点的性质以及主链动力学在促进分子间识别中所起的作用提供了新的见解。绘制界面稳定性斑块可能为旨在提高蛋白质复合物稳定性的蛋白质工程方法提供指导，并有助于设计靶向复合物界面的配体。
