Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces
Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces
复制标题
DOI：
10.1371/journal.pcbi.1003872
复制
发表时间：
2014-10-01
影响因子：
4.3
通讯作者：
Vajda, Sandor
中科院分区：
文献类型：
--
作者：
Bohnuud, Tanggis;Kozakov, Dima;Vajda, Sandor
许多蛋白质-蛋白质相互作用(PPI)是药物发现的引人注目的目标，并且在许多情况下可以被小分子破坏。本研究的主要目的是通过比较无配基和配基结合的结构来研究作为PPI靶标的蛋白质界面区域结合位点的形成机制。为了避免任何潜在的偏见，我们专注于通过核磁共振技术获得并存储在蛋白质数据库中的无配体蛋白质构象的系综，而不是专门为本研究产生的系综。用于结构比较的方法是基于检测结合热点，即对结合自由能有主要贡献的蛋白质区域。分析的主要工具是计算溶剂映射，它通过对接大量的小“探针”分子来探索蛋白质的表面。虽然我们考虑了通过核磁共振技术获得的构象系综，但分析与用于生成结构的方法无关。通过寻找能量最重要的区域，作图可以使用基于核磁共振数据的无配体模型来识别结合位点残基。此外，该方法根据结合部位的性质选择类似于某些肽结合或配体结合结构的构象。这与分子识别的构象选择模型是一致的，该模型假定这种预先存在的构象。分析还表明，在不受配体任何影响的情况下，非结合态和结合态之间的最大相似性水平。进一步向结合结构的转变假设了蛋白质-肽或蛋白质-配体的相互作用，要么选择不属于核磁共振整体的更高能量构象，要么导致诱导FIT。因此，在蛋白质-蛋白质界面上形成结合多肽并可被小配体靶向的位点总是包括构象选择，尽管也可能涉及其他识别机制。
Many protein-protein interactions (PPIs) are compelling targets for drug discovery, and in a number of cases can be disrupted by small molecules. The main goal of this study is to examine the mechanism of binding site formation in the interface region of proteins that are PPI targets by comparing ligand-free and ligand-bound structures. To avoid any potential bias, we focus on ensembles of ligand-free protein conformations obtained by nuclear magnetic resonance (NMR) techniques and deposited in the Protein Data Bank, rather than on ensembles specifically generated for this study. The measures used for structure comparison are based on detecting binding hot spots, i.e., protein regions that are major contributors to the binding free energy. The main tool of the analysis is computational solvent mapping, which explores the surface of proteins by docking a large number of small "probe'' molecules. Although we consider conformational ensembles obtained by NMR techniques, the analysis is independent of the method used for generating the structures. Finding the energetically most important regions, mapping can identify binding site residues using ligand-free models based on NMR data. In addition, the method selects conformations that are similar to some peptide-bound or ligand-bound structure in terms of the properties of the binding site. This agrees with the conformational selection model of molecular recognition, which assumes such pre-existing conformations. The analysis also shows the maximum level of similarity between unbound and bound states that is achieved without any influence from a ligand. Further shift toward the bound structure assumes protein-peptide or protein-ligand interactions, either selecting higher energy conformations that are not part of the NMR ensemble, or leading to induced fit. Thus, forming the sites in protein-protein interfaces that bind peptides and can be targeted by small ligands always includes conformational selection, although other recognition mechanisms may also be involved.