Sathyapriya R, Vishveshwara Saraswathi
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India.
Proteins. 2007 Aug 1;68(2):541-50. doi: 10.1002/prot.21401.
It is well known that proteins undergo backbone as well as side chain conformational changes upon ligand binding, which is not necessarily confined to the active site. Both the local and the global conformational changes brought out by ligand-binding have been extensively studied earlier. However, the global changes have been reported mainly at the protein backbone level. Here we present a method that explicitly takes into account the side chain interactions, yet providing a global view of the ligand-induced conformational changes. This is achieved through the analysis of Protein Structure Networks (PSN), constructed from the noncovalent side chain interactions in the protein. Here, E. coli Glutaminyl-tRNA synthetase (GlnRS) in the ligand-free and different ligand-bound states is used as a case study to assess the effect of binding of tRNA, ATP, and the amino acid Gln to GlnRS. The PSNs are constructed on the basis of the strength of noncovalent interactions existing between the side chains of amino acids. The parameters like the size of the largest cluster, edge to node ratio, and the total number of hubs are used to quantitatively assess the structure network changes. These network parameters have effectively captured the ligand-induced structural changes at a global structure network level. Hubs, the highly connected amino acids, are also identified from these networks. Specifically, we are able to characterize different types of hubs based on the comparison of structure networks of the GlnRS system. The differences in the structure networks in both the presence and the absence of the ligands are reflected in these hubs. For instance, the characterization of hubs that are present in both the ligand-free and all the ligand-bound GlnRS (the invariant hubs) might implicate their role in structural integrity. On the other hand, identification of hubs unique to a particular ligand-bound structure (the exclusive hubs) not only highlights the structural differences mediated by ligand-binding at the structure network level, but also highlights significance of these amino acids hubs in binding to the ligand and catalyzing the biochemical function. Further, the hubs identified from this study could be ideal targets for mutational studies to ascertain the ligand-induced structure-function relationships in E. coli GlnRS. The formalism used in this study is simple and can be applied to other protein-ligands in general to understand the allosteric changes mediated by the binding of ligands.
众所周知，蛋白质在结合配体时会发生主链以及侧链的构象变化，这种变化不一定局限于活性位点。配体结合所引发的局部和全局构象变化在早期已得到广泛研究。然而，此前报道的全局变化主要集中在蛋白质主链层面。在此，我们提出一种方法，该方法明确考虑了侧链相互作用，同时提供了配体诱导的构象变化的全局视图。这是通过分析由蛋白质中非共价侧链相互作用构建的蛋白质结构网络（PSN）来实现的。在此，以无配体状态以及不同配体结合状态下的大肠杆菌谷氨酰胺 - tRNA合成酶（GlnRS）为例，评估tRNA、ATP和氨基酸Gln与GlnRS结合的影响。PSN是基于氨基酸侧链之间存在的非共价相互作用强度构建的。诸如最大簇的大小、边与节点的比率以及枢纽总数等参数用于定量评估结构网络的变化。这些网络参数有效地捕捉了全局结构网络层面上配体诱导的结构变化。枢纽是高度连接的氨基酸，也可从这些网络中识别出来。具体而言，基于GlnRS系统结构网络的比较，我们能够对不同类型的枢纽进行表征。配体存在与否时结构网络的差异反映在这些枢纽中。例如，在无配体和所有配体结合的GlnRS中都存在的枢纽（不变枢纽）的表征可能暗示它们在结构完整性中的作用。另一方面，特定配体结合结构特有的枢纽（排他枢纽）的识别不仅突出了配体结合在结构网络层面介导的结构差异，还突出了这些氨基酸枢纽在与配体结合和催化生化功能方面的重要性。此外，从本研究中识别出的枢纽可能是突变研究的理想靶点，以确定大肠杆菌GlnRS中配体诱导的结构 - 功能关系。本研究中使用的形式主义很简单，一般可应用于其他蛋白质 - 配体以理解配体结合介导的变构变化。
