Structure networks of E. coli glutaminyl‐tRNA synthetase: Effects of ligand binding

Abstract

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.

Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play

“…We do not treat side-chain conformational changes, which could be substantial even in the absence of a backbone conformational change, leading to residue rewiring. 25,26 Allosteric Effects Are Cooperative Cooperativity is nonindependence. Proteins are widely believed to fold cooperatively.…”

Proteomics, networks and connectivity indices

“…Hubs, the highly connected amino acids, are also identified from these networks. Furthermore, the hubs identified with this network CIs approach could be ideal targets for mutational studies to ascertain the ligandinduced SAR [194]. The indices reviewed above are useful only to seek protein sequence-function relationships.…”

Assortative Mixing in Close-Packed Spatial Networks

“…In recent years, proteins were investigated as networks, by taking the amino-acids as nodes. Termed as residue networks (RN), edges between neighboring nodes are represented by their bonded and non-bonded interactions [16] , [17] , [18] , [19] . Several studies have shown that residue networks have small-world topology [16] , [20] , [21] , [22] , characterized by their logarithmically scaling average path lengths with network size, despite displaying high clustering.…”