Signatures of tRNAGlx -specificity in proteobacterial glutamyl-tRNA synthetases.

The canonical function of glutamyl-tRNA synthetase (GluRS) is to glutamylate tRNAGlu . Yet not all bacterial GluRSs glutamylate tRNAGlu ; many glutamylate both tRNAGlu and tRNAGln , while some glutamylate only tRNAGln and not the cognate substrate tRNAGlu . Understanding the basis of the unique specificity of tRNAGlx is important. Mutational studies have hinted at hotspot residues, both on tRNAGlx and GluRS, which play crucial roles in tRNAGlx -specificity. However, its underlying structural basis remains unexplored. The majority of biochemical studies related to tRNAGlx -specificity have been performed on GluRS from Escherichia coli and other proteobacterial species. However, since the early crystal structures of GluRS and tRNAGlu -bound GluRS were from non-proteobacterial species (Thermus thermophilus), proteobacterial biochemical data have often been interpreted in the context of non-proteobacterial GluRS structures. Marked differences between proteobacterial and non-proteobacterial GluRSs have been demonstrated; therefore, it is important to understand tRNAGlx -specificity vis-a-vis proteobacterial GluRS structures. To this end, we solved the crystal structure of a double mutant GluRS from E. coli. Using the solved structure and several other currently available proteo- and non-proteobacterial GluRS crystal structures, we probed the structural basis of the tRNAGlx -specificity of bacterial GluRSs. Specifically, our analyses suggest a unique role played by the tRNAGlx D-helix contacting loop of GluRS in the modulation of tRNAGln -specificity. While earlier studies have identified functional hotspots on tRNAGlx that control the tRNAGlx -specificity of GluRS, this is the first report of complementary signatures of tRNAGlx -specificity in GluRS.

Remote communication between unstructured and structured regions of Bcl-2 tunes its ligand binding capacity: Mechanistic insights.

Bcl-2, the prototypic, anti-apoptotic member of Bcl-2 family possesses a long Intrinsically Disordered Region (IDR) of more than sixty amino acid residues. In spite of a number of experimental evidences on the influence of IDR to regulate the function of the protein, the molecular basis is not yet established. The present work with ~8µs conformational sampling of Bcl-2, using molecular dynamics in all atom description, offers a molecular mechanistic insight into the communication between the IDR and the structured region. The results indicate a highly significant role of the IDR in controlling the movements of the atoms which form the primary binding site. Although the influence of the IDR of the wild type Bcl-2 on its structured region, especially on the binding site, seems to be ordinary, but the hidden pathway of communication gets elucidated as the perturbation due to single-site phosphorylation on S70 works as a marker of the path; the contrast brought by the data obtained after truncating the IDR highlights it further. In wild type Bcl-2, apparently there is no direct communication between the IDR and binding site. But in the phosphorylated system, a communication channel between the IDR and the binding site has been established, as evidenced from the network analysis, which results in an increased correlation between the binding pocket residues and that redistributs the sampling of conformations of the system; one of the major consequences of these changes is witnessed in its enhanced affinity for binding with its partner Bax.