A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis

Abstract

The enzymes of the family of tRNA synthetases perform their functions with high precision by synchronously recognizing the anticodon region and the aminoacylation region, which are separated by Ϸ70 Å in space. This precision in function is brought about by establishing good communication paths between the two regions. We have modeled the structure of the complex consisting of Escherichia coli methionyl-tRNA synthetase (MetRS), tRNA, and the activated methionine. Molecular dynamics simulations have been performed on the modeled structure to obtain the equilibrated structure of the complex and the cross-correlations between the residues in MetRS have been evaluated. Furthermore, the network analysis on these simulated structures has been carried out to elucidate the paths of communication between the activation site and the anticodon recognition site. This study has provided the detailed paths of communication, which are consistent with experimental results. Similar studies also have been carried out on the complexes (MetRS ؉ activated methonine) and (MetRS ؉ tRNA) along with ligand-free native enzyme. A comparison of the paths derived from the four simulations clearly has shown that the communication path is strongly correlated and unique to the enzyme complex, which is bound to both the tRNA and the activated methionine. The details of the method of our investigation and the biological implications of the results are presented in this article. The method developed here also could be used to investigate any protein system where the function takes place through longdistance communication.dynamic cross-correlations ͉ methionyl-AMP ͉ protein structure network ͉ shortest pathways of communication ͉ stacking A crucial step in the translation of the genetic code is the aminoacylation of tRNA, which involves the molecular recognition between the aminoacyl-tRNA synthetases (aaRS) and their cognate tRNA. Each synthetase consists of the catalytic domain and the anticodon domain that are separated by Ϸ70 Å. Each tRNA connects these two regions with its anticodon and the acceptor stems. The mechanism of differentiations between cognate and noncognate tRNAs depends on contacts of anticodon domain of synthetase and anticodon stem of tRNA. The efficiency of the selection mechanism controls the overall accuracy of protein synthesis (1, 2). Recognition of the protein (aaRS) and the tRNA is explained by using the induced-fit mechanism, which suggests conformational changes in protein, tRNA, or both, leading to the final bound complex (3). However, the details of communication between the anticodon region and the aminoacylation region are less understood.In all living cells, protein synthesis starts with methionine.

Dynamical networks in tRNA:protein complexes

“…Most significantly, the C-terminus half of the Rossmann fold is dynamically correlated to the motion of the anticodon, despite these regions being 55 Å apart. Although the longer simulations provided a more pronounced correlation map, the trends are similar to those observed in shorter simulations of the MetRS:tRNA Met complex (11). The simulation of the archaeal LeuRS:tRNA Leu complex displays similar coupled motion between distant regions in the complex as shown in Fig.…”

“…Conserved residues that greatly affect the CPL upon removal have been hypothesized to be important for allosteric signal transmission (10). Snapshots from a short simulation of a modeled MetRS:tRNA complex indicated that the shortest path between protein residues interacting with the anticodon and the adenylate binding site was sensitive to conformational changes in the protein (11), but the tRNA and contacts with other identity elements on the tRNA were neglected in their study of the signal transmission. Although the shortest path analysis identifies several nodes, the contribution of these nodes to communication in protein networks has not been examined, with few exceptions (12).…”

Perturbation Waves in Proteins and Protein Networks: Applications of Percolation and Game Theories in Signaling and Drug Design

“…Vibrations of nonlinear origin may be concentrated at communicationally key residue-sets, and play an important role in energy storage and transfer during specific biological functions, like enzymatic processes or signal transduction. As a good additional example for the dynamical changes in perturbation-propagation, Ghosh and Vishveshwara [67] found four major communication paths in tRNA synthase, which were connected only, when the enzyme bound both substrates. This suggests the possibility of similar specialization of perturbation propagation pathways in case of special conditions requiring a specialized function instead of a general responsiveness.…”

GraProStr – Graphs of Protein Structures: A Tool for Constructing the Graphs and Generating Graph Parameters for Protein Structures

“…Different PSNs can be constructed for the same structure for varying values of interaction strength, to describe different aspects of the structure. Diverse problems such as the identification of clusters of interacting residues at the active-site, residues important for folding and stability, stabilization of proteinprotein interfaces and the level of global connectivity have been addressed by the analyses of PSNs [6][7][8][9][10][11]. Further, PSNs are also used in elucidating important problems such as allosteric communications within proteins [10,12].…”

“…Diverse problems such as the identification of clusters of interacting residues at the active-site, residues important for folding and stability, stabilization of proteinprotein interfaces and the level of global connectivity have been addressed by the analyses of PSNs [6][7][8][9][10][11]. Further, PSNs are also used in elucidating important problems such as allosteric communications within proteins [10,12]. The *Address correspondence to this author at the Molecular Biophysics Unit, Indian Institute of Science, Banglore 560012, India; Tel: +91-80-22932611; Fax: +91-80-23600535; E-mail: sv@mbu.iisc.ernet.in # Equal contribution.…”