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

@article{citeulike:1741301, 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 {approx}70 A 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 long-distance communication. 10.1073/pnas.0704459104}, author = {Ghosh, Amit and Vishveshwara, Saraswathi}, citeulike-article-id = {1741301}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0704459104}, citeulike-linkout-1 = {http://www.pnas.org/cgi/content/abstract/104/40/15711}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17898174}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17898174}, day = {2}, doi = {10.1073/pnas.0704459104}, journal = {Proceedings of the National Academy of Sciences}, keywords = {analysis, correlation, dynamics, fullatom, md}, month = {October}, number = {40}, pages = {15711--15716}, posted-at = {2007-11-20 11:41:30}, priority = {2}, title = {A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis}, url = {http://dx.doi.org/10.1073/pnas.0704459104}, volume = {104}, year = {2007} }

TY - JOUR ID - citeulike:1741301 L3 - citeulike-article-id:1741301 N2 - 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 {approx}70 A 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 long-distance communication. 10.1073/pnas.0704459104 IS - 40 JF - Proceedings of the National Academy of Sciences EP - 15716 TI - A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis VL - 104 SP - 15711 KW - analysis KW - correlation KW - dynamics KW - fullatom KW - md AU - Ghosh, Amit AU - Vishveshwara, Saraswathi PY - 2007/10/02/ UR - http://dx.doi.org/10.1073/pnas.0704459104 ER -