Use of Analogues of Methionine and Methionyl Adenylate to Sample Conformational Changes During Catalysis in Escherichia coli Methionyl-tRNA Synthetase

Crépin, Thibaut; Schmitt, Emmanuelle; Mechulam, Yves; Sampson, Peter B.; Vaughan, Mark D.; Honek, John F.; Blanquet, Sylvain

doi:10.1016/s0022-2836(03)00917-3

Cited by 73 publications

(102 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The crystal structure of the complex of E. coli MetRS with tRNA Met is not available, although the structures of tRNA Met (26) and MetRS (27,28) are available. Hence, we modeled the structure of MetRStRNA f Met complex by using the Aquifex aeolicus (29) as a template.…”

Section: Resultsmentioning

confidence: 99%

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

Ghosh

Vishveshwara

2007

Proc. Natl. Acad. Sci. U.S.A.

230

288

View full text Add to dashboard Cite

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.

show abstract

Section: Resultsmentioning

confidence: 99%

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

Ghosh

Vishveshwara

2007

Proc. Natl. Acad. Sci. U.S.A.

230

288

View full text Add to dashboard Cite

show abstract

“…Highresolution crystal structures of E. coli MetRS are available both without (20) and with (21) Met bound. Additional structures are available for MetRS bound to several analogs of Met and methionyl-AMP (22). This wealth of structural data allows informed selection of residues for saturation mutagenesis in the binding pocket of MetRS.…”

mentioning

confidence: 99%

“…These residues have been suggested to be critical to Met binding; the backbone amide of L13 and the hydroxyl group of Y260 form hydrogen bonds with the sulfur atom of bound Met (21). H301 also is believed to form a hydrogen bond to the sulfur atom, whereas W253 forms hydrophobic contacts with the Met side chain (22). Four of these five residues, excluding W253, were selected for mutagenesis to all other possible amino acids; their orientations with respect to bound Met are shown in Fig.…”

mentioning

confidence: 99%

Discovery of aminoacyl-tRNA synthetase activity through cell-surface display of noncanonical amino acids

Link

Vink

Agard

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

175

154

View full text Add to dashboard Cite

The incorporation of noncanonical amino acids into recombinant proteins in Escherichia coli can be facilitated by the introduction of new aminoacyl-tRNA synthetase activity into the expression host. We describe here a screening procedure for the identification of new aminoacyl-tRNA synthetase activity based on the cell surface display of noncanonical amino acids. Screening of a saturation mutagenesis library of the E. coli methionyl-tRNA synthetase (MetRS) led to the discovery of three MetRS mutants capable of incorporating the long-chain amino acid azidonorleucine into recombinant proteins with modest efficiency. The Leu-13 3 Gly (L13G) mutation is found in each of the three MetRS mutants, and the MetRS variant containing this single mutation is highly efficient in producing recombinant proteins that contain azidonorleucine.azide-alkyne ligation ͉ azidohomoalanine ͉ azidonorleucine ͉ click chemistry

show abstract

“…The three-di- (Table 1). [17][18][19][20][21][22][23][24] Virtual library of 48 compounds used for this study were developed based on four scaffolds (Table 2-5) and followed by database generation carried out using MDL ISIS/Base and ISIS/Draw. 25 All the 48 compounds are converted into 3D structures and performed energy minimization in Inisght II software before proceeding to molecular docking simulations.…”

Section: Methodsmentioning

confidence: 99%

Molecular Docking Study of Aminoacyl-tRNA Synthetases with Ligand Molecules from Four Different Scaffolds

Bharatham¹,

Bharatham²,

Lee³

et al. 2010

Bulletin of the Korean Chemical Society

View full text Add to dashboard Cite

Aminoacyl-tRNA synthetases (aaRSs) play vital roles in protein biosynthesis of living organisms and are interesting antibacterial drug targets. In order to find out new inhibitor candidate molecules as antibacterial agent, the binding modes of the candidate molecules were investigated at the active sites of aaRSs by molecular docking study. The docking simulations were performed with 48 compounds from four different scaffolds into the eight different aaRSs. The results show that scaffolds 3 and 4 compounds have consistently better binding capabilities, specifically for HisRS (E. coli) and IleRS (S. aureus). The binding modes of the best compounds with the proteins were well compatible with those of two ligands in crystal structures. Therefore, we expect that the final compounds we present may have reasonable aaRS inhibitory activity.

show abstract

Use of Analogues of Methionine and Methionyl Adenylate to Sample Conformational Changes During Catalysis in Escherichia coli Methionyl-tRNA Synthetase

Cited by 73 publications

References 58 publications

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

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

Discovery of aminoacyl-tRNA synthetase activity through cell-surface display of noncanonical amino acids

Molecular Docking Study of Aminoacyl-tRNA Synthetases with Ligand Molecules from Four Different Scaffolds

Contact Info

Product

Resources

About