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Selectivity and specificity of substrate binding in methionyl-tRNA synthetase

Materials and Process Simulation Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA

(RECEIVED April 7, 2004; FINAL REVISION June 25, 2004; ACCEPTED June 25, 2004)

The accuracy of in vivo incorporation of amino acids during protein biosynthesis is controlled to a significant extent by aminoacyl-tRNA synthetases (aaRS). This paper describes the application of the HierDock computational method to study the molecular basis of amino acid binding to the Escherichia coli methionyl tRNA synthetase (MetRS). Starting with the protein structure from the MetRS cocrystal, the HierDock calculations predict the binding site of methionine in MetRS to a root mean square deviation in coordinates (CRMS) of 0.55 Å for all the atoms, compared with the crystal structure. The MetRS conformation in the cocrystal structure shows good discrimination between cognate and the 19 noncognate amino acids. In addition, the calculated binding energies of a set of five methionine analogs show a good correlation (R² = 0.86) to the relative free energies of binding derived from the measured in vitro kinetic parameters, K_m and k_cat. Starting with the crystal structure of MetRS without the methionine (apo-MetRS), the putative binding site of methionine was predicted. We demonstrate that even the apo-MetRS structure shows a preference for binding methionine compared with the 19 other natural amino acids. On comparing the calculated binding energies of the 20 natural amino acids for apo-MetRS with those for the cocrystal structure, we observe that the discrimination against the noncognate substrate increases dramatically in the second step of the physical binding process associated with the conformation change in the protein.

Keywords: HierDock; synthetase; methionine; MetRS; selectivity; conformational change

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04792204.

Reprint requests to: William A. Goddard III, Materials and Process Simulation Center (MC 139-74), Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; e-mail: wag{at}wag.caltech.edu; fax: (626) 585-0918.

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				C. L. McClendon, N. Vaidehi, V. W. T. Kam, D. Zhang, and W. A. Goddard III Fidelity of seryl-tRNA synthetase to binding of natural amino acids from HierDock first principles computations Protein Eng. Des. Sel., May 1, 2006; 19(5): 195 - 203. [Abstract] [Full Text] [PDF]