ONIOM and ab-initio calculations on the mechanism of uncatalyzed peptide bond formation

Monajemi, H. and Daud, Mohammad Noh and Zain, Sharifuddin Md and Wan Abdullah, Wan Ahmad Tajuddin (2012) ONIOM and ab-initio calculations on the mechanism of uncatalyzed peptide bond formation. Biochemistry and Cell Biology, 90 (6). pp. 691-700. ISSN 0829-8211, DOI https://doi.org/10.1139/o2012-027.

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Official URL: http://www.nrcresearchpress.com/doi/abs/10.1139/o2...


Finding a proper transition structure for the peptide bond formation process can lead one to a better understanding of the role of ribosome in catalyzing this reaction. Using computer simulations, we performed the potential energy surface scan on the ester bond dissociation of P-site aminoacyl-tRNA and the peptide bond formation of P-site and A-site amino acids. The full fragments of initiator tRNA(i)(met) and elongator tRNA(phe) are attached to both cognate and non-cognate amino acids as the P-site substrate. The A-site amino acid for all four calculations is methionine. We used ONIOM calculations to reduce the computational cost. Our study illustrates the reduced rate of peptide bond formation for misacylated tRNA(i)(met) in the absence of ribosomal bases. The misacylated elongator tRNA(phe), however, did not show any difference in its PES compared with that for the phe-tRNA(phe). This demonstrates the structural specification of initiator tRNA(i)(met) for the amino acids side chain.

Item Type: Article
Additional Information: Department of Chemistry, Faculty of Science Building, University of Malaya, 50603 Kuala Lumpur, MALAYSIA
Subjects: Q Science > QD Chemistry
Divisions: Faculty of Science > Department of Chemistry
Depositing User: Miss Malisa Diana
Date Deposited: 21 May 2013 02:06
Last Modified: 25 Oct 2019 09:18
URI: http://eprints.um.edu.my/id/eprint/6094

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