Computational outlook on the ribosome as an entropy trap

Monajemi, H. and Wan Abdullah, W.A.T. and Zain, S.M. (2011) Computational outlook on the ribosome as an entropy trap. Computational and Theoretical Chemistry, 976 (1-3). pp. 148-152. ISSN 2210271X

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Abstract

Recent progress in the study of transition structure of peptide bond formation indicates that ribosome acts as a water trap. However, considering experimental approaches, it is hard to overlook the role of ribosomal bases in catalyzing the reaction by substrate stabilization. In this study, we employ ab initio quantum chemistry methods to calculate the transition structure of the peptide bond formation in the absence of ribosomal bases. This will allow us to compare the transition structure in the process with the ones obtained computationally in the presence of ribosomal bases, and also the reaction rate with the experimental results. To save calculation time this study was carried out using short fragments of the A and P site aminoacyl-tRNAs. Based on our observation, the absence of ribosome results in a more favorable enthalpy but a less favorable entropy. Overall, the lower rate of reaction compared to that in the ribosomal environment indicates the role of ribosomal bases in catalyzing the reaction 'entropically'. © 2011 Elsevier B.V.

Item Type: Article
Additional Information: Department of Chemistry, Faculty of Science Building, University of Malaya, 50603 Kuala Lumpur, MALAYSIA
Uncontrolled Keywords: Density Functional Theory, Peptide bond formation, Ribosome, Transition state
Subjects: Q Science > QD Chemistry
Divisions: Faculty of Science > Dept of Chemistry
Depositing User: Miss Malisa Diana
Date Deposited: 13 May 2013 01:05
Last Modified: 13 May 2013 01:05
URI: http://eprints.um.edu.my/id/eprint/6070

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