Computational outlook on the ribosome as an entropy trap
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 emplo...
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| Format: | Article |
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2011
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| author | Monajemi, H. Wan Abdullah, W.A.T. Zain, Sharifuddin Md |
| author_facet | Monajemi, H. Wan Abdullah, W.A.T. Zain, Sharifuddin Md |
| author_sort | Monajemi, H. |
| collection | UM |
| description | 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. |
| first_indexed | 2024-03-06T05:15:53Z |
| format | Article |
| id | um.eprints-6070 |
| institution | Universiti Malaya |
| last_indexed | 2024-03-06T05:15:53Z |
| publishDate | 2011 |
| record_format | dspace |
| spelling | um.eprints-60702019-10-25T09:15:31Z http://eprints.um.edu.my/6070/ Computational outlook on the ribosome as an entropy trap Monajemi, H. Wan Abdullah, W.A.T. Zain, Sharifuddin Md QD Chemistry 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. 2011 Article PeerReviewed Monajemi, H. and Wan Abdullah, W.A.T. and Zain, Sharifuddin Md (2011) Computational outlook on the ribosome as an entropy trap. Computational and Theoretical Chemistry, 976 (1-3). pp. 148-152. ISSN 2210271X, DOI https://doi.org/10.1016/j.comptc.2011.08.017 <https://doi.org/10.1016/j.comptc.2011.08.017>. http://www.scopus.com/inward/record.url?eid=2-s2.0-84555190831&partnerID=40&md5=21851bd2434435d664aef4f2d05ae93e 10.1016/j.comptc.2011.08.017 |
| spellingShingle | QD Chemistry Monajemi, H. Wan Abdullah, W.A.T. Zain, Sharifuddin Md Computational outlook on the ribosome as an entropy trap |
| title | Computational outlook on the ribosome as an entropy trap |
| title_full | Computational outlook on the ribosome as an entropy trap |
| title_fullStr | Computational outlook on the ribosome as an entropy trap |
| title_full_unstemmed | Computational outlook on the ribosome as an entropy trap |
| title_short | Computational outlook on the ribosome as an entropy trap |
| title_sort | computational outlook on the ribosome as an entropy trap |
| topic | QD Chemistry |
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