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Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation—A Theoretical Study
In this work, we have investigated a novel distal proton shuttle mechanism of ribosome catalyzed peptide bond formation reaction. The reaction was found to follow a two-step mechanism. A distal water molecule located about 6.1 Å away from the attacking amine plays as a proton acceptor and results in...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6154465/ https://www.ncbi.nlm.nih.gov/pubmed/28362358 http://dx.doi.org/10.3390/molecules22040571 |
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author | Zhang, Xiaotong Jiang, Yafei Mao, Qiuyun Tan, Hongwei Li, Xichen Chen, Guangju Jia, Zongchao |
author_facet | Zhang, Xiaotong Jiang, Yafei Mao, Qiuyun Tan, Hongwei Li, Xichen Chen, Guangju Jia, Zongchao |
author_sort | Zhang, Xiaotong |
collection | PubMed |
description | In this work, we have investigated a novel distal proton shuttle mechanism of ribosome catalyzed peptide bond formation reaction. The reaction was found to follow a two-step mechanism. A distal water molecule located about 6.1 Å away from the attacking amine plays as a proton acceptor and results in a charge-separated intermediate that is stabilized by the N terminus of L27 and the A-site A76 5′-phosphate. The ribose A2451 bridges the proton shuttle pathway, thus plays critical role in the reaction. The calculated 27.64 kcal·mol(−1) free energy barrier of the distal proton shuttle mechanism is lower than that of eight-membered ring transition state. The distal proton shuttle mechanism studied in this work can provide new insights into the important biological peptide synthesis process. |
format | Online Article Text |
id | pubmed-6154465 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-61544652018-11-13 Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation—A Theoretical Study Zhang, Xiaotong Jiang, Yafei Mao, Qiuyun Tan, Hongwei Li, Xichen Chen, Guangju Jia, Zongchao Molecules Article In this work, we have investigated a novel distal proton shuttle mechanism of ribosome catalyzed peptide bond formation reaction. The reaction was found to follow a two-step mechanism. A distal water molecule located about 6.1 Å away from the attacking amine plays as a proton acceptor and results in a charge-separated intermediate that is stabilized by the N terminus of L27 and the A-site A76 5′-phosphate. The ribose A2451 bridges the proton shuttle pathway, thus plays critical role in the reaction. The calculated 27.64 kcal·mol(−1) free energy barrier of the distal proton shuttle mechanism is lower than that of eight-membered ring transition state. The distal proton shuttle mechanism studied in this work can provide new insights into the important biological peptide synthesis process. MDPI 2017-03-31 /pmc/articles/PMC6154465/ /pubmed/28362358 http://dx.doi.org/10.3390/molecules22040571 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Zhang, Xiaotong Jiang, Yafei Mao, Qiuyun Tan, Hongwei Li, Xichen Chen, Guangju Jia, Zongchao Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation—A Theoretical Study |
title | Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation—A Theoretical Study |
title_full | Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation—A Theoretical Study |
title_fullStr | Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation—A Theoretical Study |
title_full_unstemmed | Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation—A Theoretical Study |
title_short | Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation—A Theoretical Study |
title_sort | distal proton shuttle mechanism of ribosome catalysed peptide bond formation—a theoretical study |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6154465/ https://www.ncbi.nlm.nih.gov/pubmed/28362358 http://dx.doi.org/10.3390/molecules22040571 |
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