title: Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation-A Theoretical Study.
abstract: 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.
authors.affiliation: Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China. ZhangXiT@hotmail.com.
authors.forename: Xiaotong
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China. yafei.jiang@mail.bnu.edu.cn.
authors.forename: Yafei
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China. 201631150035@mail.bnu.edu.cn.
authors.forename: Qiuyun
authors.initials: Q
authors.lastname: Mao
authors.affiliation: Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China. hongwei.tan@bnu.edu.cn.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Tan
authors.affiliation: Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China. xcli@bnu.edu.cn.
authors.forename: Xichen
authors.initials: X
authors.lastname: Li
authors.affiliation: Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China. gjchen@bnu.edu.cn.
authors.forename: Guangju
authors.initials: G
authors.lastname: Chen
authors.affiliation: Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7N 3L6, Canada jia@queensu.ca. jia@queensu.ca.
authors.forename: Zongchao
authors.initials: Z
authors.lastname: Jia
mesh_terms: D002384:Catalysis; D008958:Models, Molecular; D008968:Molecular Conformation; D010455:Peptides / Q000378:metabolism*; D010710:Phosphates / Q000737:chemistry; D011522:Protons; D011789:Quantum Theory; D012270:Ribosomes / Q000378:metabolism*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D010455:Peptides; D010710:Phosphates; D011522:Protons; D014867:Water
keywords: Density Functional Theory; peptide bond formation; proton shuttle mechanism