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Mudryi V, Peske F, Rodnina M. Translation Factor Accelerating Peptide Bond Formation on the Ribosome: EF-P and eIF5A as Entropic Catalysts and a Potential Drug Targets. BBA ADVANCES 2023; 3:100074. [PMID: 37082265 PMCID: PMC10074943 DOI: 10.1016/j.bbadva.2023.100074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
Elongation factor P (EF-P) and its eukaryotic homolog eIF5A are auxiliary translation factors that facilitate peptide bond formation when several sequential proline (Pro) residues are incorporated into the nascent chain. EF-P and eIF5A bind to the exit (E) site of the ribosome and contribute to favorable entropy of the reaction by stabilizing tRNA binding in the peptidyl transferase center of the ribosome. In most organisms, EF-P and eIF5A carry a posttranslational modification that is crucial for catalysis. The chemical nature of the modification varies between different groups of bacteria and between pro- and eukaryotes, making the EF-P-modification enzymes promising targets for antibiotic development. In this review, we summarize our knowledge of the structure and function of EF-P and eIF5A, describe their modification enzymes, and present an approach for potential drug screening aimed at EarP, an enzyme that is essential for EF-P modification in several pathogenic bacteria.
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2
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Wang Q, Su H. A Tale of Water Molecules in the Ribosomal Peptidyl Transferase Reaction. Biochemistry 2022; 61:2241-2247. [PMID: 36178262 DOI: 10.1021/acs.biochem.2c00098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The peptidyl transferase center (PTC) in the large subunit of the ribosome plays a critical role in protein synthesis by catalyzing the formation of peptide bonds with an astounding speed of about 15 to 20 peptide bonds per second. The ribosome coordinates the nucleophilic attack and deprotonation in the rate-limiting step at the PTC. However, the details of peptide bond formation within the ribosome, particularly the precise role of the two water molecules in the PTC, remain unclear. Here, we propose a novel stepwise "proton shuttle" mechanism which corroborates all the reported experimental measurements so far. In this mechanism, a water molecule close to A76 of peptidyl-tRNA 2'- and 3'-O stabilizes the transition state. The other one adjacent to the carbonyl oxygen of peptidyl-tRNA actively participates in the proton shuttle, playing the catalytic role of ribosome-catalyzed peptide bond formation.
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Affiliation(s)
- Qiang Wang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China
| | - Haibin Su
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong 999077, China.,HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen 518048, China
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3
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Tan Z, Song Z, Xue T, Zheng L, Jiang L, Jiang Y, Fu Z, Nguyen A, Leal C, Cheng J. Open-air synthesis of oligo(ethylene glycol)-functionalized polypeptides from non-purified N-carboxyanhydrides. Biomater Sci 2021; 9:4120-4126. [PMID: 33949455 DOI: 10.1039/d1bm00223f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
With PEG-like properties, such as hydrophilicity and stealth effect against protein absorption, oligo(ethylene glycol) (OEG)-functionalized polypeptides have emerged as a new class of biomaterials alternative to PEG with polypeptide-like properties. Synthesis of this class of materials, however, has been demonstrated very challenging, as the synthesis and purification of OEG-functionalized N-carboxyanhydrides (OEG-NCAs) in high purity, which is critical for the success in polymerization, is tedious and often results in low yield. OEG-functionalized polypeptides are therefore only accessible to a few limited labs with expertise in this specialized NCA chemistry and materials. Here, we report the controlled synthesis of OEG-functionalized polypeptides in high yield directly from the OEG-functionalized amino acids via easy and reproducible polymerization of non-purified OEG-NCAs. The prepared amphiphilic block copolypeptides can self-assemble into narrowly dispersed nanoparticles in water, which show properties suitable for drug delivery applications.
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Affiliation(s)
- Zhengzhong Tan
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Ziyuan Song
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Tianrui Xue
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lining Zheng
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Lei Jiang
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. and State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Yunjiang Jiang
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Zihuan Fu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Anh Nguyen
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Cecilia Leal
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Jianjun Cheng
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA and Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA and Materials Research Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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4
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Zhang L, Wang Y, Dai H, Zhou J. Structural and functional studies revealed key mechanisms underlying elongation step of protein translation. Acta Biochim Biophys Sin (Shanghai) 2020; 52:749-756. [PMID: 32400848 DOI: 10.1093/abbs/gmaa046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Indexed: 11/12/2022] Open
Abstract
The ribosome is an ancient and universally conserved macromolecular machine that synthesizes proteins in all organisms. Since the discovery of the ribosome by electron microscopy in the mid-1950s, rapid progress has been made in research on it, regarding its architecture and functions. As a machine that synthesizes polypeptides, the sequential addition of amino acids to a growing polypeptide chain occurs during a phase called the elongation cycle. This is the core step of protein translation and is highly conserved between bacteria and eukarya. The elongation cycle involves codon recognition by aminoacyl tRNAs, catalysis of peptide bond formation, and the most complex operation of translation-translocation. In this review, we discuss the fundamental results from structural and functional studies over the past decades that have led to understanding of the three key questions underlying translation.
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Affiliation(s)
- Ling Zhang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yinghui Wang
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Hong Dai
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jie Zhou
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
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5
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Kazemi M, Socan J, Himo F, Åqvist J. Mechanistic alternatives for peptide bond formation on the ribosome. Nucleic Acids Res 2019; 46:5345-5354. [PMID: 29746669 PMCID: PMC6009655 DOI: 10.1093/nar/gky367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 04/26/2018] [Indexed: 02/04/2023] Open
Abstract
The peptidyl transfer reaction on the large ribosomal subunit depends on the protonation state of the amine nucleophile and exhibits a large kinetic solvent isotope effect (KSIE ∼8). In contrast, the related peptidyl-tRNA hydrolysis reaction involved in termination shows a KSIE of ∼4 and a pH-rate profile indicative of base catalysis. It is, however, unclear why these reactions should proceed with different mechanisms, as the experimental data suggests. One explanation is that two competing mechanisms may be operational in the peptidyl transferase center (PTC). Herein, we explored this possibility by re-examining the previously proposed proton shuttle mechanism and testing the feasibility of general base catalysis also for peptide bond formation. We employed a large cluster model of the active site and different reaction mechanisms were evaluated by density functional theory calculations. In these calculations, the proton shuttle and general base mechanisms both yield activation energies comparable to the experimental values. However, only the proton shuttle mechanism is found to be consistent with the experimentally observed pH-rate profile and the KSIE. This suggests that the PTC promotes the proton shuttle mechanism for peptide bond formation, while prohibiting general base catalysis, although the detailed mechanism by which general base catalysis is excluded remains unclear.
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Affiliation(s)
- Masoud Kazemi
- Department of Cell and Molecular Biology, Box 596, Uppsala University, BMC, SE-751 24 Uppsala, Sweden.,Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jaka Socan
- Department of Cell and Molecular Biology, Box 596, Uppsala University, BMC, SE-751 24 Uppsala, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Box 596, Uppsala University, BMC, SE-751 24 Uppsala, Sweden
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6
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Synthesis of polypeptides via bioinspired polymerization of in situ purified N-carboxyanhydrides. Proc Natl Acad Sci U S A 2019; 116:10658-10663. [PMID: 31088971 DOI: 10.1073/pnas.1901442116] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribozymes synthesize proteins in a highly regulated local environment to minimize side reactions caused by various competing species. In contrast, it is challenging to prepare synthetic polypeptides from the polymerization of N-carboxyanhydrides (NCAs) in the presence of water and impurities, which induce monomer degradations and chain terminations, respectively. Inspired by natural protein synthesis, we herein report the preparation of well-defined polypeptides in the presence of competing species, by using a water/dichloromethane biphasic system with macroinitiators anchored at the interface. The impurities are extracted into the aqueous phase in situ, and the localized macroinitiators allow for NCA polymerization at a rate which outpaces water-induced side reactions. Our polymerization strategy streamlines the process from amino acids toward high molecular weight polypeptides with low dispersity by circumventing the tedious NCA purification and the demands for air-free conditions, enabling low-cost, large-scale production of polypeptides that has potential to change the paradigm of polypeptide-based biomaterials.
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7
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Lilley DMJ. How RNA acts as a nuclease: some mechanistic comparisons in the nucleolytic ribozymes. Biochem Soc Trans 2017; 45:683-691. [PMID: 28620029 DOI: 10.1042/bst20160158] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 02/11/2024]
Abstract
Recent structural and mechanistic studies have shed considerable light on the catalytic mechanisms of nucleolytic ribozymes. The discovery of several new ribozymes in this class has now allowed comparisons to be made, and the beginnings of mechanistic groupings to emerge.
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Affiliation(s)
- David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, U.K.
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8
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Theoretical study of a proton wire mechanism for the peptide bond formation in the ribosome. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2066-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Protein Elongation, Co-translational Folding and Targeting. J Mol Biol 2016; 428:2165-85. [DOI: 10.1016/j.jmb.2016.03.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 11/18/2022]
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10
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11
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Świderek K, Marti S, Tuñón I, Moliner V, Bertran J. Peptide Bond Formation Mechanism Catalyzed by Ribosome. J Am Chem Soc 2015; 137:12024-34. [PMID: 26325003 PMCID: PMC4582011 DOI: 10.1021/jacs.5b05916] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM potentials, where the chemical system has been described by the M06-2X functional and the environment by means of the AMBER force field. According to our results, the most favorable mechanism in the ribosome would proceed through an eight-membered ring transition state, involving a proton shuttle mechanism through the hydroxyl group of the sugar and a water molecule. This transition state is similar to that described for the reaction in solution (J. Am. Chem. Soc. 2013, 135, 8708-8719), but the reaction mechanisms are noticeably different. Our simulations reproduce the experimentally determined catalytic effect of ribosome that can be explained by the different behavior of the two environments. While the solvent reorganizes during the chemical process involving an entropic penalty, the ribosome is preorganized in the formation of the Michaelis complex and does not suffer important changes along the reaction, dampening the charge redistribution of the chemical system.
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Affiliation(s)
- Katarzyna Świderek
- Departament de Química Física i Analítica; Universitat Jaume I, 12071 Castellón (Spain)
- Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, (Poland)
| | - Sergio Marti
- Departament de Química Física i Analítica; Universitat Jaume I, 12071 Castellón (Spain)
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjasot, (Spain)
| | - Vicent Moliner
- Departament de Química Física i Analítica; Universitat Jaume I, 12071 Castellón (Spain)
| | - Juan Bertran
- Departament de Química; Universitat Autònoma de Barcelona, 08193 Bellaterra, (Spain)
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12
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A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome. Nat Struct Mol Biol 2014; 21:787-93. [PMID: 25132179 PMCID: PMC4156881 DOI: 10.1038/nsmb.2871] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 07/14/2014] [Indexed: 11/12/2022]
Abstract
During peptide bond formation on the ribosome the α-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of pre-attack and post-catalysis complexes of the Thermus thermophilus 70S ribosome at ∼2.6 Å resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. Unlike earlier models, we propose that the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule.
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14
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Abstract
A201A, a unique nucleoside antibiotic with potent antibacterial activities, has been synthesized for the first time in a total of 47 steps in a highly modular and linear manner, highlighting the elaboration/incorporation of an unprecedented hexofuranoside unit bearing an exocyclic enol ether moiety.
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Affiliation(s)
- Shenyou Nie
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai 200032, China
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15
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Affiliation(s)
| | - V. Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
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16
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Rodnina MV. The ribosome as a versatile catalyst: reactions at the peptidyl transferase center. Curr Opin Struct Biol 2013; 23:595-602. [PMID: 23711800 DOI: 10.1016/j.sbi.2013.04.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 04/10/2013] [Indexed: 11/29/2022]
Abstract
In all contemporary organisms, the active site of the ribosome--the peptidyl transferase center--catalyzes two distinct reactions, peptide bond formation between peptidyl-tRNA and aminoacyl-tRNA as well as the hydrolysis of peptidyl-tRNA with the help of a release factor. However, when provided with appropriate substrates, ribosomes can also catalyze a broad range of other chemical reaction, which provides the basis for orthogonal translation and synthesis of alloproteins from unnatural building blocks. Advances in understanding the mechanisms of the two ubiquitous reactions, the peptide bond formation and peptide release, provide insights into the versatility of the active site of the ribosome. Release factors 1 and 2 and elongation factor P are auxiliary factors that augment the intrinsic catalytic activity of the ribosome in special cases.
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Affiliation(s)
- Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Goettingen, Germany.
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17
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Syrén PO. The solution of nitrogen inversion in amidases. FEBS J 2013; 280:3069-83. [DOI: 10.1111/febs.12241] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/06/2013] [Accepted: 03/08/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Per-Olof Syrén
- Institute of Technical Biochemistry; University of Stuttgart; Germany
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18
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Aqvist J, Lind C, Sund J, Wallin G. Bridging the gap between ribosome structure and biochemistry by mechanistic computations. Curr Opin Struct Biol 2012; 22:815-23. [PMID: 22884263 DOI: 10.1016/j.sbi.2012.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 06/14/2012] [Accepted: 07/09/2012] [Indexed: 11/18/2022]
Abstract
The wealth of structural and biochemical data now available for protein synthesis on the ribosome presents major new challenges for computational biochemistry. Apart from technical difficulties in modeling ribosome systems, the complexity of the overall translation cycle with a multitude of different kinetic steps presents a formidable problem for computational efforts where we have only seen the beginning. However, a range of methodologies including molecular dynamics simulations, free energy calculations, molecular docking and quantum chemical approaches have already been put to work with promising results. In particular, the combined efforts of structural biology, biochemistry, kinetics and computational modeling can lead towards a quantitative structure-based description of translation.
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Affiliation(s)
- Johan Aqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.
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19
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Kingery DA, Strobel SA. Analysis of enzymatic transacylase Brønsted studies with application to the ribosome. Acc Chem Res 2012; 45:495-503. [PMID: 22122380 DOI: 10.1021/ar100162b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Preferential binding of an enzyme to the transition state relative to the ground state is a key strategy for enzyme catalysis. When there is a difference between the ground and transition state charge distributions, enzymes maximize electrostatic interactions to achieve this enhanced transition state binding. Although the transition state is difficult to observe directly by structural methods, the chemical details of this transient species can be characterized by studies of substituent effects (Brønsted, Hammett, Swain-Scott, etc.) and isotope effects. Brønsted analysis can provide an estimate of transition state charges for the nucleophile and leaving group of a reaction. This Account will discuss the theoretical basis of Brønsted analysis and describe its practical application to the study of transacylase enzyme systems including the peptidyl transferase reaction of the ribosome. The Brønsted coefficient is derived from the linear free energy relationship (LFER) that correlates the acidity (pK(a)) of a reactive atom to the log of its rate constant. The Brønsted coefficient establishes the change in atomic charge as the reaction proceeds from the ground state to the transition state. Bonding events alter the electrostatics of atoms and the extent of bonding can be extrapolated from transition state charges. Therefore, well-defined nucleophile and leaving group transition state charges limit the number of mechanisms that are consistent with a particular transition state. Brønsted results are most informative when interpreted in the context of other mechanistic data, especially for enzymatic studies where an active site may promote a transition state that differs significantly from a prediction based on uncatalyzed solution reactions. Here we review Brønsted analyses performed on transacylases to illustrate how these data enhanced the enzymatic mechanistic studies. Through a systematic comparison of five enzymes, we reveal a wide spectrum of Brønsted values that are possible for what otherwise appear to be similar chemical reactions. The variations in the Brønsted coefficients predict different transition states for the various enzymes. This Account explores an overriding theme in the enzymatic mechanisms that catalysis enhances commensurate bond formation and proton abstraction events. The extent of the two bonding events in relationship to each other can be inferred from the Brønsted coefficient. When viewed in the context of recent ribosomal studies, this interpretation provides mechanistic insights into peptide bond formation.
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Affiliation(s)
- David A. Kingery
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520, United States
| | - Scott A. Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520, United States
- Department of Chemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520, United States
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20
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Quantum-Mechanical Study on the Mechanism of Peptide Bond Formation in the Ribosome. J Am Chem Soc 2012; 134:5817-31. [DOI: 10.1021/ja209558d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Vicenç Branchadell
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Antoni Oliva
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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21
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Abstract
The ability of RNA to both store genetic information and catalyse chemical reactions has led to the hypothesis that it predates DNA and proteins. While there is no doubt that RNA is capable of storing the genetic information of a primitive organism, only two classes of reactions-phosphoryl transfer and peptide bond formation-have been observed to be catalysed by RNA in nature. However, these naturally occurring ribozymes use a wide range of catalytic strategies that could be applied to other reactions. Furthermore, RNA can bind several cofactors that are used by protein enzymes to facilitate a wide variety of chemical processes. Despite its limited functional groups, these observations indicate RNA is a versatile molecule that could, in principle, catalyse the myriad reactions necessary to sustain life.
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Affiliation(s)
- David A Hiller
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
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22
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Abstract
Ribozymes are RNA molecules that act as chemical catalysts. In contemporary cells, most known ribozymes carry out phosphoryl transfer reactions. The nucleolytic ribozymes comprise a class of five structurally-distinct species that bring about site-specific cleavage by nucleophilic attack of the 2'-O on the adjacent 3'-P to form a cyclic 2',3'-phosphate. In general, they will also catalyse the reverse reaction. As a class, all these ribozymes appear to use general acid-base catalysis to accelerate these reactions by about a million-fold. In the Varkud satellite ribozyme, we have shown that the cleavage reaction is catalysed by guanine and adenine nucleobases acting as general base and acid, respectively. The hairpin ribozyme most probably uses a closely similar mechanism. Guanine nucleobases appear to be a common choice of general base, but the general acid is more variable. By contrast, the larger ribozymes such as the self-splicing introns and RNase P act as metalloenzymes.
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Affiliation(s)
- David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, MSI/WTB Complex, Dow Street, Dundee DD1 5EH, UK.
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23
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Pech M, Nierhaus KH. The thorny way to the mechanism of ribosomal peptide-bond formation. Chembiochem 2012; 13:189-92. [PMID: 22213275 DOI: 10.1002/cbic.201100660] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Pech
- Department, AG Ribosomen, Abteilung Vingron, Max-Planck-Insitut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany
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24
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Carrasco N, Hiller DA, Strobel SA. Minimal Transition State Charge Stabilization of the Oxyanion during Peptide Bond Formation by the Ribosome. Biochemistry 2011; 50:10491-8. [DOI: 10.1021/bi201290s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Nicolas Carrasco
- Departments of Molecular Biophysics & Biochemistry and Chemistry, Yale University, 260 Whitney Ave., New Haven, Connecticut 06520-81114, United States
| | - David A. Hiller
- Departments of Molecular Biophysics & Biochemistry and Chemistry, Yale University, 260 Whitney Ave., New Haven, Connecticut 06520-81114, United States
| | - Scott A. Strobel
- Departments of Molecular Biophysics & Biochemistry and Chemistry, Yale University, 260 Whitney Ave., New Haven, Connecticut 06520-81114, United States
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25
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Kuhlenkoetter S, Wintermeyer W, Rodnina MV. Different substrate-dependent transition states in the active site of the ribosome. Nature 2011; 476:351-4. [PMID: 21804565 DOI: 10.1038/nature10247] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/03/2011] [Indexed: 11/09/2022]
Abstract
The active site of the ribosome, the peptidyl transferase centre, catalyses two reactions, namely, peptide bond formation between peptidyl-tRNA and aminoacyl-tRNA as well as the release-factor-dependent hydrolysis of peptidyl-tRNA. Unlike peptide bond formation, peptide release is strongly impaired by mutations of nucleotides within the active site, in particular by base exchanges at position A2602 (refs 1, 2). The 2'-OH group of A76 of the peptidyl-tRNA substrate seems to have a key role in peptide release. According to computational analysis, the 2'-OH may take part in a concerted 'proton shuttle' by which the leaving group is protonated, in analogy to similar current models of peptide bond formation. Here we report kinetic solvent isotope effects and proton inventories (reaction rates measured in buffers with increasing content of deuterated water, D(2)O) of the two reactions catalysed by the active site of the Escherichia coli ribosome. The transition state of the release factor 2 (RF2)-dependent hydrolysis reaction is characterized by the rate-limiting formation of a single strong hydrogen bond. This finding argues against a concerted proton shuttle in the transition state of the hydrolysis reaction. In comparison, the proton inventory for peptide bond formation indicates the rate-limiting formation of three hydrogen bonds with about equal contributions, consistent with a concerted eight-membered proton shuttle in the transition state. Thus, the ribosome supports different rate-limiting transition states for the two reactions that take place in the peptidyl transferase centre.
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Affiliation(s)
- Stephan Kuhlenkoetter
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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A two-step chemical mechanism for ribosome-catalysed peptide bond formation. Nature 2011; 476:236-9. [PMID: 21765427 PMCID: PMC3154986 DOI: 10.1038/nature10248] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/03/2011] [Indexed: 01/18/2023]
Abstract
The chemical step of natural protein synthesis, peptide bond formation, is catalysed by the large subunit of the ribosome. Crystal structures have shown that the active site for peptide bond formation is composed entirely of RNA. Recent work has focused on how an RNA active site is able to catalyse this fundamental biological reaction at a suitable rate for protein synthesis. On the basis of the absence of important ribosomal functional groups, lack of a dependence on pH, and the dominant contribution of entropy to catalysis, it has been suggested that the role of the ribosome is limited to bringing the substrates into close proximity. Alternatively, the importance of the 2'-hydroxyl of the peptidyl-transfer RNA and a Brønsted coefficient near zero have been taken as evidence that the ribosome coordinates a proton-transfer network. Here we report the transition state of peptide bond formation, based on analysis of the kinetic isotope effect at five positions within the reaction centre of a peptidyl-transfer RNA mimic. Our results indicate that in contrast to the uncatalysed reaction, formation of the tetrahedral intermediate and proton transfer from the nucleophilic nitrogen both occur in the rate-limiting step. Unlike in previous proposals, the reaction is not fully concerted; instead, breakdown of the tetrahedral intermediate occurs in a separate fast step. This suggests that in addition to substrate positioning, the ribosome is contributing to chemical catalysis by changing the rate-limiting transition state.
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Leung EKY, Suslov N, Tuttle N, Sengupta R, Piccirilli JA. The Mechanism of Peptidyl Transfer Catalysis by the Ribosome. Annu Rev Biochem 2011; 80:527-55. [DOI: 10.1146/annurev-biochem-082108-165150] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Nikolai Suslov
- Department of Biochemistry and Molecular Biology, Chicago, Illinois 60637
| | - Nicole Tuttle
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637;
| | - Raghuvir Sengupta
- Department of Biochemistry, Stanford University, Stanford, California 94305
| | - Joseph Anthony Piccirilli
- Department of Biochemistry and Molecular Biology, Chicago, Illinois 60637
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637;
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Krishnakumar KS, Goudedranche S, Bouchu D, Strazewski P. The Shortest Synthetic Route to Puromycin Analogues Using a Modified Robins Approach. J Org Chem 2011; 76:2253-6. [DOI: 10.1021/jo102178h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kollappillil S. Krishnakumar
- Laboratoire de Synthèse de Biomolécules (UMR 5246, ICBMS), Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Sébastien Goudedranche
- Laboratoire de Synthèse de Biomolécules (UMR 5246, ICBMS), Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Denis Bouchu
- Laboratoire de Synthèse de Biomolécules (UMR 5246, ICBMS), Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Peter Strazewski
- Laboratoire de Synthèse de Biomolécules (UMR 5246, ICBMS), Université Claude Bernard Lyon 1, 43 boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France
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Krishnakumar KS, Michel BY, Nguyen-Trung NQ, Fenet B, Strazewski P. Intrinsic pKa values of 3′-N-α-l-aminoacyl-3′-aminodeoxyadenosines determined by pH dependent 1H NMR in H2O. Chem Commun (Camb) 2011; 47:3290-2. [DOI: 10.1039/c0cc05136e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Fonvielle M, Chemama M, Lecerf M, Villet R, Busca P, Bouhss A, Ethève-Quelquejeu M, Arthur M. Decoding the Logic of the tRNA Regiospecificity of Nonribosomal FemXWv Aminoacyl Transferase. Angew Chem Int Ed Engl 2010; 49:5115-9. [DOI: 10.1002/anie.201001473] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Fonvielle M, Chemama M, Lecerf M, Villet R, Busca P, Bouhss A, Ethève-Quelquejeu M, Arthur M. Decoding the Logic of the tRNA Regiospecificity of Nonribosomal FemXWv Aminoacyl Transferase. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001473] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hiller DA, Zhong M, Singh V, Strobel SA. Transition states of uncatalyzed hydrolysis and aminolysis reactions of a ribosomal P-site substrate determined by kinetic isotope effects. Biochemistry 2010; 49:3868-78. [PMID: 20359191 PMCID: PMC2864349 DOI: 10.1021/bi901458x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The ester bond of peptidyl-tRNA undergoes nucleophilic attack in solution and when catalyzed by the ribosome. To characterize the uncatalyzed hydrolysis reaction, a model of peptide release, the transition state structure for hydrolysis of a peptidyl-tRNA mimic was determined. Kinetic isotope effects were measured at several atoms that potentially undergo a change in bonding in the transition state. Large kinetic isotope effects of carbonyl (18)O and alpha-deuterium substitutions on uncatalyzed hydrolysis indicate the transition state is nearly tetrahedral. Kinetic isotope effects were also measured for aminolysis by hydroxylamine to study a reaction similar to the formation of a peptide bond. In contrast to hydrolysis, the large leaving group (18)O isotope effect indicates the C-O3' bond has undergone significant scission in the transition state. The smaller carbonyl (18)O and alpha-deuterium effects are consistent with a later transition state. The assay developed here can also be used to measure isotope effects for the ribosome-catalyzed reactions. These uncatalyzed reactions serve as a basis for determining what aspects of the transition states are stabilized by the ribosome to achieve a rate enhancement.
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Affiliation(s)
- David A Hiller
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven CT 06511 USA
| | | | - Vipender Singh
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven CT 06511 USA
| | - Scott A Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven CT 06511 USA
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The transition state for peptide bond formation reveals the ribosome as a water trap. Proc Natl Acad Sci U S A 2010; 107:1888-93. [PMID: 20080677 DOI: 10.1073/pnas.0914192107] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent progress in elucidating the peptide bond formation process on the ribosome has led to notion of a proton shuttle mechanism where the 2'-hydroxyl group of the P-site tRNA plays a key role in mediating proton transfer between the nucleophile and leaving group, whereas ribosomal groups do not actively participate in the reaction. Despite these advances, the detailed nature of the transition state for peptidyl transfer and the role of several trapped water molecules in the peptidyl transferase center remain major open questions. Here, we employ high-level quantum chemical ab initio calculations to locate and characterize global transition states for the reaction, described by a molecular model encompassing all the key elements of the reaction center. The calculated activation enthalpy as well as structures are in excellent agreement with experimental data and point to feasibility of an eight-membered "double proton shuttle" mechanism in which an auxiliary water molecule, observed both in computer simulations and crystal structures, actively participates. A second conserved water molecule is found to be of key importance for stabilizing developing negative charge on the substrate oxyanion and its presence is catalytically favorable both in terms of activation enthalpy and entropy. Transition states calculated both for six- and eight-membered mechanisms are invariably late and do not involve significant charge development on the attacking amino group. Predicted kinetic isotope effects consistent with this picture are similar to those observed for uncatalyzed ester aminolysis reactions in solution.
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Simonović M, Steitz TA. A structural view on the mechanism of the ribosome-catalyzed peptide bond formation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:612-23. [PMID: 19595805 DOI: 10.1016/j.bbagrm.2009.06.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 06/23/2009] [Accepted: 06/25/2009] [Indexed: 10/20/2022]
Abstract
The ribosome is a large ribonucleoprotein particle that translates genetic information encoded in mRNA into specific proteins. Its highly conserved active site, the peptidyl-transferase center (PTC), is located on the large (50S) ribosomal subunit and is comprised solely of rRNA, which makes the ribosome the only natural ribozyme with polymerase activity. The last decade witnessed a rapid accumulation of atomic-resolution structural data on both ribosomal subunits as well as on the entire ribosome. This has allowed studies on the mechanism of peptide bond formation at a level of detail that surpasses that for the classical protein enzymes. A current understanding of the mechanism of the ribosome-catalyzed peptide bond formation is the focus of this review. Implications on the mechanism of peptide release are discussed as well.
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Affiliation(s)
- Miljan Simonović
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, MBRB 1170, 900 S Ashland Ave., Chicago, IL 60607, USA
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Mizusawa K, Abe K, Sando S, Aoyama Y. Synthesis of puromycin derivatives with backbone-elongated substrates and associated translation inhibitory activities. Bioorg Med Chem 2009; 17:2381-7. [DOI: 10.1016/j.bmc.2009.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 02/05/2009] [Accepted: 02/06/2009] [Indexed: 10/21/2022]
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37
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Okuda K, Hirota T, Kingery DA, Nagasawa H. Synthesis of a Fluorine-Substituted Puromycin Derivative for Brønsted Studies of Ribosomal-Catalyzed Peptide Bond Formation. J Org Chem 2009; 74:2609-12. [DOI: 10.1021/jo802611t] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kensuke Okuda
- Gifu Pharmaceutical University, Gifu 502-8585, Japan, Faculty of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan, and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114
| | - Takashi Hirota
- Gifu Pharmaceutical University, Gifu 502-8585, Japan, Faculty of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan, and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114
| | - David A. Kingery
- Gifu Pharmaceutical University, Gifu 502-8585, Japan, Faculty of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan, and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114
| | - Hideko Nagasawa
- Gifu Pharmaceutical University, Gifu 502-8585, Japan, Faculty of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan, and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114
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Wohlgemuth I, Brenner S, Beringer M, Rodnina MV. Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates. J Biol Chem 2008; 283:32229-35. [PMID: 18809677 DOI: 10.1074/jbc.m805316200] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ribosome catalyzes peptide bond formation between peptidyl-tRNA in the P site and aminoacyl-tRNA in the A site. Here, we show that the nature of the C-terminal amino acid residue in the P-site peptidyl-tRNA strongly affects the rate of peptidyl transfer. Depending on the C-terminal amino acid of the peptidyl-tRNA, the rate of reaction with the small A-site substrate puromycin varied between 100 and 0.14 s(-1), regardless of the tRNA identity. The reactivity decreased in the order Lys = Arg > Ala > Ser > Phe = Val > Asp >> Pro, with Pro being by far the slowest. However, when Phe-tRNA(Phe) was used as A-site substrate, the rate of peptide bond formation with any peptidyl-tRNA was approximately 7 s(-1), which corresponds to the rate of binding of Phe-tRNA(Phe) to the A site (accommodation). Because accommodation is rate-limiting for peptide bond formation, the reaction rate is uniform for all peptidyl-tRNAs, regardless of the variations of the intrinsic chemical reactivities. On the other hand, the 50-fold increase in the reaction rate for peptidyl-tRNA ending with Pro suggests that full-length aminoacyl-tRNA in the A site greatly accelerates peptide bond formation.
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Affiliation(s)
- Ingo Wohlgemuth
- Institute of Physical Biochemistry, University of Witten/Herdecke, Stockumer Strasse 10, D-58448 Witten, Germany
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Huang KS, Carrasco N, Pfund E, Strobel SA. Transition state chirality and role of the vicinal hydroxyl in the ribosomal peptidyl transferase reaction. Biochemistry 2008; 47:8822-7. [PMID: 18672893 DOI: 10.1021/bi800299u] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ribosomal peptidyl transferase is a biologically essential catalyst responsible for protein synthesis. The reaction is expected to proceed through a transition state approaching tetrahedral geometry with a specific chirality. To establish that stereospecificity, we synthesized two diastereomers of a transition state inhibitor with mimics for each of the four ligands around the reactive chiral center. Preferential binding of the inhibitor that mimics a transition state with S chirality establishes the spatial position of the nascent peptide and the oxyanion and places the amine near the critical A76 2'-OH group on the P-site tRNA. Another inhibitor series with 2'-NH 2 and 2'-SH substitutions at the critical 2'-OH group was used to test the neutrality of the 2'-OH group as predicted if the hydroxyl functions as a proton shuttle in the transition state. The lack of significant pH-dependent binding by these inhibitors argues that the 2'-OH group remains neutral in the transition state. Both of these observations are consistent with a proton shuttle mechanism for the peptidyl transferase reaction.
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Affiliation(s)
- Kevin S Huang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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