51
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Affiliation(s)
| | - V. Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
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52
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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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53
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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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54
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Quantum Mechanical Study on the Mechanism of Peptide Release in the Ribosome. J Phys Chem B 2013; 117:3503-15. [DOI: 10.1021/jp3110248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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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55
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Davydov II, Wohlgemuth I, Artamonova II, Urlaub H, Tonevitsky AG, Rodnina MV. Evolution of the protein stoichiometry in the L12 stalk of bacterial and organellar ribosomes. Nat Commun 2013; 4:1387. [DOI: 10.1038/ncomms2373] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 12/12/2012] [Indexed: 01/08/2023] Open
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56
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Byun BJ, Kang YK. A mechanistic study supports a two-step mechanism for peptide bond formation on the ribosome. Phys Chem Chem Phys 2013; 15:14931-5. [DOI: 10.1039/c3cp51082d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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57
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Shaw JJ, Trobro S, He SL, Åqvist J, Green R. A Role for the 2' OH of peptidyl-tRNA substrate in peptide release on the ribosome revealed through RF-mediated rescue. ACTA ACUST UNITED AC 2012; 19:983-93. [PMID: 22921065 DOI: 10.1016/j.chembiol.2012.06.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 05/12/2012] [Accepted: 06/01/2012] [Indexed: 11/25/2022]
Abstract
The 2' OH of the peptidyl-tRNA substrate is thought to be important for catalysis of both peptide bond formation and peptide release in the ribosomal active site. The release reaction also specifically depends on a release factor protein (RF) to hydrolyze the ester linkage of the peptidyl-tRNA upon recognition of stop codons in the A site. Here, we demonstrate that certain amino acid substitutions (in particular those containing hydroxyl or thiol groups) in the conserved GGQ glutamine of release factor RF1 can rescue defects in the release reaction associated with peptidyl-tRNA substrates lacking a 2' OH. We explored this rescue effect through biochemical and computational approaches that support a model where the 2' OH of the P-site substrate is critical for orienting the nucleophile in a hydrogen-bonding network productive for catalysis.
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Affiliation(s)
- Jeffrey J Shaw
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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58
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Fukushima K, Iwahashi H, Nishikimi M. ONIOM Study of a Proton Shuttle-Catalyzed Stepwise Mechanism for Peptide Bond Formation in the Ribosome. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2012. [DOI: 10.1246/bcsj.20120144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
| | | | - Morimitsu Nishikimi
- Department of Food Science and Nutrition, Faculty of Human Life and Environmental Sciences, Nagoya Women’s University
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59
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Xu J, Zhang JZH, Xiang Y. Ab Initio QM/MM Free Energy Simulations of Peptide Bond Formation in the Ribosome Support an Eight-Membered Ring Reaction Mechanism. J Am Chem Soc 2012; 134:16424-9. [DOI: 10.1021/ja3076605] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun Xu
- State Key Laboratory of Precision
Spectroscopy, Institute of Theoretical and Computational Science,
Department of Physics, East China Normal University, Shanghai 200062, China
| | - John Z. H. Zhang
- State Key Laboratory of Precision
Spectroscopy, Institute of Theoretical and Computational Science,
Department of Physics, East China Normal University, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United
States
| | - Yun Xiang
- State Key Laboratory of Precision
Spectroscopy, Institute of Theoretical and Computational Science,
Department of Physics, East China Normal University, Shanghai 200062, China
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60
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Nahalka J. Glycocodon theory--the first table of glycocodons. J Theor Biol 2012; 307:193-204. [PMID: 22609469 DOI: 10.1016/j.jtbi.2012.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 04/11/2012] [Accepted: 05/09/2012] [Indexed: 01/24/2023]
Abstract
Hydrophobic cellular membranes separate cells from an environment that is generally based on water. Therefore, it is not surprising that hydrophilic glycans and glycoproteins are exposed on the lipidic surface of membranes and that the glycocalyx has evolved in all basic cell types. During the evolution of multicellular life, the surface exposed protein-glycan interactions were taken as the origin of the language of cell-cell communication. The bioinformatics analysis presented here reveals that the amino acid triplets, the glycocodons, can be deduced for each glycan letter (monosaccharide). This theory proposes to distinguish between the "sugar code" (the sugar sequence) and the "glycocode" (evolutionary selected amino acids recognising the mono-sugar). Similarly to genetic code, original glycocodons are related to G, A, V, and D amino acids. Modern glycocodons can be deduced from GAVD-glycocodons using hydropathic similarity. In general, the amino acid triplets can be assembled from one dipeptide that is specific to a monosaccharide plus a polar amino acid. This theory may shed a different light on the reason for WWD conservation in the active sites of oligosaccharyltransferases and for GGQ in the active sites of ribosomes.
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Affiliation(s)
- Jozef Nahalka
- Institute of Chemistry, Centre for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84538 Bratislava, Slovak Republic.
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61
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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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62
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Cantillo D, Ávalos M, Babiano R, Cintas P, Jiménez JL, Palacios JC. On the prebiotic synthesis of D-sugars catalyzed by L-peptides: assessments from first-principles calculations. Chemistry 2012; 18:8795-9. [PMID: 22689139 DOI: 10.1002/chem.201200466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Indexed: 11/11/2022]
Abstract
What accounts for a particular chiral selection in the case of a few sugars of prebiotic relevance, thereby mirroring the asymmetry observed in nature? By using first-principles calculations, the generation of pentoses from glycolaldehyde (the initial product of the autocatalytic formose reaction), which has been detected in outer space), has been modeled by using L-Val-L-Val as a primeval catalyst. Our theoretical study provides insight into the mechanism of this reaction and satisfactorily explains a few key molecular events. Our rationale agrees with the reported experimental data and shows that the D-configuration is only favored for ribose. L-pentoses are usually favored in the presence of L-configured dipeptides, as observed experimentally, although no chiral selection could be observed in the case of xylose. These results confirm that a prebiotic sugar soup could be fine-tuned in the presence of shorter peptides as catalysts and that D-ribose would have also resulted in an advantageous imbalance for further amplification and chemical evolution.
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Affiliation(s)
- David Cantillo
- Department of Organic and Inorganic Chemistry, University of Extremadura, Avda. de Elvas s/n, 06006 Badajoz, Spain.
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63
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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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64
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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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65
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Quality control of mRNA decoding on the bacterial ribosome. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 86:95-128. [PMID: 22243582 DOI: 10.1016/b978-0-12-386497-0.00003-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ribosome is a major player in providing accurate gene expression in the cell. The fidelity of substrate selection is tightly controlled throughout the translation process, including the initiation, elongation, and termination phases. Although each phase of translation involves different players, that is, translation factors and tRNAs, the general principles of selection appear surprisingly similar for very different substrates. At essentially every step of translation, differences in complex stabilities as well as induced fit are sources of selectivity. A view starts to emerge of how the ribosome uses local and global conformational switches to govern induced-fit mechanisms that ensure fidelity. This review describes the mechanisms of tRNA and mRNA selection at all phases of protein synthesis in bacteria.
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66
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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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