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Latipudin D, Tumilaar SG, Ramdani Y, Dudi D, Kurnia D. Potential Piperolactam A Isolated From Piper betle as Natural Inhibitors of Brucella Species Aminoacyl-tRNA Synthetase for Livestock Infections: In Silico Approach. Vet Med Sci 2024; 10:e70042. [PMID: 39315732 PMCID: PMC11420939 DOI: 10.1002/vms3.70042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 08/12/2024] [Accepted: 08/30/2024] [Indexed: 09/25/2024] Open
Abstract
Brucellosis is an important global zoonosis caused by the bacterium Brucella sp. Brucellosis causes abortions, reproductive failure and reduced milk production, resulting in significant economic losses. Brucella species are reported to be resistant to antibiotics, which makes treatment difficult. The urgency of discovering new drug candidates to combat Brucella's infection necessitates the exploration of novel alternative agents with unique protein targets. Aminoacyl-tRNA synthetases (aaRSs), which have fundamental functions in translation, inhibit this process, stop protein synthesis and ultimately inhibit bacterial growth. The purpose of this study was to isolate piperolactam A compounds from the methanol extract of Piper betle leaves that have potential as antibacterials to inhibit the growth of Brucella sp. causing brucellosis in livestock and to analyse the mechanism of inhibitory activity of piperolactam A compounds against the aaRS enzyme through a molecular docking approach in silico. Piperolactam A was isolated from P. betle by column chromatography and characterized by UV, IR, 1D and 2D NMRs and MS, then tested for their inhibition mechanism against the enzymes threonyl-tRNA synthetase, leucyl-tRNA synthetase (LeuRS) and methionyl-tRNA synthetase in silico. The result in silico test is that piperolactam A has the potential to inhibit LeuRS enzyme with the greater binding affinity.
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Affiliation(s)
- Diding Latipudin
- Department of Animal Nutrition, Faculty of Animal Husbandry, Universitas Padjadjaran, Sumedang, West Java, Indonesia
| | - Sefren Geiner Tumilaar
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, West Java, Indonesia
| | - Yoga Ramdani
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, West Java, Indonesia
| | - Dudi Dudi
- Department of Animal Nutrition, Faculty of Animal Husbandry, Universitas Padjadjaran, Sumedang, West Java, Indonesia
| | - Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, West Java, Indonesia
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Sagiroglugil M, Yasar F. Catalytic Reaction Mechanism of Bacterial GH92 α-1,2-Mannosidase: A QM/MM Metadynamics Study. Chemphyschem 2023; 24:e202300628. [PMID: 37782219 DOI: 10.1002/cphc.202300628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/23/2023] [Accepted: 10/01/2023] [Indexed: 10/03/2023]
Abstract
The catalytic mechanism of aC a + 2 ${C{a}^{+2}}$ -dependent family 92 α ${{\rm \alpha }}$ -mannosidase, which is abundantly present in human gut flora and malfunctions leading to the lysosomal storage disease α-mannosidosis, has been investigated using quantum mechanics/molecular mechanics and metadynamics methods. Computational efforts show that the enzyme follows a conformational itinerary of and theC a + 2 ${C{a}^{+2}}$ ion serves a dual purpose, as it not only distorts the sugar ring but also plays a crucial role in orchestrating the arrangement of catalytic residues. This orchestration, in turn, contributes to the facilitation of O S 2 ${{{\rm \ }}^{{\rm O}}{{\rm S}}_{2}}$ conformers for the ensuing reaction. This mechanistic insight is well-aligned with the experimental predictions of the catalytic pathway, and the computed energies are of the same order of magnitude as the experimental estimations. Hence, our results extend the mechanistic understanding of glycosidases.
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Affiliation(s)
- Mert Sagiroglugil
- Department of Physics Engineering, Hacettepe University, Üniversiteler Mahallesi Beytepe Kampüsü, 06800, Ankara, Turkey
- Current Address: Departament de Química Inorgànica i Orgànica (Seccióde Química Orgànica), Institut de Química Teòrica i Computacional (IQTCUB) Universitat de Barcelona, Carrer de Martí i Franquès, 1, 08028, Barcelona, Spain
| | - Fatih Yasar
- Department of Physics Engineering, Hacettepe University, Üniversiteler Mahallesi Beytepe Kampüsü, 06800, Ankara, Turkey
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3
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Badu S, Melnik R, Singh S. Mathematical and computational models of RNA nanoclusters and their applications in data-driven environments. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1804564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shyam Badu
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Roderick Melnik
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
- BCAM-Basque Center for Applied Mathematics, Bilbao, Spain
| | - Sundeep Singh
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
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4
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Substrate-assisted mechanism of catalytic hydrolysis of misaminoacylated tRNA required for protein synthesis fidelity. Biochem J 2019; 476:719-732. [PMID: 30718305 DOI: 10.1042/bcj20180910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/28/2019] [Accepted: 02/01/2019] [Indexed: 11/17/2022]
Abstract
d-aminoacyl-tRNA-deacylase (DTD) prevents the incorporation of d-amino acids into proteins during translation by hydrolyzing the ester bond between mistakenly attached amino acids and tRNAs. Despite extensive study of this proofreading enzyme, the precise catalytic mechanism remains unknown. Here, a combination of biochemical and computational investigations has enabled the discovery of a new substrate-assisted mechanism of d-Tyr-tRNATyr hydrolysis by Thermus thermophilus DTD. Several functional elements of the substrate, misacylated tRNA, participate in the catalysis. During the hydrolytic reaction, the 2'-OH group of the А76 residue of d-Tyr-tRNATyr forms a hydrogen bond with a carbonyl group of the tyrosine residue, stabilizing the transition-state intermediate. Two water molecules participate in this reaction, attacking and assisting ones, resulting in a significant decrease in the activation energy of the rate-limiting step. The amino group of the d-Tyr aminoacyl moiety is unprotonated and serves as a general base, abstracting the proton from the assisting water molecule and forming a more nucleophilic ester-attacking species. Quantum chemical methodology was used to investigate the mechanism of hydrolysis. The DFT-calculated deacylation reaction is in full agreement with the experimental data. The Gibbs activation energies for the first and second steps were 10.52 and 1.05 kcal/mol, respectively, highlighting that the first step of the hydrolysis process is the rate-limiting step. Several amino acid residues of the enzyme participate in the coordination of the substrate and water molecules. Thus, the present work provides new insights into the proofreading details of misacylated tRNAs and can be extended to other systems important for translation fidelity.
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Harada R. Simple, yet Efficient Conformational Sampling Methods for Reproducing/Predicting Biologically Rare Events of Proteins. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180170] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan
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6
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Dulic M, Cvetesic N, Zivkovic I, Palencia A, Cusack S, Bertosa B, Gruic-Sovulj I. Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase. J Mol Biol 2018; 430:1-16. [DOI: 10.1016/j.jmb.2017.10.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/02/2017] [Accepted: 10/08/2017] [Indexed: 10/18/2022]
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Richardson CJ, First EA. Hyperactive Editing Domain Variants Switch the Stereospecificity of Tyrosyl-tRNA Synthetase. Biochemistry 2016; 55:2526-37. [DOI: 10.1021/acs.biochem.6b00157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Charles J. Richardson
- Department of Biochemistry
and Molecular Biology, Louisiana State University Health Sciences Center in Shreveport, 1501 Kings Highway, Shreveport, Louisiana 71130, United States
| | - Eric A. First
- Department of Biochemistry
and Molecular Biology, Louisiana State University Health Sciences Center in Shreveport, 1501 Kings Highway, Shreveport, Louisiana 71130, United States
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8
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Boyarshin KS, Priss AE, Rayevskiy AV, Ilchenko MM, Dubey IY, Kriklivyi IA, Yaremchuk AD, Tukalo MA. A new mechanism of post-transfer editing by aminoacyl-tRNA synthetases: catalysis of hydrolytic reaction by bacterial-type prolyl-tRNA synthetase. J Biomol Struct Dyn 2016; 35:669-682. [PMID: 26886480 DOI: 10.1080/07391102.2016.1155171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Aminoacyl tRNA synthetases are enzymes that specifically attach amino acids to cognate tRNAs for use in the ribosomal stage of translation. For many aminoacyl tRNA synthetases, the required level of amino acid specificity is achieved either by specific hydrolysis of misactivated aminoacyl-adenylate intermediate (pre-transfer editing) or by hydrolysis of the mischarged aminoacyl-tRNA (post-transfer editing). To investigate the mechanism of post-transfer editing of alanine by prolyl-tRNA synthetase from the pathogenic bacteria Enterococcus faecalis, we used molecular modeling, molecular dynamic simulations, quantum mechanical (QM) calculations, site-directed mutagenesis of the enzyme, and tRNA modification. The results support a new tRNA-assisted mechanism of hydrolysis of misacylated Ala-tRNAPro. The most important functional element of this catalytic mechanism is the 2'-OH group of the terminal adenosine 76 of Ala-tRNAPro, which forms an intramolecular hydrogen bond with the carbonyl group of the alanine residue, strongly facilitating hydrolysis. Hydrolysis was shown by QM methods to proceed via a general acid-base catalysis mechanism involving two functionally distinct water molecules. The transition state of the reaction was identified. Amino acid residues of the editing active site participate in the coordination of substrate and both attacking and assisting water molecules, performing the proton transfer to the 3'-O atom of A76.
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Affiliation(s)
- Konstantin S Boyarshin
- a Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine.,b State Key Laboratory of Molecular and Cellular Biology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Anastasia E Priss
- b State Key Laboratory of Molecular and Cellular Biology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Alexsey V Rayevskiy
- a Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine.,b State Key Laboratory of Molecular and Cellular Biology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Mykola M Ilchenko
- c Department of Synthetic Bioregulators , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Igor Ya Dubey
- c Department of Synthetic Bioregulators , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Ivan A Kriklivyi
- a Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine.,b State Key Laboratory of Molecular and Cellular Biology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Anna D Yaremchuk
- a Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine.,b State Key Laboratory of Molecular and Cellular Biology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
| | - Michael A Tukalo
- a Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine.,b State Key Laboratory of Molecular and Cellular Biology , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Zabolotnogo Str, 03680 Kyiv , Ukraine
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9
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Harada R, Takano Y, Baba T, Shigeta Y. Simple, yet powerful methodologies for conformational sampling of proteins. Phys Chem Chem Phys 2016; 17:6155-73. [PMID: 25659594 DOI: 10.1039/c4cp05262e] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Several biological functions, such as molecular recognition, enzyme catalysis, signal transduction, allosteric regulation, and protein folding, are strongly related to conformational transitions of proteins. These conformational transitions are generally induced as slow dynamics upon collective motions, including biologically relevant large-amplitude fluctuations of proteins. Although molecular dynamics (MD) simulation has become a powerful tool for extracting conformational transitions of proteins, it might still be difficult to reach time scales of the biological functions because the accessible time scales of MD simulations are far from biological time scales, even if straightforward conventional MD (CMD) simulations using massively parallel computers are employed. Thus, it is desirable to develop efficient methods to achieve canonical ensembles with low computational costs. From this perspective, we review several enhanced conformational sampling techniques of biomolecules developed by us. In our methods, multiple independent short-time MD simulations are employed instead of single straightforward long-time CMD simulations. Our basic strategy is as follows: (i) selection of initial seeds (initial structures) for the conformational sampling in restarting MD simulations. Here, the seeds should be selected as candidates with high potential to transit. (ii) Resampling from the selected seeds by initializing velocities in restarting short-time MD simulations. A cycle of these simple protocols might drastically promote the conformational transitions of biomolecules. (iii) Once reactive trajectories extracted from the cycles of short-time MD simulations are obtained, a free energy profile is evaluated by means of umbrella sampling (US) techniques with the weighted histogram analysis method (WHAM) as a post-processing technique. For the selection of the initial seeds, we proposed four different choices: (1) Parallel CaScade molecular dynamics (PaCS-MD), (2) Fluctuation Flooding Method (FFM), (3) Outlier FLOODing (OFLOOD) method, and (4) TaBoo SeArch (TBSA) method. We demonstrate applications of our methods to several biological systems, such as domain motions of proteins with large-amplitude fluctuations, conformational transitions upon ligand binding, and protein folding/refolding to native structures of proteins. Finally, we show the conformational sampling efficiencies of our methods compared with those by CMD simulations and other previously developed enhanced conformational sampling methods.
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Affiliation(s)
- Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8571, Japan.
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10
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Zhao H, Palencia A, Seiradake E, Ghaemi Z, Cusack S, Luthey-Schulten Z, Martinis S. Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism. ACS Chem Biol 2015; 10:2277-85. [PMID: 26172575 DOI: 10.1021/acschembio.5b00291] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new class of antimicrobial benzoxaborole compounds was identified as a potent inhibitor of leucyl-tRNA synthetase (LeuRS) and therefore of protein synthesis. In a novel mechanism, AN2690 (5-fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole) blocks fungal cytoplasmic LeuRS by covalently trapping tRNA(Leu) in the editing site of the enzyme's CP1 domain. However, some resistant mutation sites are located outside of the CP1 hydrolytic editing active site. Thus, their mode of action that undermines drug inhibition was not understood. A combination of X-ray crystallography, molecular dynamics, metadynamics, biochemical experiments, and mutational analysis of a distal benzoxaborole-resistant mutant uncovered a eukaryote-specific tyrosine "switch" that is critical to tRNA-dependent post-transfer editing. The tyrosine "switch" has three states that shift between interactions with a lysine and the 3'-hydroxyl of the tRNA terminus, to inhibit or promote post-transfer editing. The oxaborole's mechanism of action capitalizes upon one of these editing active site states. This tunable editing mechanism in eukaryotic and archaeal LeuRSs is proposed to facilitate precise quality control of aminoacylation fidelity. These mechanistic distinctions could also be capitalized upon for development of the benzoxaboroles as a broad spectrum antibacterial.
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Affiliation(s)
| | - Andres Palencia
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, BP181, 38042 Grenoble Cedex 9, France
| | - Elena Seiradake
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, BP181, 38042 Grenoble Cedex 9, France
| | | | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 71 Avenue des Martyrs, BP181, 38042 Grenoble Cedex 9, France
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Ardèvol A, Rovira C. Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations. J Am Chem Soc 2015; 137:7528-47. [DOI: 10.1021/jacs.5b01156] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Albert Ardèvol
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
| | - Carme Rovira
- Departament
de Química Orgànica and Institut de Química Teòrica
i Computacional (IQTCUB), Universitat de Barcelona, Martí
i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08018 Barcelona, Spain
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12
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Universal pathway for posttransfer editing reactions: insights from the crystal structure of TtPheRS with puromycin. Proc Natl Acad Sci U S A 2015; 112:3967-72. [PMID: 25775602 DOI: 10.1073/pnas.1414852112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
At the amino acid binding and recognition step, phenylalanyl-tRNA synthetase (PheRS) faces the challenge of discrimination between cognate phenylalanine and closely similar noncognate tyrosine. Resampling of Tyr-tRNA(Phe) to PheRS increasing the number of correctly charged tRNA molecules has recently been revealed. Thus, the very same editing site of PheRS promotes hydrolysis of misacylated tRNA species, associated both with cis- and trans-editing pathways. Here we report the crystal structure of Thermus thermophilus PheRS (TtPheRS) at 2.6 Å resolution, in complex with phenylalanine and antibiotic puromycin mimicking the A76 of tRNA acylated with tyrosine. Starting from the complex structure and using a hybrid quantum mechanics/molecular mechanics approach, we investigate the pathways of editing reaction catalyzed by TtPheRS. We show that both 2' and 3' isomeric esters undergo mutual transformation via the cyclic intermediate orthoester, and the editing site can readily accommodate a model of Tyr-tRNA(Phe) where deacylation occurs from either the 2'- or 3'-OH. The suggested pathway of the hydrolytic reaction at the editing site of PheRS is of sufficient generality to warrant comparison with other class I and class II aminoacyl-tRNA synthetases.
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Baba T, Boero M, Kamiya K, Ando H, Negoro S, Nakano M, Shigeta Y. Unraveling the degradation of artificial amide bonds in nylon oligomer hydrolase: from induced-fit to acylation processes. Phys Chem Chem Phys 2015; 17:4492-504. [DOI: 10.1039/c4cp04419c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To unravel the factor that provides the ability to degrade non-biological amide bond with nylon oligomer hydrolase, we investigated the process from induced-fit to acylation by a combination of different theoretical methods.
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Affiliation(s)
- Takeshi Baba
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | - Mauro Boero
- Institut de Physique et Chimie des Matériaux de Strasbourg
- UMR 7504 CNRS and University of Strasbourg
- 67034 Strasbourg
- France
| | - Katsumasa Kamiya
- Center for Basic Education and Integrated Learning
- Kanagawa Institute of Technology
- Atsugi
- Japan
| | - Hiroyuki Ando
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | - Seiji Negoro
- Department of Material Science and Chemistry
- Graduate School of Engineering
- University of Hyogo
- Himeji
- Japan
| | - Masayoshi Nakano
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | - Yasuteru Shigeta
- Department of Physics
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
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14
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Zheng S, Pfaendtner J. Enhanced sampling of chemical and biochemical reactions with metadynamics. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.923574] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Baba T, Harada R, Nakano M, Shigeta Y. On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase. J Comput Chem 2014; 35:1240-7. [DOI: 10.1002/jcc.23614] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/04/2014] [Accepted: 03/28/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Takeshi Baba
- Department of Materials Engineering Science; Graduate School of Engineering Science; Osaka University; Toyonaka 560-8531 Japan
| | - Ryuhei Harada
- RIKEN, Advanced Institute for Computational Science; 7-1-26 Minatojima-minami-machi Chuo-Ku, Kobe Hyogo 650-0047 Japan
- JST, CREST; 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
| | - Masayoshi Nakano
- Department of Materials Engineering Science; Graduate School of Engineering Science; Osaka University; Toyonaka 560-8531 Japan
| | - Yasuteru Shigeta
- Department of Materials Engineering Science; Graduate School of Engineering Science; Osaka University; Toyonaka 560-8531 Japan
- JST, CREST; 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
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16
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Motta A, Fragalà IL, Marks TJ. Insight into Group 4 Metallocenium-Mediated Olefin Polymerization Reaction Coordinates Using a Metadynamics Approach. J Chem Theory Comput 2013; 9:3491-7. [DOI: 10.1021/ct400259a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alessandro Motta
- Dipartimento
di Scienze Chimiche, Università di Catania, and INSTM, UdR Catania, Viale A. Doria 6, 95125
Catania, Italy
| | - Ignazio L. Fragalà
- Dipartimento
di Scienze Chimiche, Università di Catania, and INSTM, UdR Catania, Viale A. Doria 6, 95125
Catania, Italy
| | - Tobin J. Marks
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
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17
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Rovira C. The description of electronic processes inside proteins from Car-Parrinello molecular dynamics: chemical transformations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1153] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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18
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Biological applications of hybrid quantum mechanics/molecular mechanics calculation. J Biomed Biotechnol 2012; 2012:236157. [PMID: 22536015 PMCID: PMC3321478 DOI: 10.1155/2012/236157] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 10/27/2011] [Accepted: 11/11/2011] [Indexed: 12/17/2022] Open
Abstract
Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs) and molecular mechanics (MMs) calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD) simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction) in leucyl-tRNA synthetase complexed with the misaminoacylated tRNA(Leu), and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.
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Kumar S, Das M, Hadad CM, Musier-Forsyth K. Substrate and enzyme functional groups contribute to translational quality control by bacterial prolyl-tRNA synthetase. J Phys Chem B 2012; 116:6991-9. [PMID: 22458656 DOI: 10.1021/jp300845h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Aminoacyl-tRNA synthetases activate specific amino acid substrates and attach them via an ester linkage to cognate tRNA molecules. In addition to cognate proline, prolyl-tRNA synthetase (ProRS) can activate cysteine and alanine and misacylate tRNA(Pro). Editing of the misacylated aminoacyl-tRNA is required for error-free protein synthesis. An editing domain (INS) appended to bacterial ProRS selectively hydrolyzes Ala-tRNA(Pro), whereas Cys-tRNA(Pro) is cleared by a freestanding editing domain, YbaK, through a unique mechanism involving substrate sulfhydryl chemistry. The detailed mechanism of catalysis by INS is currently unknown. To understand the alanine specificity and mechanism of catalysis by INS, we have explored several possible mechanisms of Ala-tRNA(Pro) deacylation via hybrid QM/MM calculations. Experimental studies were also performed to test the role of several residues in the INS active site as well as various substrate functional groups in catalysis. Our results support a critical role for the tRNA 2'-OH group in substrate binding and catalytic water activation. A role is also proposed for the protein's conserved GXXXP loop in transition state stabilization and for the main chain atoms of Gly261 in a proton relay that contributes substantially to catalysis.
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Affiliation(s)
- Sandeep Kumar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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