1
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Fu Y, Yu J, Fan F, Wang B, Cao Z. Elucidating the Enzymatic Mechanism of Dihydrocoumarin Degradation: Insight into the Functional Evolution of Methyl-Parathion Hydrolase from QM/MM and MM MD Simulations. J Phys Chem B 2024; 128:5567-5575. [PMID: 38814729 DOI: 10.1021/acs.jpcb.4c00970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Methyl-parathion hydrolase (MPH), which evolved from dihydrocoumarin hydrolase, offers one of the most efficient enzymes for the hydrolysis of methyl-parathion. Interestingly, the substrate preference of MPH shifts from the methyl-parathion to the lactone dihydrocoumarin (DHC) after its mutation of five specific residues (R72L, L273F, L258H, T271I, and S193Δ, m5-MPH). Here, extensive QM/MM calculations and MM MD simulations have been used to delve into the structure-function relationship of MPH enzymes and plausible mechanisms for the chemical and nonchemical steps, including the transportation and binding of the substrate DHC to the active site, the hydrolysis reaction, and the product release. The results reveal that the five mutations remodel the active pocket and reposition DHC within the active site, leading to stronger enzyme-substrate interactions. The MM/GBSA-estimated binding free energies are about -20.7 kcal/mol for m5-MPH and -17.1 kcal/mol for wild-type MPH. Furthermore, this conformational adjustment of the protein may facilitate the chemical step of DHC hydrolysis and the product release, although there is a certain influence on the substrate transport. The hydrolytic reaction begins with the nucleophilic attack of the bridging OH- with the energy barriers of 22.0 and 18.0 kcal/mol for the wild-type and m5-MPH enzymes, respectively, which is rate-determining for the entire process. Unraveling these mechanistic intricacies may help in the understanding of the natural evolution of enzymes for diverse substrates and establish the enzyme structure-function relationship.
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Affiliation(s)
- Yuzhuang Fu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jun Yu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fangfang Fan
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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2
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Wang QQ, Song J, Wei D. Origin of Chemoselectivity of Halohydrin Dehalogenase-Catalyzed Epoxide Ring-Opening Reactions. J Chem Inf Model 2024; 64:4530-4541. [PMID: 38808649 DOI: 10.1021/acs.jcim.4c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
By performing molecular dynamics (MD), quantum mechanical/molecular mechanical (QM/MM) calculations, and QM cluster calculations, the origin of chemoselectivity of halohydrin dehalogenase (HHDH)-catalyzed ring-opening reactions of epoxide with the nucleophilic reagent NO2- has been explored. Four possible chemoselective pathways were considered, and the computed results indicate that the pathway associated with the nucleophilic attack on the Cα position of epoxide by NO2- is most energetically favorable and has an energy barrier of 12.9 kcal/mol, which is close to 14.1 kcal/mol derived from experimental kinetic data. A hydrogen bonding network formed by residues Ser140, Tyr153, and Arg157 can strengthen the electrophilicity of the active site of the epoxide substrate to affect chemoselectivity. To predict the energy barrier trends of the chemoselective transition states, multiple analyses including distortion analysis and electrophilic Parr function (Pk+) analysis were carried out with or without an enzyme environment. The obtained insights should be valuable for the rational design of enzyme-catalyzed and biomimetic organocatalytic epoxide ring-opening reactions with special chemoselectivity.
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Affiliation(s)
- Qian-Qian Wang
- College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Jinshuai Song
- College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
| | - Donghui Wei
- College of Chemistry, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, Henan, P. R. China
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3
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Meelua W, Wanjai T, Thinkumrob N, Friedman R, Jitonnom J. Multiscale QM/MM Simulations Identify the Roles of Asp239 and 1-OH···Nucleophile in Transition State Stabilization in Arabidopsis thaliana Cell-Wall Invertase 1. J Chem Inf Model 2023; 63:4827-4838. [PMID: 37503869 DOI: 10.1021/acs.jcim.3c00796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Arabidopsis thaliana cell-wall invertase 1 (AtCWIN1), a key enzyme in sucrose metabolism in plants, catalyzes the hydrolysis of sucrose into fructose and glucose. AtCWIN1 belongs to the glycoside hydrolase GH-J clan, where two carboxylate residues (Asp23 and Glu203 in AtCWIN1) are well documented as a nucleophile and an acid/base catalyst. However, details at the atomic level about the role of neighboring residues and enzyme-substrate interactions during catalysis are not fully understood. Here, quantum mechanical/molecular mechanical (QM/MM) free-energy simulations were carried out to clarify the origin of the observed decreased rates in Asp239Ala, Asp239Asn, and Asp239Phe in AtCWIN1 compared to the wild type and delineate the role of Asp239 in catalysis. The glycosylation and deglycosylation steps were considered in both wild type and mutants. Deglycosylation is predicted to be the rate-determining step in the reaction, with a calculated overall free-energy barrier of 15.9 kcal/mol, consistent with the experimental barrier (15.3 kcal/mol). During the reaction, the -1 furanosyl ring underwent a conformational change corresponding to 3E ↔ [E2]⧧ ↔ 1E according to the nomenclature of saccharide structures along the full catalytic reaction. Asp239 was found to stabilize not only the transition state but also the fructosyl-enzyme intermediate, which explains findings from previous structural and mutagenesis experiments. The 1-OH···nucleophile interaction has been found to provide an important contribution to the transition state stabilization, with a contribution of ∼7 kcal/mol, and affected glycosylation more significantly than deglycosylation. This study provides molecular insights that improve the current understanding of sucrose binding and hydrolysis in members of clan GH-J, which may benefit protein engineering research. Finally, a rationale on the sucrose inhibitor configuration in chicory 1-FEH IIa, proposed a long time ago in the literature, is also provided based on the QM/MM calculations.
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Affiliation(s)
- Wijitra Meelua
- Demonstration School, University of Phayao, Phayao 56000, Thailand
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao 56000, Thailand
| | - Tanchanok Wanjai
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao 56000, Thailand
| | - Natechanok Thinkumrob
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao 56000, Thailand
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, Kalmar SE-391 82, Sweden
| | - Jitrayut Jitonnom
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao 56000, Thailand
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4
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Meelua W, Wanjai T, Thinkumrob N, Oláh J, Cairns JRK, Hannongbua S, Ryde U, Jitonnom J. A computational study of the reaction mechanism and stereospecificity of dihydropyrimidinase. Phys Chem Chem Phys 2023; 25:8767-8778. [PMID: 36912034 DOI: 10.1039/d2cp05262h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Dihydropyrimidinase (DHPase) is a key enzyme in the pyrimidine pathway, the catabolic route for synthesis of β-amino acids. It catalyses the reversible conversion of 5,6-dihydrouracil (DHU) or 5,6-dihydrothymine (DHT) to the corresponding N-carbamoyl-β-amino acids. This enzyme has the potential to be used as a tool in the production of β-amino acids. Here, the reaction mechanism and origin of stereospecificity of DHPases from Saccharomyces kluyveri and Sinorhizobium meliloti CECT4114 were investigated and compared using a quantum mechanical cluster approach based on density functional theory. Two models of the enzyme active site were designed from the X-ray crystal structure of the native enzyme: a small cluster to characterize the mechanism and the stationary points and a large model to probe the stereospecificity and the role of stereo-gate-loop (SGL) residues. It is shown that a hydroxide ion first performs a nucleophilic attack on the substrate, followed by the abstraction of a proton by Asp358, which occurs concertedly with protonation of the ring nitrogen by the same residue. For the DHT substrate, the enzyme displays a preference for the L-configuration, in good agreement with experimental observation. Comparison of the reaction energetics of the two models reveals the importance of SGL residues in the stereospecificity of catalysis. The role of the conserved Tyr172 residue in transition-state stabilization is confirmed as the Tyr172Phe mutation increases the activation barrier of the reaction by ∼8 kcal mol-1. A detailed understanding of the catalytic mechanism of the enzyme could offer insight for engineering in order to enhance its activity and substrate scope.
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Affiliation(s)
- Wijitra Meelua
- Demonstration School, University of Phayao, Phayao 56000, Thailand
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao 56000, Thailand.
| | - Tanchanok Wanjai
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao 56000, Thailand.
| | - Natechanok Thinkumrob
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao 56000, Thailand.
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rakpart 3, Budapest H-1111, Hungary
| | - James R Ketudat Cairns
- Center for Biomolecular Structure, Function and Application and School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, Lund SE-221 00, Sweden
| | - Jitrayut Jitonnom
- Unit of Excellence in Computational Molecular Science and Catalysis, and Division of Chemistry, School of Science, University of Phayao, Phayao 56000, Thailand.
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Comparative QM/MM study on the inhibition mechanism of β-Hydroxynorvaline to Threonyl-tRNA synthetase. J Mol Graph Model 2022; 115:108224. [DOI: 10.1016/j.jmgm.2022.108224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/26/2022] [Accepted: 05/13/2022] [Indexed: 11/18/2022]
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Role of water coordination at zinc binding site and its catalytic pathway of dizinc creatininase: insights from quantum cluster approach. J Comput Aided Mol Des 2022; 36:279-289. [PMID: 35384596 DOI: 10.1007/s10822-022-00451-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/17/2022] [Indexed: 10/18/2022]
Abstract
Creatininase is a key enzyme of creatinine-metabolizing pathway in mammals, and has a great potential for diagnostic application. It catalyzes the reversible conversion of creatinine to creatine. Here, we investigated its reaction mechanism with density functional theory in conjunction with the quantum cluster approach. Three reaction pathways in which several possible proton transfers assisted by either His178 or a water ligand to Zn1 (Wat2) or both were considered. DFT calculations reveal, depending on Wat2 coordination mode at Zn1, two competitive ring-opening pathways where His178 playing a central role as a proton shuttle or both His178 and Wat2 serving as a dual catalytic role as a base and an acid, respectively. Three elementary steps were proposed for the reaction: the first involves nucleophilic attack by a bridging hydroxide to the substrate and forms a gem-diolate intermediate, followed by a proton transfer from the gem-diolate to His178 (His178 protonation is a required step for efficient proton transfers). Finally, the second proton transfer from the protonated His178 or Wat2 to the amide of substrate leads to the ring opening. The first proton transfer is the rate-limiting step of the whole reaction, in consistent with previous experimental and computational studies. A detailed understanding of the reaction mechanism of the creatininase enzyme family will also be helpful for developing a biosensor for kidney function.
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Meelua W, Wanjai T, Thinkumrob N, Oláh J, Mujika JI, Ketudat-Cairns JR, Hannongbua S, Jitonnom J. Active site dynamics and catalytic mechanism in arabinan hydrolysis catalyzed by GH43 endo-arabinanase from QM/MM molecular dynamics simulation and potential energy surface. J Biomol Struct Dyn 2021; 40:7439-7449. [PMID: 33715601 DOI: 10.1080/07391102.2021.1898469] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The endo-1,5-α-L-arabinanases, belonging to glycoside hydrolase family 43 (GH43), catalyse the hydrolysis of α-1,5-arabinofuranosidic bonds in arabinose-containing polysaccharides. These enzymes are proposed targets for industrial and medical applications. Here, molecular dynamics (MD), potential energy surface and free energy (potential of mean force) simulations are undertaken using hybrid quantum mechanical/molecular mechanical (QM/MM) potentials to understand the active site dynamics, catalytic mechanism and the electrostatic influence of active site residues of the GH43 endo-arabinanase from G. stearothermophilus. The calculated results give support to the single-displacement mechanism proposed for the inverting GH43 enzymes: first a proton is transferred from the general acid E201 to the substrate, followed by a nucleophilic attack by water, activated by the general base D27, on the anomer carbon. A conformational change (2E ↔E3 ↔ 4E) in the -1 sugar ring is observed involving a transition state featuring an oxocarbenium ion character. Residues D87, K106, H271 are highlighted as potential targets for future mutation experiments in order to increase the efficiency of the reaction. To our knowledge, this is the first QM/MM study providing molecular insights into the glycosidic bond hydrolysis of a furanoside substrate by an inverting GH in solution.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wijitra Meelua
- Demonstration School, University of Phayao, Phayao, Thailand.,Division of Chemistry, School of Science, University of Phayao, Phayao, Thailand
| | | | | | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Jon I Mujika
- Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, and Donostia International Physics Center (DIPC), Donostia, Euskadi, Spain
| | - James R Ketudat-Cairns
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Jitrayut Jitonnom
- Division of Chemistry, School of Science, University of Phayao, Phayao, Thailand
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Velasco J, Oliva B, Gonçalves AL, Lima AS, Ferreira G, França BA, Mulinari EJ, Gonçalves TA, Squina FM, Kadowaki MAS, Maiorano A, Polikarpov I, Oliveira LCD, Segato F. Functional characterization of a novel thermophilic exo-arabinanase from Thermothielavioides terrestris. Appl Microbiol Biotechnol 2020; 104:8309-8326. [PMID: 32813063 DOI: 10.1007/s00253-020-10806-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/06/2020] [Accepted: 08/02/2020] [Indexed: 10/23/2022]
Abstract
Arabinanases from glycoside hydrolase family GH93 are enzymes with exo-activity that hydrolyze the α-1,5 bonds between arabinose residues present on arabinan. Currently, several initiatives aiming to use byproducts rich in arabinan such as pectin and sugar beet pulp as raw material to produce various compounds of interest are being developed. However, it is necessary to use robust enzymes that have an optimal performance under pH and temperature conditions used in the industrial processes. In this work, the first GH93 from the thermophilic fungus Thermothielavioides terrestris (Abn93T) was heterologously expressed in Aspergillus nidulans, purified and biochemically characterized. The enzyme is a thermophilic glycoprotein (optimum activity at 70 °C) with prolonged stability in acid pHs (4.0 to 6.5). The presence of glycosylation affected slightly the hydrolytic capacity of the enzyme, which was further increased by 34% in the presence of 1 mM CoCl2. Small-angle X-ray scattering results show that Abn93T is a globular-like-shaped protein with a slight bulge at one end. The hydrolytic mechanism of the enzyme was elucidated using capillary zone electrophoresis and molecular docking calculations. Abn93T has an ability to produce (in synergism with arabinofuranosidases) arabinose and arabinobiose from sugar beet arabinan, which can be explored as fermentable sugars and prebiotics. KEY POINTS: • Thermophilic exo-arabinanase from family GH93 • Molecular basis of arabinan depolymerization.
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Affiliation(s)
- Josman Velasco
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Bianca Oliva
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Aline Larissa Gonçalves
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Awana Silva Lima
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Gislene Ferreira
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Bruno Alves França
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Evandro José Mulinari
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Thiago Augusto Gonçalves
- Departamento de Bioquímica, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.,Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - Fábio Márcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - Marco Antonio Seiki Kadowaki
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Alfredo Maiorano
- Instituto de Pesquisas Tecnológicas do Estado de São Paulo, Diretoria de Operações e Negócios, Núcleo de Bionanomanufatura, São Paulo, SP, Brazil
| | - Igor Polikarpov
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Leandro Cristante de Oliveira
- Department of Physics - Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil
| | - Fernando Segato
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil.
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Wu X, Yu H, Yuan M, Cao H, Ye T, Yu J, Xu F. H-bond interactions between arsenite and deoxynucleotides at different pH values: A combined computational and experimental study. CHEMOSPHERE 2020; 251:126395. [PMID: 32155498 DOI: 10.1016/j.chemosphere.2020.126395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 02/23/2020] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
Deoxynucleotides can be good monomers for arsenite ion-imprinted polymers (IIPs) due to the successful obtainment of aptamers which can specifically recognize arsenite. However, the recognition and interaction mechanism between arsenite and deoxynucleotides is still not clear. In this work, the binding interactions between arsenite and deoxynucleotides (dAMP, dTMP, dGMP, dCMP) as pH changing from 1 to 14 were investigated using density functional theory calculations as well as spectroscopy analysis. dGMP was calculated to have the largest affinity towards arsenite. H3AsO30-dGMP0 binding at phosphate group, H3AsO30-dAMP2-, H3AsO30-dCMP0 and H3AsO30-dTMP2- binding around nucleobase were found to be the most stable complexes. This suggests the optimal pH ranges for binding interactions of dAMP, dCMP, dGMP and dTMP towards arsenite might be 6.10-9.23, 1.00-4.50, 1.00-2.40 and 6.40-9.23, respectively, which agree with UV/VIS experimental results. Reduced Density Gradient method indicated that the binding interactions of arsenite with deoxynucleotides are mainly attributed to hydrogen bonds (H-bond). The strengths of these H-bonds are affected by pH. FT-IR and NMR spectroscopy analysis also provided essential H-bonding information, giving direct evidence to support the computational conclusions.
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Affiliation(s)
- Xiuxiu Wu
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Huaxing Yu
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Min Yuan
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Hui Cao
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Tai Ye
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Jinsong Yu
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Fei Xu
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, 200093, China.
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10
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Mu X, Xu D. QM/MM investigation of substrate binding of subclass B3 metallo-β-lactamase SMB-1 from Serratia marcescents: insights into catalytic mechanism. J Mol Model 2020; 26:71. [PMID: 32146530 DOI: 10.1007/s00894-020-4330-y] [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: 06/11/2019] [Accepted: 02/23/2020] [Indexed: 11/25/2022]
Abstract
Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel B3 subclass MβL, which could inactivate nearly all β-lactam-containing antibiotics, e.g., cephalosporins and carbapenems. It represents a new round of worrisome bacterial resistance. In this work, the Michaelis model of SMB-1 in complex with ampicillin was simulated using combined quantum mechanical and molecular mechanical method. Similar with other dizinc MβLs, a Zn-bridged hydroxide ion was simulated as the nucleophile for the hydrolysis reaction assisted by D120. The protonation of D120 could lead to the loss of Oδ2-Zn2 coordination bond, whereas the C3 carboxylate group moves down to become a new ligand to Zn2. The initial β-lactam ring-opening reaction leads to a conserved nitrogen anionic intermediate, which forms a new ligation between the resulted nitrogen anion and Zn2. The corresponding reaction free energy barrier for the first step of lactam ring-opening reaction was calculated to be 19.2 kcal/mol. During the reaction, Q157 serves as the putative "oxyanion hole" rather than Zn1 in L1 enzyme, which was confirmed via the site-directed mutagenesis simulation of Q157A. Our theoretical studies showed some insights into the substrate binding and catalytic mechanism of the SMB-1 metallo-β-lactamase.
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Affiliation(s)
- Xia Mu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China
| | - Dingguo Xu
- College of Chemistry, MOE Key Laboratory of Green Chemistry and Technology, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China. .,Research Center for Material Genome Engineering, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
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11
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Yu H, Yuan M, Cao H, Ye T, Yu J, Xu F. A computational investigation of the interaction between As3+ and deoxynucleotides. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1587761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Huaxing Yu
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
| | - Min Yuan
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
| | - Hui Cao
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
| | - Tai Ye
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
| | - Jinsong Yu
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
| | - Fei Xu
- Institute of Food Quality and Safety, University of Shanghai for Science and Technology, Shanghai, People’s Republic of China
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12
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Paiva P, Sousa SF, Ramos MJ, Fernandes PA. Understanding the Catalytic Machinery and the Reaction Pathway of the Malonyl-Acetyl Transferase Domain of Human Fatty Acid Synthase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00577] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pedro Paiva
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Sérgio F. Sousa
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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Wang WJ, Wei WJ, Liao RZ. Deciphering the chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase. Phys Chem Chem Phys 2018; 20:15784-15794. [DOI: 10.1039/c8cp02683a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
QM/MM calculations were performed to elucidate the reaction mechanism and chemoselectivity of 2,4-QueD. The protonation state of the first-shell ligand Glu74 plays an important role in dictating the selectivity.
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Affiliation(s)
- Wen-Juan Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Wen-Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
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