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Romero-Téllez S, Cruz A, Masgrau L, González-Lafont À, Lluch JM. Accounting for the instantaneous disorder in the enzyme-substrate Michaelis complex to calculate the Gibbs free energy barrier of an enzyme reaction. Phys Chem Chem Phys 2021; 23:13042-13054. [PMID: 34100037 DOI: 10.1039/d1cp01338f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Many enzyme reactions present instantaneous disorder. These dynamic fluctuations in the enzyme-substrate Michaelis complexes generate a wide range of energy barriers that cannot be experimentally observed, but that determine the measured kinetics of the reaction. These individual energy barriers can be calculated using QM/MM methods, but then the problem is how to deal with this dispersion of energy barriers to provide kinetic information. So far, the most usual procedure has implied the so-called exponential average of the energy barriers. In this paper, we discuss the foundations of this method, and we use the free energy perturbation theory to derive an alternative equation to get the Gibbs free energy barrier of the enzyme reaction. In addition, we propose a practical way to implement it. We have chosen four enzyme reactions as examples. In particular, we have studied the hydrolysis of a glycosidic bond catalyzed by the enzyme Thermus thermophilus β-glycosidase, and the mutant Y284P Ttb-gly, and the hydrogen abstraction reactions from C13 and C7 of arachidonic acid catalyzed by the enzyme rabbit 15-lipoxygenase-1.
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Affiliation(s)
- Sonia Romero-Téllez
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain and Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Alejandro Cruz
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Laura Masgrau
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain and Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain and Zymvol Biomodeling, Carrer Roc Boronat, 117, 08018 Barcelona, Spain.
| | - Àngels González-Lafont
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain and Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain and Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
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2
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Ambrus V, Hoffka G, Fuxreiter M. Asymmetric dynamic coupling promotes alternative evolutionary pathways in an enzyme dimer. Sci Rep 2020; 10:18866. [PMID: 33139795 PMCID: PMC7608688 DOI: 10.1038/s41598-020-75772-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 10/16/2020] [Indexed: 11/09/2022] Open
Abstract
The importance of dynamic factors in enzyme evolution is gaining recognition. Here we study how the evolution of a new enzymatic activity exploits conformational tinkering and demonstrate that conversion of a dimeric phosphotriesterase to an arylesterase in Pseudomonas diminuta is accompanied by structural divergence between the two subunits. Deviations in loop conformations increase with promiscuity, leading to functionally distinct states, while they decrease during specialisation for the new function. We show that opposite loop movements in the two subunits are due to a dynamic coupling with the dimer interface, the importance of which is also corroborated by the co-evolution of the loop and interface residues. These results illuminate how protein dynamics promotes conformational heterogeneity in a dimeric enzyme, leading to alternative evolutionary pathways for the emergence of a new function.
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Affiliation(s)
- V Ambrus
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Gy Hoffka
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - M Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary. .,Department of Biomedical Sciences, University of Padova, Padua, Italy.
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3
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Soler J, González-Lafont À, Lluch JM. A protocol to obtain multidimensional quantum tunneling corrections derived from QM(DFT)/MM calculations for an enzyme reaction. Phys Chem Chem Phys 2020; 22:27385-27393. [DOI: 10.1039/d0cp05265e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The multidimensional small-curvature tunneling (SCT) method with Electrostatic Embedding calculations is a compromise between an accessible computational cost and the attainment of an accurate enough estimation of tunneling for an enzyme reaction.
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Affiliation(s)
- Jordi Soler
- Departament de Química Universitat Autònoma de Barcelona
- Bellaterra
- Spain
| | - Àngels González-Lafont
- Departament de Química Universitat Autònoma de Barcelona
- Bellaterra
- Spain
- Institut de Biotecnologia i de Biomedicina (IBB)
- Universitat Autònoma de Barcelona
| | - José M. Lluch
- Departament de Química Universitat Autònoma de Barcelona
- Bellaterra
- Spain
- Institut de Biotecnologia i de Biomedicina (IBB)
- Universitat Autònoma de Barcelona
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4
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McClory J, Hu GX, Zou JW, Timson DJ, Huang M. Phosphorylation Mechanism of N-Acetyl-l-glutamate Kinase, a QM/MM Study. J Phys Chem B 2019; 123:2844-2852. [PMID: 30848915 DOI: 10.1021/acs.jpcb.9b00547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In microorganisms and plants, N-acetyl-l-glutamate kinase (NAGK) catalyzes the second step in l-arginine synthesis, the phosphorylation of N-Acetyl-l-glutamate (NAG) to give N-acetyl-l-glutamate-5-phosphate. NAGK is only present in microorganisms and plants but absent in mammals, which makes it an attractive target for antimicrobial or biocidal development. Understanding the substrate binding mode and reaction mechanism of NAGK is crucial for targeting the kinase to develop potential therapies. Here, the substrate binding mode was studied by comparing the conformational change of NAGK in the presence and in the absence of the NAG substrate based on molecular dynamics simulations. We revealed that with substrate binding, the catalytic site of the kinase involving three loops in NAGK exhibits a closed conformation, which is predominantly controlled by an interaction between Arg98 and the α-COO- of NAG. Lys41 is found to guide phosphate transfer through the interactions with the β-,γ-, and γ-phosphate oxygen atoms of adenosine 5'-triphosphate surrounded by two highly conserved glycine residues (Gly44 and Gly76), while Arg98 helps to position the NAG substrate in the catalytic site, which facilitates the phosphate transfer. Furthermore, we elucidated phosphate-transfer reaction mechanism using hybrid density functional theory-based quantum mechanics/molecular mechanics calculations (B97D/AMBER99) and found that the catalysis follows a dissociative mechanism.
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Affiliation(s)
- James McClory
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast BT9 5AG , Northern Ireland , U.K
| | - Gui-Xiang Hu
- School of Biotechnology and Chemical Engineering, Ningbo Institute of Technology , Zhejiang University , 1 Xuefu Rd , Yinzhou Dist. Ningbo 315100 , China
| | - Jian-Wei Zou
- School of Biotechnology and Chemical Engineering, Ningbo Institute of Technology , Zhejiang University , 1 Xuefu Rd , Yinzhou Dist. Ningbo 315100 , China
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences , The University of Brighton , Huxley Building, Lewes Road , Brighton BN2 4GJ , U.K
| | - Meilan Huang
- School of Chemistry and Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast BT9 5AG , Northern Ireland , U.K
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5
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Santos-Martins D, Calixto AR, Fernandes PA, Ramos MJ. A Buried Water Molecule Influences Reactivity in α-Amylase on a Subnanosecond Time Scale. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04400] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Diogo Santos-Martins
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Ana R. Calixto
- 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
| | - 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
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Ryde U. How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging. J Chem Theory Comput 2017; 13:5745-5752. [DOI: 10.1021/acs.jctc.7b00826] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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7
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Sousa SF, Ribeiro AJM, Neves RPP, Brás NF, Cerqueira NMFSA, Fernandes PA, Ramos MJ. Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1281] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Sérgio Filipe Sousa
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - António J. M. Ribeiro
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Rui P. P. Neves
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Natércia F. Brás
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Nuno M. F. S. A. Cerqueira
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Pedro A. Fernandes
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
| | - Maria João Ramos
- Departamento de Química e Bioquímica, Faculdade de Ciências UCIBIO, REQUIMTE, Universidade do Porto Porto Portugal
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8
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Li Y, Zhang R, Du L, Zhang Q, Wang W. How Many Conformations of Enzymes Should Be Sampled for DFT/MM Calculations? A Case Study of Fluoroacetate Dehalogenase. Int J Mol Sci 2016; 17:E1372. [PMID: 27556449 PMCID: PMC5000767 DOI: 10.3390/ijms17081372] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 11/16/2022] Open
Abstract
The quantum mechanics/molecular mechanics (QM/MM) method (e.g., density functional theory (DFT)/MM) is important in elucidating enzymatic mechanisms. It is indispensable to study "multiple" conformations of enzymes to get unbiased energetic and structural results. One challenging problem, however, is to determine the minimum number of conformations for DFT/MM calculations. Here, we propose two convergence criteria, namely the Boltzmann-weighted average barrier and the disproportionate effect, to tentatively address this issue. The criteria were tested by defluorination reaction catalyzed by fluoroacetate dehalogenase. The results suggest that at least 20 conformations of enzymatic residues are required for convergence using DFT/MM calculations. We also tested the correlation of energy barriers between small QM regions and big QM regions. A roughly positive correlation was found. This kind of correlation has not been reported in the literature. The correlation inspires us to propose a protocol for more efficient sampling. This saves 50% of the computational cost in our current case.
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Affiliation(s)
- Yanwei Li
- Environment Research Institute, Shandong University, Jinan 250100, China.
| | - Ruiming Zhang
- Environment Research Institute, Shandong University, Jinan 250100, China.
| | - Likai Du
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China..
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Jinan 250100, China.
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Jinan 250100, China.
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Oliveira EF, Cerqueira NMFSA, Ramos MJ, Fernandes PA. QM/MM study of the mechanism of reduction of 3-hydroxy-3-methylglutaryl coenzyme A catalyzed by human HMG-CoA reductase. Catal Sci Technol 2016. [DOI: 10.1039/c6cy00356g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Detailing with atomistic resolution the reaction mechanism of human HMG-CoA reductase (HMG-CoA-R) might provide valuable insights for the development of new cholesterol-lowering drugs.
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Affiliation(s)
- Eduardo F. Oliveira
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
- 4169-007 Porto
| | | | - Maria J. Ramos
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
- 4169-007 Porto
| | - Pedro A. Fernandes
- REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências
- Universidade do Porto
- 4169-007 Porto
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10
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Ribeiro AJM, Santos-Martins D, Russo N, Ramos MJ, Fernandes PA. Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00759] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- António J. M. Ribeiro
- UCBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Dipartimento
di Chimica, Università della Calabria, 87036 Arcavacata
di Rende, Italia
| | - Diogo Santos-Martins
- UCBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Nino Russo
- Dipartimento
di Chimica, Università della Calabria, 87036 Arcavacata
di Rende, Italia
| | - Maria J. Ramos
- UCBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
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11
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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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Radusky LG, Hassan S, Lanzarotti E, Tiwari S, Jamal S, Ali J, Ali A, Ferreira R, Barh D, Silva A, Turjanski AG, Azevedo VA. An integrated structural proteomics approach along the druggable genome of Corynebacterium pseudotuberculosis species for putative druggable targets. BMC Genomics 2015; 16 Suppl 5:S9. [PMID: 26041381 PMCID: PMC4460585 DOI: 10.1186/1471-2164-16-s5-s9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background The bacterium Corynebacterium pseudotuberculosis (Cp) causes caseous lymphadenitis (CLA), mastitis, ulcerative lymphangitis, and oedema in a number of hosts, comprising ruminants, thereby intimidating economic and dairy industries worldwide. So far there is no effective drug or vaccine available against Cp. Previously, a pan-genomic analysis was performed for both biovar equi and biovar ovis and a Pathogenicity Islands (PAIS) analysis within the strains highlighted a large set of proteins that could be relevant therapeutic targets for controlling the onset of CLA. In the present work, a structural druggability analysis pipeline was accomplished along 15 previously sequenced Cp strains from both biovar equi and biovar ovis. Methods and results We computed the whole modelome of a reference strain Cp1002 (NCBI Accession: NC_017300.1) and then the homology models of proteins, of 14 different Cp strains, with high identity (≥ 85%) to the reference strain were also done. Druggability score of all proteins pockets was calculated and only those targets that have a highly druggable (HD) pocket in all strains were kept, a set of 58 proteins. Finally, this information was merged with the previous PAIS analysis giving two possible highly relevant targets to conduct drug discovery projects. Also, off-targeting information against host organisms, including Homo sapiens and a further analysis for protein essentiality provided a final set of 31 druggable, essential and non-host homologous targets, tabulated in table S4, additional file 1. Out of 31 globally druggable targets, 9 targets have already been reported in other pathogenic microorganisms, 3 of them (3-isopropylmalate dehydratase small subunit, 50S ribosomal protein L30, Chromosomal replication initiator protein DnaA) in C. pseudotuberculosis. Conclusion Overall we provide valuable information of possible targets against C. pseudotuberculosis where some of these targets have already been reported in other microorganisms for drug discovery projects, also discarding targets that might be physiologically relevant but are not amenable for drug binding. We propose that the constructed in silico dataset might serve as a guidance for the scientific community to have a better understanding while selecting putative therapeutic protein candidates as druggable ones as effective measures against C. pseudotuberculosis.
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