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Bím D, Navrátil M, Gutten O, Konvalinka J, Kutil Z, Culka M, Navrátil V, Alexandrova AN, Bařinka C, Rulíšek L. Predicting Effects of Site-Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II. J Phys Chem B 2022; 126:132-143. [PMID: 34978450 DOI: 10.1021/acs.jpcb.1c09240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Quantum and molecular mechanics (QM/MM) and QM-only (cluster model) modeling techniques represent the two workhorses in mechanistic understanding of enzyme catalysis. One of the stringent tests for QM/MM and/or QM approaches is to provide quantitative answers to real-world biochemical questions, such as the effect of single-point mutations on enzyme kinetics. This translates into predicting the relative activation energies to 1-2 kcal·mol-1 accuracy; such predictions can be used for the rational design of novel enzyme variants with desired/improved characteristics. Herein, we employ glutamate carboxypeptidase II (GCPII), a dizinc metallopeptidase, also known as the prostate specific membrane antigen, as a model system. The structure and activity of this major cancer antigen have been thoroughly studied, both experimentally and computationally, which makes it an ideal model system for method development. Its reaction mechanism is quite well understood: the reaction coordinate comprises a "tetrahedral intermediate" and two transition states and experimental activation Gibbs free energy of ∼17.5 kcal·mol-1 can be inferred for the known kcat ≈ 1 s-1. We correlate experimental kinetic data (including the E424H variant, newly characterized in this work) for various GCPII mutants (kcat = 8.6 × 10-5 s-1 to 2.7 s-1) with the energy profiles calculated by QM/MM and QM-only (cluster model) approaches. We show that the near-quantitative agreement between the experimental values and the calculated activation energies (ΔH⧧) can be obtained and recommend the combination of the two protocols: QM/MM optimized structures and cluster model (QM) energetics. The trend in relative activation energies is mostly independent of the QM method (DFT functional) used. Last but not least, a satisfactory correlation between experimental and theoretical data allows us to provide qualitative and fairly simple explanations of the observed kinetic effects which are thus based on a rigorous footing.
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Affiliation(s)
- Daniel Bím
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.,Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Michal Navrátil
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 2120 00 Prague, Czech Republic
| | - Zsófia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Václav Navrátil
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Cyril Bařinka
- Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
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2
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Wei WM, Xu YL, Zheng RH, Zhao T, Fang W, Qin YD. Theoretical Study on the Mechanism of the Acylate Reaction of β-Lactamase. ACS OMEGA 2021; 6:12598-12604. [PMID: 34056410 PMCID: PMC8154126 DOI: 10.1021/acsomega.1c00592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 05/25/2023]
Abstract
Using density functional theory and a cluster approach, we study the reaction potential surface and compute Gibbs free energies for the acylate reaction of β-lactamase with penicillin G, where the solvent effect is important and taken into consideration. Two reaction paths are investigated: one is a multi-step process with a rate-limit energy barrier of 19.1 kcal/mol, which is relatively small, and the reaction can easily occur; the other is a one-step process with a barrier of 45.0 kcal/mol, which is large and thus makes the reaction hard to occur. The reason why the two paths have different barriers is explained.
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Affiliation(s)
- Wen-Mei Wei
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
| | - Yan-Li Xu
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
| | - Ren-Hui Zheng
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory for
Structural Chemistry of Unstable and Stable Species, Institute of
Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, P. R. China
| | - Tingting Zhao
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
| | - Weijun Fang
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
| | - Yi-De Qin
- School
of Basic Medical Sciences, Anhui Medical
University, Hefei, Anhui 230032, P.
R. China
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3
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QM study of carbon dioxide (CO2) and carbonyl sulfide (COS) degradation by cluster model of Carbonic anhydrase enzyme. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Prejanò M, Romeo I, Russo N, Marino T. On the Catalytic Activity of the Engineered Coiled-Coil Heptamer Mimicking the Hydrolase Enzymes: Insights from a Computational Study. Int J Mol Sci 2020; 21:E4551. [PMID: 32604744 PMCID: PMC7352413 DOI: 10.3390/ijms21124551] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 01/22/2023] Open
Abstract
Recently major advances were gained on the designed proteins aimed to generate biomolecular mimics of proteases. Although such enzyme-like catalysts must still suffer refinements for improving the catalytic activity, at the moment, they represent a good example of artificial enzymes to be tested in different fields. Herein, a de novo designed homo-heptameric peptide assembly (CC-Hept) where the esterase activity towards p-nitro-phenylacetate was obtained for introduction of the catalytic triad (Cys-His-Glu) into the hydrophobic matrix, is the object of the present combined molecular dynamics and quantum mechanics/molecular mechanics investigation. Constant pH Molecular Dynamics simulations on the apoform of CC-Hept suggested that the Cys residues are present in the protonated form. Molecular dynamics (MD) simulations of the enzyme-substrate complex evidenced the attitude of the enzyme-like system to retain water molecules, necessary in the hydrolytic reaction, in correspondence of the active site, represented by the Cys-His-Glu triad on each of the seven chains, without significant structural perturbations. A detailed reaction mechanism of esterase activity of CC-Hept-Cys-His-Glu was investigated on the basis of the quantum mechanics/molecular mechanics calculations employing a large quantum mechanical (QM) region of the active site. The proposed mechanism is consistent with available esterases kinetics and structural data. The roles of the active site residues were also evaluated. The deacylation phase emerged as the rate-determining step, in agreement with esterase activity of other natural proteases.
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Affiliation(s)
| | | | - Nino Russo
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy; (M.P.); (I.R.)
| | - Tiziana Marino
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy; (M.P.); (I.R.)
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Chauhan P, Gupta K, Ravikumar G, Saini DK, Chakrapani H. Carbonyl Sulfide (COS) Donor Induced Protein Persulfidation Protects against Oxidative Stress. Chem Asian J 2019; 14:4717-4724. [DOI: 10.1002/asia.201901148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/07/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Preeti Chauhan
- Department of ChemistryIndian Institute of Science Education and Research Pune Dr. Homi Bhabha Road, Pashan Pune 411 008 Maharashtra India
| | - Kavya Gupta
- Department of Molecular Reproduction, Development and GeneticsIndian Institute of Science Bangalore 560012 Karnataka India
| | - Govindan Ravikumar
- Department of ChemistryIndian Institute of Science Education and Research Pune Dr. Homi Bhabha Road, Pashan Pune 411 008 Maharashtra India
| | - Deepak K. Saini
- Department of Molecular Reproduction, Development and GeneticsIndian Institute of Science Bangalore 560012 Karnataka India
| | - Harinath Chakrapani
- Department of ChemistryIndian Institute of Science Education and Research Pune Dr. Homi Bhabha Road, Pashan Pune 411 008 Maharashtra India
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Steiger AK, Zhao Y, Pluth MD. Emerging Roles of Carbonyl Sulfide in Chemical Biology: Sulfide Transporter or Gasotransmitter? Antioxid Redox Signal 2018; 28:1516-1532. [PMID: 28443679 PMCID: PMC5930797 DOI: 10.1089/ars.2017.7119] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 04/16/2017] [Indexed: 12/19/2022]
Abstract
SIGNIFICANCE Carbonyl sulfide (COS) is the most prevalent sulfur-containing gas in the Earth's atmosphere, and it plays important roles in the global sulfur cycle. COS has been implicated in origin of life peptide ligation, is the primary energy source for certain bacteria, and has been detected in mammalian systems. Despite this long and intertwined history with terrestrial biology, limited attention has focused on potential roles of COS as a biological mediator. Recent Advances: Although bacterial COS production is well documented, definitive sources of mammalian COS production have not been confirmed. Enzymatic COS consumption in mammals, however, is well documented and occurs primarily by carbonic anhydrase (CA)-mediated conversion to hydrogen sulfide (H2S). COS has been detected in ex vivo mammalian tissue culture, as well as in exhaled breath as a potential biomarker for different disease pathologies, including cystic fibrosis and organ rejection. Recently, chemical tools for COS delivery have emerged and are poised to advance future investigations into the role of COS in different biological contexts. CRITICAL ISSUES Possible roles of COS as an important biomolecule, gasotransmitter, or sulfide transport intermediate remain to be determined. Key advances in both biological and chemical tools for COS research are needed to further investigate these questions. FUTURE DIRECTIONS Further evaluation of the biological roles of COS and disentangling the chemical biology of COS from that of H2S are needed to further elucidate these interactions. Chemical tools for COS delivery and modulation may provide a first avenue of investigative tools to answer many of these questions. Antioxid. Redox Signal. 28, 1516-1532.
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Affiliation(s)
- Andrea K Steiger
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, Materials Science Institute, University of Oregon , Eugene, Oregon
| | - Yu Zhao
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, Materials Science Institute, University of Oregon , Eugene, Oregon
| | - Michael D Pluth
- Department of Chemistry and Biochemistry, Institute of Molecular Biology, Materials Science Institute, University of Oregon , Eugene, Oregon
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7
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Prejanò M, Marino T, Rizzuto C, Madrid Madrid JC, Russo N, Toscano M. Reaction Mechanism of Low-Spin Iron(III)- and Cobalt(III)-Containing Nitrile Hydratases: A Quantum Mechanics Investigation. Inorg Chem 2017; 56:13390-13400. [DOI: 10.1021/acs.inorgchem.7b02121] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mario Prejanò
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Tiziana Marino
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Carmen Rizzuto
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Josè Carlos Madrid Madrid
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Nino Russo
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
| | - Marirosa Toscano
- Department of Chemistry
and
Chemical Technologies, Università della Calabria, Via P. Bucci, I-87036 Arcavacata di Rende, Italy
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8
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Piazzetta P, Marino T, Russo N, Salahub DR. The role of metal substitution in the promiscuity of natural and artificial carbonic anhydrases. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Abstract
The quantum chemical cluster approach is a powerful method for investigating enzymatic reactions. Over the past two decades, a large number of highly diverse systems have been studied and a great wealth of mechanistic insight has been developed using this technique. This Perspective reviews the current status of the methodology. The latest technical developments are highlighted, and challenges are discussed. Some recent applications are presented to illustrate the capabilities and progress of this approach, and likely future directions are outlined.
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Affiliation(s)
- Fahmi Himo
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University , SE-106 91 Stockholm, Sweden
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10
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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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Vullo D, Del Prete S, De Luca V, Carginale V, Ferraroni M, Dedeoglu N, Osman SM, AlOthman Z, Capasso C, Supuran CT. Anion inhibition studies of the β-carbonic anhydrase from the pathogenic bacterium Vibrio cholerae. Bioorg Med Chem Lett 2016; 26:1406-10. [PMID: 26853167 DOI: 10.1016/j.bmcl.2016.01.072] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 01/22/2016] [Accepted: 01/23/2016] [Indexed: 02/06/2023]
Abstract
The genome of the pathogenic bacterium Vibrio cholerae encodes for three carbonic anhydrases (CAs, EC 4.2.1.1) belonging to the α-, β- and γ-classes. Here we report and anion inhibition study of the β-CA, VchCAβ with anions and other small molecules which inhibit metalloenzymes. The best VchCAβ anion inhibitors were sulfamide, sulfamate, phenylboronic acid and phenylarsonic acid, which showed KIs in the range of 54-86μM. Diethyldithiocarbonate was also an effective VchCAβ inhibitor, with an inhibition constant of 0.73mM. The halides, cyanate, thiocyanate, cyanide, bicarbonate, carbonate, nitrate, nitrite, stannate, selenate, tellurate, divanadate, tetraborate, perrhenate, perruthenate, peroxydisulfate, selenocyanide, trithiocarbonate, and fluorosulfonate showed affinity in the low millimolar range, with KIs of 2.3-9.5mM. Identification of selective inhibitors of VchCAβ (over the human CA isoforms) may lead to pharmacological tools useful for understanding the physiological role(s) of this under-investigated enzyme.
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Affiliation(s)
- Daniela Vullo
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Sonia Del Prete
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy; Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Viviana De Luca
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Vincenzo Carginale
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy
| | - Marta Ferraroni
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Nurcan Dedeoglu
- Università degli Studi di Firenze, Dipartimento Di Chimica, Laboratorio di Chimica Bioinorganica, Polo Scientifico, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Sameh M Osman
- King Saud University, Department of Chemistry, Riyadh, Saudi Arabia
| | - Zeid AlOthman
- King Saud University, Department of Chemistry, Riyadh, Saudi Arabia
| | - Clemente Capasso
- Istituto di Bioscienze e Biorisorse, CNR, Via Pietro Castellino 81, Napoli, Italy.
| | - Claudiu T Supuran
- King Saud University, Department of Chemistry, Riyadh, Saudi Arabia; Università degli Studi di Firenze, Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
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