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Carbonic anhydrase activity identified in the powdered nacreous layer of Pinctada fucata. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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2
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Tsikas D, Gambaryan S. Nitrous anhydrase activity of carbonic anhydrase II: cysteine is required for nitric oxide (NO) dependent phosphorylation of VASP in human platelets. J Enzyme Inhib Med Chem 2021; 36:525-534. [PMID: 33508993 PMCID: PMC7875556 DOI: 10.1080/14756366.2021.1874946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The carbonic anhydrase (CA) family does not only catalyse the reversible hydration of CO2 to bicarbonate, but it also possesses esterase and phosphatase activity. Recently, bovine CA II and human CA II have been reported to convert inorganic nitrite (O=N-O−) to nitric oxide (NO) and nitrous anhydride (N2O3). Given the ability of NO to mediate vasodilation and inhibit platelet aggregation, this CA II activity would represent a bioactivation of nitrite. There are contradictory reports in the literature and the physiological role of CA II nitrite bioactivation is still disputed. Here, we provide new experimental data in support of the nitrous anhydrase activity of CA II and the key role L-cysteine in the bioactivation of nitrite by CA II. Using washed human platelets and by measuring VASP phosphorylation we provide evidence that exogenous nitrite (10 µM) is bioactivated to NO in a manner strongly depending on L-cysteine (100 and 200 µM). The process is not inhibitable by acetazolamide, a potent CA inhibitor. The contradictory results of recently published studies in this area are thoroughly discussed.
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Affiliation(s)
- Dimitrios Tsikas
- Institute of Toxicology, Core Unit Proteomics, Hannover Medical School, Hannover, Germany
| | - Stepan Gambaryan
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Petersburg, Russia
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3
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De Simone G, Di Fiore A, Truppo E, Langella E, Vullo D, Supuran CT, Monti SM. Exploration of the residues modulating the catalytic features of human carbonic anhydrase XIII by a site-specific mutagenesis approach. J Enzyme Inhib Med Chem 2019; 34:1506-1510. [PMID: 31431090 PMCID: PMC6713127 DOI: 10.1080/14756366.2019.1653290] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Carbonic anhydrases (CAs) are ubiquitous metallo-enzymes that catalyse the reversible hydration of carbon dioxide to bicarbonate and proton. In humans there are 15 isoforms among which only 12 are catalytically active. Since active human (h) CAs show different efficiency, the understanding of the molecular determinants affecting it is a matter of debate. Here we investigated, by a site-specific mutagenesis approach, residues modulating the catalytic features of one of the least investigated cytosolic isoform, i.e. hCA XIII. Results showed that residues assisting the formation of an ordered solvent network within the catalytic site as well as those forming a histidine cluster on the protein surface are important to guarantee an efficient proton transfer.
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Affiliation(s)
| | - Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-CNR , Naples , Italy
| | | | - Emma Langella
- Istituto di Biostrutture e Bioimmagini-CNR , Naples , Italy
| | - Daniela Vullo
- Neurofarba Department, Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche e Nutraceutiche , Sesto Fiorentino , Florence , Italy
| | - Claudiu T Supuran
- Neurofarba Department, Università degli Studi di Firenze, Sezione di Scienze Farmaceutiche e Nutraceutiche , Sesto Fiorentino , Florence , Italy
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4
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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q Rev Biophys 2019; 51:e10. [PMID: 30912486 DOI: 10.1017/s0033583518000082] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.
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KILIÇ D, ERDOĞAN O, KÜFREVİOĞLU Öİ. Effect of mutation in active site residue Trp209 to Val, Leu, Ile and Pro on the catalytic activity and affinity for some benzenesulfonamides of human carbonic anhydrase II. Turk J Biol 2017. [DOI: 10.3906/biy-1705-37] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Taraphder S, Maupin CM, Swanson JJ, Voth GA. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II. J Phys Chem B 2016; 120:8389-404. [PMID: 27063577 PMCID: PMC5003118 DOI: 10.1021/acs.jpcb.6b02166] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/06/2016] [Indexed: 11/28/2022]
Abstract
The role of protein dynamics in enzyme catalysis is one of the most highly debated topics in enzymology. The main controversy centers around what may be defined as functionally significant conformational fluctuations and how, if at all, these fluctuations couple to enzyme catalyzed events. To shed light on this debate, the conformational dynamics along the transition path surmounting the highest free energy barrier have been herein investigated for the rate limiting proton transport event in human carbonic anhydrase (HCA) II. Special attention has been placed on whether the motion of an excess proton is correlated with fluctuations in the surrounding protein and solvent matrix, which may be rare on the picosecond and subpicosecond time scales of molecular motions. It is found that several active site residues, which do not directly participate in the proton transport event, have a significant impact on the dynamics of the excess proton. These secondary participants are shown to strongly influence the active site environment, resulting in the creation of water clusters that are conducive to fast, moderately slow, or slow proton transport events. The identification and characterization of these secondary participants illuminates the role of protein dynamics in the catalytic efficiency of HCA II.
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Affiliation(s)
- Srabani Taraphder
- Department
of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - C. Mark Maupin
- Department
of Chemical and Biological Engineering, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United
States
| | - Jessica
M. J. Swanson
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Institute for Biophysical Dynamics, James Frank Institute,
and Computation Institute, University of
Chicago, 5735 South Ellis
Avenue, Chicago, Illinois 60637, United States
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7
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Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer. Proc Natl Acad Sci U S A 2015; 112:5673-8. [PMID: 25902526 DOI: 10.1073/pnas.1502255112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human carbonic anhydrase II (HCA II) uses a Zn-bound OH(-)/H2O mechanism to catalyze the reversible hydration of CO2. This catalysis also involves a separate proton transfer step, mediated by an ordered solvent network coordinated by hydrophilic residues. One of these residues, Tyr7, was previously shown to be deprotonated in the neutron crystal structure at pH 10. This observation indicated that Tyr7 has a perturbed pKa compared with free tyrosine. To further probe the pKa of this residue, NMR spectroscopic measurements of [(13)C]Tyr-labeled holo HCA II (with active-site Zn present) were preformed to titrate all Tyr residues between pH 5.4-11.0. In addition, neutron studies of apo HCA II (with Zn removed from the active site) at pH 7.5 and holo HCA II at pH 6 were conducted. This detailed interrogation of tyrosines in HCA II by NMR and neutron crystallography revealed a significantly lowered pKa of Tyr7 and how pH and Tyr proximity to Zn affect hydrogen-bonding interactions.
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Boone CD, Pinard M, McKenna R, Silverman D. Catalytic mechanism of α-class carbonic anhydrases: CO2 hydration and proton transfer. Subcell Biochem 2014; 75:31-52. [PMID: 24146373 DOI: 10.1007/978-94-007-7359-2_3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The carbonic anhydrases (CAs; EC 4.2.1.1) are a family of metalloenzymes that catalyze the reversible hydration of carbon dioxide (CO2) and dehydration of bicarbonate (HCO3 (-)) in a two-step ping-pong mechanism: [Formula: see text] CAs are ubiquitous enzymes and are categorized into five distinct classes (α, β, γ, δ and ζ). The α-class is found primarily in vertebrates (and the only class of CA in mammals), β is observed in higher plants and some prokaryotes, γ is present only in archaebacteria whereas the δ and ζ classes have only been observed in diatoms.The focus of this chapter is on α-CAs as the structure-function relationship is best understood for this class, in particular for humans. The reader is referred to other reviews for an overview of the structure and catalytic mechanism of the other CA classes. The overall catalytic site structure and geometry of α-CAs are described in the first section of this chapter followed by the kinetic studies, binding of CO2, and the proton shuttle network.
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Affiliation(s)
- Christopher D Boone
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA,
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Appraisal of sildenafil binding on the structure and promiscuous esterase activity of native and histidine-modified forms of carbonic anhydrase II. Biophys Chem 2013; 175-176:1-16. [DOI: 10.1016/j.bpc.2013.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 11/17/2022]
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Fisher Z, Boone CD, Biswas SM, Venkatakrishnan B, Aggarwal M, Tu C, Agbandje-McKenna M, Silverman D, McKenna R. Kinetic and structural characterization of thermostabilized mutants of human carbonic anhydrase II. Protein Eng Des Sel 2012; 25:347-55. [PMID: 22691706 DOI: 10.1093/protein/gzs027] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Carbonic anhydrases (CAs) are ubiquitous enzymes that catalyze the reversible hydration/dehydration of carbon dioxide/bicarbonate. As such, there is enormous industrial interest in using CA as a bio-catalyst for carbon sequestration and biofuel production. However, to ensure cost-effective use of the enzyme under harsh industrial conditions, studies were initiated to produce variants with enhanced thermostability while retaining high solubility and catalytic activity. Kinetic and structural studies were conducted to determine the structural and functional effects of these mutations. X-ray crystallography revealed that a gain in surface hydrogen bonding contributes to stability while retaining proper active site geometry and electrostatics to sustain catalytic efficiency. The kinetic profiles determined under a variety of conditions show that the surface mutations did not negatively impact the carbon dioxide hydration or proton transfer activity of the enzyme. Together these results show that it is possible to enhance the thermal stability of human carbonic anhydrase II by specific replacements of surface hydrophobic residues of the enzyme. In addition, combining these stabilizing mutations with strategic active site changes have resulted in thermostable mutants with desirable kinetic properties.
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Affiliation(s)
- Zoë Fisher
- Bioscience Division, TA-53 Bldg 622, Mailstop H805, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Turkoglu S, Maresca A, Alper M, Kockar F, Işık S, Sinan S, Ozensoy O, Arslan O, Supuran CT. Mutation of active site residues Asn67 to Ile, Gln92 to Val and Leu204 to Ser in human carbonic anhydrase II: Influences on the catalytic activity and affinity for inhibitors. Bioorg Med Chem 2012; 20:2208-13. [DOI: 10.1016/j.bmc.2012.02.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/06/2012] [Accepted: 02/08/2012] [Indexed: 11/15/2022]
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12
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Mikulski R, Domsic JF, Ling G, Tu C, Robbins AH, Silverman DN, McKenna R. Structure and catalysis by carbonic anhydrase II: role of active-site tryptophan 5. Arch Biochem Biophys 2011; 516:97-102. [PMID: 22001224 DOI: 10.1016/j.abb.2011.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/27/2011] [Accepted: 09/28/2011] [Indexed: 11/25/2022]
Abstract
The tryptophan residue Trp5, highly conserved in the α class of carbonic anhydrases including human carbonic anhydrase II (HCA II), is positioned at the entrance of the active site cavity and forms a π-stacking interaction with the imidazole ring of the proton shuttle His64 in its outward orientation. We have observed that replacement of Trp5 in HCA II caused significant structural changes, as determined by X-ray diffraction, in the conformation of 11 residues at the N-terminus and in the orientation of the proton shuttle residue His64. Most significantly, two variants W5H and W5E HCA II had His64 predominantly outward in orientation, while W5F and wild type showed the superposition of both outward and inward orientations in crystal structures. Although Trp5 influences the orientation of the proton shuttle His64, this orientation had no significant effect on the rate constant for proton transfer near 1μs(-1), determined by exchange of (18)O between CO(2) and water measured by mass spectrometry. The apparent values of the pK(a) of the zinc-bound water and the proton shuttle residue suggest that different active-site conformations influence the two stages of catalysis, the proton transfer stage and the interconversion of CO(2) and bicarbonate.
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Affiliation(s)
- Rose Mikulski
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, United States
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