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Gigli L, Silva JM, Cerofolini L, Macedo AL, Geraldes CFGC, Suturina EA, Calderone V, Fragai M, Parigi G, Ravera E, Luchinat C. Machine Learning-Enhanced Quantum Chemistry-Assisted Refinement of the Active Site Structure of Metalloproteins. Inorg Chem 2024; 63:10713-10725. [PMID: 38805564 DOI: 10.1021/acs.inorgchem.4c01274] [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
Understanding the fine structural details of inhibitor binding at the active site of metalloenzymes can have a profound impact on the rational drug design targeted to this broad class of biomolecules. Structural techniques such as NMR, cryo-EM, and X-ray crystallography can provide bond lengths and angles, but the uncertainties in these measurements can be as large as the range of values that have been observed for these quantities in all the published structures. This uncertainty is far too large to allow for reliable calculations at the quantum chemical (QC) levels for developing precise structure-activity relationships or for improving the energetic considerations in protein-inhibitor studies. Therefore, the need arises to rely upon computational methods to refine the active site structures well beyond the resolution obtained with routine application of structural methods. In a recent paper, we have shown that it is possible to refine the active site of cobalt(II)-substituted MMP12, a metalloprotein that is a relevant drug target, by matching to the experimental pseudocontact shifts (PCS) those calculated using multireference ab initio QC methods. The computational cost of this methodology becomes a significant bottleneck when the starting structure is not sufficiently close to the final one, which is often the case with biomolecular structures. To tackle this problem, we have developed an approach based on a neural network (NN) and a support vector regression (SVR) and applied it to the refinement of the active site structure of oxalate-inhibited human carbonic anhydrase 2 (hCAII), another prototypical metalloprotein target. The refined structure gives a remarkably good agreement between the QC-calculated and the experimental PCS. This study not only contributes to the knowledge of CAII but also demonstrates the utility of combining machine learning (ML) algorithms with QC calculations, offering a promising avenue for investigating other drug targets and complex biological systems in general.
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Affiliation(s)
- Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - José Malanho Silva
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Anjos L Macedo
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB─Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Carlos F G C Geraldes
- Department of Life Sciences, Faculty of Science and Technology, 3000-393 Coimbra, Portugal
- Coimbra Chemistry Center─Institute of Molecular Sciences (CCC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
| | | | - Vito Calderone
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
- Florence Data Science, University of Florence, Florence 50134, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino 50019, Italy
- Giotto Biotech, S.R.L., Sesto Fiorentino 50019, Italy
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Silva JM, Cerofolini L, Carvalho AL, Ravera E, Fragai M, Parigi G, Macedo AL, Geraldes CFGC, Luchinat C. Elucidating the concentration-dependent effects of thiocyanate binding to carbonic anhydrase. J Inorg Biochem 2023; 244:112222. [PMID: 37068394 DOI: 10.1016/j.jinorgbio.2023.112222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/28/2023] [Accepted: 04/09/2023] [Indexed: 04/19/2023]
Abstract
Many proteins naturally carry metal centers, with a large share of them being in the active sites of several enzymes. Paramagnetic effects are a powerful source of structural information and, therefore, if the native metal is paramagnetic, or it can be functionally substituted with a paramagnetic one, paramagnetic effects can be used to study the metal sites, as well as the overall structure of the protein. One notable example is cobalt(II) substitution for zinc(II) in carbonic anhydrase. In this manuscript we investigate the effects of sodium thiocyanate on the chemical environment of the metal ion of the human carbonic anhydrase II. The electron paramagnetic resonance (EPR) titration of the cobalt(II) protein with thiocyanate shows that the EPR spectrum changes from A-type to C-type on passing from 1:1 to 1:1000-fold ligand excess. This indicates the occurrence of a change in the electronic structure, which may reflect a sizable change in the metal coordination environment in turn caused by a modification of the frozen solvent glass. However, paramagnetic nuclear magnetic resonance (NMR) data indicate that the metal coordination cage remains unperturbed even in 1:1000-fold ligand excess. This result proves that the C-type EPR spectrum observed at large ligand concentration should be ascribed to the low temperature at which EPR measurements are performed, which impacts on the structure of the protein when it is destabilized by a high concentration of a chaotropic agent.
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Affiliation(s)
- José Malanho Silva
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Ana Luísa Carvalho
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Anjos L Macedo
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Carlos F G C Geraldes
- Department of Life Sciences, Faculty of Science and Technology, 3000-393 Coimbra, Portugal; Coimbra Chemistry Center- Institute of Molecular Sciences (CCC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy; Giotto Biotech, S.R.L, Sesto Fiorentino, Florence 50019, Italy.
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McConnell KD, Fitzkee NC, Emerson JP. Metal Ion Binding Induces Local Protein Unfolding and Destabilizes Human Carbonic Anhydrase II. Inorg Chem 2022; 61:1249-1253. [PMID: 34989562 PMCID: PMC8919859 DOI: 10.1021/acs.inorgchem.1c03271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Human carbonic anhydrase II (HCA) is a robust metalloprotein and an excellent biological model system to study the thermodynamics of metal ion coordination. Apo-HCA binds one zinc ion or two copper ions. We studied these binding processes at five temperatures (15-35 °C) using isothermal titration calorimetry, yielding thermodynamic parameters corrected for pH and buffer effects. We then sought to identify binding-induced structural changes. Our data suggest that binding at the active site organizes 6-8 residues; however, copper binding near the N-terminus results in a net unfolding of 6-7 residues. This surprising destabilization was confirmed using circular dichroism and protein stability measurements. Metal binding induced unfolding may represent an important regulatory mechanism, but it may be easily missed by NMR and X-ray crystallography. Thus, in addition to highlighting a highly novel binding-induced unfolding event, we demonstrate the value of calorimetry for studying the structural implications of metal binding.
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Affiliation(s)
- Kayla D. McConnell
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Nicholas C. Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Joseph P. Emerson
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
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Krishnamoorthy GK, Alluvada P, Hameed Mohammed Sherieff S, Kwa T, Krishnamoorthy J. Isothermal titration calorimetry and surface plasmon resonance analysis using the dynamic approach. Biochem Biophys Rep 2020; 21:100712. [PMID: 31890903 PMCID: PMC6926116 DOI: 10.1016/j.bbrep.2019.100712] [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: 10/04/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/24/2022] Open
Abstract
Biophysical techniques such as isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) are routinely used to ascertain the global binding mechanisms of protein-protein or protein-ligand interaction. Recently, Dumas etal, have explicitly modelled the instrument response of the ligand dilution and analysed the ITC thermogram to obtain kinetic rate constants. Adopting a similar approach, we have integrated the dynamic instrument response with the binding mechanism to simulate the ITC profiles of equivalent and independent binding sites, equivalent and sequential binding sites and aggregating systems. The results were benchmarked against the standard commercial software Origin-ITC. Further, the experimental ITC chromatograms of 2′-CMP + RNASE and BH3I-1 + hBCLXL interactions were analysed and shown to be comparable with that of the conventional analysis. Dynamic approach was applied to simulate the SPR profiles of a two-state model, and could reproduce the experimental profile accurately. Incorporated instrument response within the kinetic framework using dynamic approach to analyse ITC and SPR data. Different modelling approaches for instrument response such as lumped and kinetic modelling were compared and their equivalence were shown. (1) equivalent single site, (2) equivalent sequential sites, (3) equivalent parallel sites and (4) aggregating molecular system were modelled using dynamic approach.
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Giri A, Pant D. Carbonic anhydrase modification for carbon management. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:1294-1318. [PMID: 31797268 DOI: 10.1007/s11356-019-06667-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
Carbonic anhydrase modification (chemical and biological) is an attractive strategy for its diverse application to accelerate the absorption of CO2 from a flue gas with improved activity and stability. This article reports various possibilities of CA modification using metal-ligand homologous chemistry, cross-linking agents, and residue- and group-specific and genetic modifications, and assesses their role in carbon management. Chemically modified carbonic anhydrase is able to improve the absorption of carbon dioxide from a gas stream into mediation compounds with enhanced sequestration and mineral formation. Genetically modified CA polypeptide can also increase carbon dioxide conversion. Chemical modification of CA can be categorized in terms of (i) residue-specific modification (involves protein-ligand interaction in terms of substitution/addition) and group-specific modifications (based on the functional groups of the target CA). For every sustainable change, there should be no/limited toxic or immunological response. In this review, several CA modification pathways and biocompatibility rules are proposed as a theoretical support for emerging research in this area.
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Affiliation(s)
- Anand Giri
- Department of Environmental Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Deepak Pant
- School of Chemical Sciences, Central University of Haryana, Mahendragarh, Haryana, 123029, India.
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6
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Witkowska D, Rowińska-Żyrek M. Biophysical approaches for the study of metal-protein interactions. J Inorg Biochem 2019; 199:110783. [PMID: 31349072 DOI: 10.1016/j.jinorgbio.2019.110783] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/10/2019] [Accepted: 07/15/2019] [Indexed: 12/17/2022]
Abstract
Protein-protein interactions play important roles for a variety of cell functions, often involving metal ions; in fact, metal-ion binding mediates and regulates the activity of a wide range of biomolecules. Enlightening all of the specific features of metal-protein and metal-mediated protein-protein interactions can be a very challenging task; a detailed knowledge of the thermodynamic and spectroscopic parameters and the structural changes of the protein is normally required. For this purpose, many experimental techniques are employed, embracing all fields of Analytical and Bioinorganic Chemistry. In addition, the use of peptide models, reproducing the primary sequence of the metal-binding sites, is also proved to be useful. In this paper, a review of the most useful techniques for studying ligand-protein interactions with a special emphasis on metal-protein interactions is provided, with a critical summary of their strengths and limitations.
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Affiliation(s)
- Danuta Witkowska
- Public Higher Medical Professional School in Opole, Katowicka 68, 45060 Opole, Poland.
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7
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Cerofolini L, Silva JM, Ravera E, Romanelli M, Geraldes CFGC, Macedo AL, Fragai M, Parigi G, Luchinat C. How Do Nuclei Couple to the Magnetic Moment of a Paramagnetic Center? A New Theory at the Gauntlet of the Experiments. J Phys Chem Lett 2019; 10:3610-3614. [PMID: 31181162 DOI: 10.1021/acs.jpclett.9b01128] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The recent derivation, based on pure quantum chemistry (QC) first-principles, of the pseudocontact shifts (PCSs) caused by a paramagnetic metal center on far away nuclei has cast doubts on the validity of the semiempirical (SE) theory, predicting PCSs to arise from the metal magnetic susceptibility anisotropy. The SE theory has been used and applied countless times, especially in the last 2 decades, to obtain structural information on proteins containing paramagnetic metal ions. We show here that the QC and SE predictions can be directly tested against experiments, provided a suitable macromolecular system is used. The SE approach yields a good prediction of the experimental PCSs while the QC one does not. It appears that the classic theory is able to grasp satisfactorily the underlying physics.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
| | - José Malanho Silva
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Life Sciences and Coimbra Chemistry Center , University of Coimbra , Coimbra 3004-531 , Portugal
- UCIBIO-Requimte, Faculty of Sciences and Technology , Universidade NOVA de Lisboa , Caparica 2829-516 , Portugal
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Chemistry , University of Florence , Sesto Fiorentino 50019 , Italy
| | - Maurizio Romanelli
- Department of Earth Sciences , University of Florence , Sesto Fiorentino 50019 , Italy
| | - Carlos F G C Geraldes
- Department of Life Sciences and Coimbra Chemistry Center , University of Coimbra , Coimbra 3004-531 , Portugal
| | - Anjos L Macedo
- UCIBIO-Requimte, Faculty of Sciences and Technology , Universidade NOVA de Lisboa , Caparica 2829-516 , Portugal
| | - Marco Fragai
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Chemistry , University of Florence , Sesto Fiorentino 50019 , Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Chemistry , University of Florence , Sesto Fiorentino 50019 , Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) , University of Florence, and Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP) , via Sacconi 6 , Sesto Fiorentino 50019 , Italy
- Department of Chemistry , University of Florence , Sesto Fiorentino 50019 , Italy
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Tabbì G, Magrì A, Rizzarelli E. The copper(II) binding centres of carbonic anhydrase are differently affected by reductants that ensure the redox intracellular environment. J Inorg Biochem 2019; 199:110759. [PMID: 31299377 DOI: 10.1016/j.jinorgbio.2019.110759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/18/2019] [Accepted: 07/01/2019] [Indexed: 01/25/2023]
Abstract
Copper is involved in several biological processes. The static and labile copper pools are controlled by means of a network of influx and efflux transporters, storage proteins, chaperones, transcription factors and small molecules as glutathione (GSH), which contributes to the cell reducing environment. To follow the fate of intracellular copper labile pool, a variant of human apocarbonic anhydrase has been proposed as fluorescent probe to monitor cytoplasmic Cu2+. Aware that in this cellular compartment copper ion is present as Cu+, electron spin resonance technique (ESR) was used to ascertain whether (bovine or human) carbonic anhydrase (CA) was able to accommodate Cu+ in the same sites occupied by Cu2+, in the presence of naturally occurring reducing agents such as ascorbate and GSH. Our ESR results on Cu2+ complexes with CA allow for a complete characterization of the two metal binding sites of the protein in solution. The use of the reported affinity constants of zinc in the catalytic site and of Cu2+ in the peripheral and catalytic site, allow us to obtain the speciation of copper species mimicking the spectroscopic study conditions. The different Cu2+ coordination features in the catalytic and the peripheral (the N-terminus cleft mouth) binding sites influence the chemical reduction effect of the two main naturally occurring reductants. Ascorbate reversibly reduces the Cu2+ complex with CA, while glutathione irreversibly induces the formation of Cu2+ complex with its oxidized form (GSSG). Our results questioned the use of CA as intracellular Cu2+ sensor. Furthermore, translating these findings to intracellular environment, the conversion of GSH in GSSG can significantly alter the metallostasis.
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Affiliation(s)
- Giovanni Tabbì
- Institute of Crystallography, National Council of Research, CNR, S.S. Catania, via P. Gaifami 18, Catania, Italy
| | - Antonio Magrì
- Institute of Crystallography, National Council of Research, CNR, S.S. Catania, via P. Gaifami 18, Catania, Italy
| | - Enrico Rizzarelli
- Institute of Crystallography, National Council of Research, CNR, S.S. Catania, via P. Gaifami 18, Catania, Italy; Department of Chemical Sciences, University of Catania, Viale A. Doria 6, Catania, Italy; Consorzio Interuniversitario per la Ricerca dei Metalli nei Sistemi Biologici, Via Ulpiani 27, Bari, Italy.
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9
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Ferraroni M, Gaspari R, Scozzafava A, Cavalli A, Supuran CT. Dioxygen, an unexpected carbonic anhydrase ligand. J Enzyme Inhib Med Chem 2018; 33:999-1005. [PMID: 29806484 PMCID: PMC6010096 DOI: 10.1080/14756366.2018.1475371] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Carbonic anhydrases (CAs, EC 4.2.1.1) are ubiquitous metalloenzymes, grouped into seven different classes, which catalyze the reaction of CO2 hydration to bicarbonate and protons. All of the fifteen human isoforms reported to date belong to the α-class and contain zinc as a cofactor. The structure of human Zn,Cu-CA II has been solved which contains a copper ion bound at its N-terminal, coordinated to His4 and His64. In the active site a dioxygen molecule is coordinated to the zinc ion. Since dioxygen is a rather unexpected CA ligand, molecular dynamics (MD) simulations were performed which suggested a superoxide character of the zinc bound O2.
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Affiliation(s)
- Marta Ferraroni
- a Dipartimento di Chimica , Università di Firenze , Sesto Fiorentino (FI) , Italia
| | | | - Andrea Scozzafava
- a Dipartimento di Chimica , Università di Firenze , Sesto Fiorentino (FI) , Italia
| | - Andrea Cavalli
- c Dipartimento di Farmacia e Biotecnologie , Università di Bologna , Bologna , Italia
| | - Claudiu T Supuran
- d Dipartimento NEUROFARBA - Pharmaceutical and Nutraceutical Section , Sesto Fiorentino (FI) , Italia
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10
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Catalytic Water Oxidation by Iridium-Modified Carbonic Anhydrase. Chem Asian J 2018; 13:334-341. [DOI: 10.1002/asia.201701543] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/24/2017] [Indexed: 11/07/2022]
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11
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Coordination contributions to protein stability in metal-substituted carbonic anhydrase. J Biol Inorg Chem 2016; 21:659-67. [DOI: 10.1007/s00775-016-1375-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 06/20/2016] [Indexed: 10/21/2022]
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12
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The Complex Relationship between Metals and Carbonic Anhydrase: New Insights and Perspectives. Int J Mol Sci 2016; 17:ijms17010127. [PMID: 26797606 PMCID: PMC4730368 DOI: 10.3390/ijms17010127] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/01/2016] [Indexed: 12/22/2022] Open
Abstract
Carbonic anhydrase is a ubiquitous metalloenzyme, which catalyzes the reversible hydration of CO2 to HCO3− and H+. Metals play a key role in the bioactivity of this metalloenzyme, although their relationships with CA have not been completely clarified to date. The aim of this review is to explore the complexity and multi-aspect nature of these relationships, since metals can be cofactors of CA, but also inhibitors of CA activity and modulators of CA expression. Moreover, this work analyzes new insights and perspectives that allow translating new advances in basic science on the interaction between CA and metals to applications in several fields of research, ranging from biotechnology to environmental sciences.
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13
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Quinn CF, Carpenter MC, Croteau ML, Wilcox DE. Isothermal Titration Calorimetry Measurements of Metal Ions Binding to Proteins. Methods Enzymol 2016; 567:3-21. [PMID: 26794348 DOI: 10.1016/bs.mie.2015.08.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
ITC measurements involving metal ions are susceptible to a number of competing reactions (oxidation, precipitation, and hydrolysis) and coupled reactions involving the buffer and protons. Stabilization and delivery of the metal ion as a well-defined and well-characterized complex with the buffer, or a specific ligand, can suppress undesired solution chemistry and, depending on the stability of the metal complex, allow accurate measurements of higher affinity protein-binding sites. This requires, however, knowledge of the thermodynamics of formation of the metal complex and accounting for its contribution to the experimentally measured values (KITC and ΔHITC) through a post hoc analysis that provides the condition-independent binding thermodynamics (K, ΔG(o), ΔH, ΔS, and ΔCP). This analysis also quantifies the number of protons that are displaced when the metal ion binds to the protein.
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Affiliation(s)
- Colette F Quinn
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA
| | | | - Molly L Croteau
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA
| | - Dean E Wilcox
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA.
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14
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Nettles WL, Song H, Farquhar ER, Fitzkee NC, Emerson JP. Characterization of the Copper(II) Binding Sites in Human Carbonic Anhydrase II. Inorg Chem 2015; 54:5671-80. [PMID: 26010488 PMCID: PMC4482258 DOI: 10.1021/acs.inorgchem.5b00057] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human carbonic anhydrase (CA) is a well-studied, robust, mononuclear Zn-containing metalloprotein that serves as an excellent biological ligand system to study the thermodynamics associated with metal ion coordination chemistry in aqueous solution. The apo form of human carbonic anhydrase II (CA) binds 2 equiv of copper(II) with high affinity. The Cu(2+) ions bind independently forming two noncoupled type II copper centers in CA (CuA and CuB). However, the location and coordination mode of the CuA site in solution is unclear, compared to the CuB site that has been well-characterized. Using paramagnetic NMR techniques and X-ray absorption spectroscopy we identified an N-terminal Cu(2+) binding location and collected information on the coordination mode of the CuA site in CA, which is consistent with a four- to five-coordinate N-terminal Cu(2+) binding site reminiscent to a number of N-terminal copper(II) binding sites including the copper(II)-amino terminal Cu(2+) and Ni(2+) and copper(II)-β-amyloid complexes. Additionally, we report a more detailed analysis of the thermodynamics associated with copper(II) binding to CA. Although we are still unable to fully deconvolute Cu(2+) binding data to the high-affinity CuA site, we derived pH- and buffer-independent values for the thermodynamics parameters K and ΔH associated with Cu(2+) binding to the CuB site of CA to be 2 × 10(9) and -17.4 kcal/mol, respectively.
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Affiliation(s)
- Whitnee L. Nettles
- Mississippi State University: Department of Chemistry Box 9573 Mississippi State University Mississippi State, MS 39762-9573
| | - He Song
- Mississippi State University: Department of Chemistry Box 9573 Mississippi State University Mississippi State, MS 39762-9573
| | - Erik R. Farquhar
- Case Western Reserve University Center for Synchrotron Biosciences, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nicholas C. Fitzkee
- Mississippi State University: Department of Chemistry Box 9573 Mississippi State University Mississippi State, MS 39762-9573
| | - Joseph P. Emerson
- Mississippi State University: Department of Chemistry Box 9573 Mississippi State University Mississippi State, MS 39762-9573
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