1
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Raum HN, Fisher SZ, Weininger U. Energetics and dynamics of the proton shuttle of carbonic anhydrase II. Cell Mol Life Sci 2023; 80:286. [PMID: 37688664 PMCID: PMC10492700 DOI: 10.1007/s00018-023-04936-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/26/2023] [Accepted: 08/23/2023] [Indexed: 09/11/2023]
Abstract
Human carbonic anhydrase II catalyzes the reversible reaction of carbon dioxide and water to form bicarbonate and a proton. His64-mediated proton shuttling between the active site and the bulk solvent is rate limiting. Here we investigate the protonation behavior of His64 as well as its structural and dynamic features in a pH dependent way. We derive two pKa values for His64, 6.25 and 7.60, that we were able to assign to its inward and outward conformation. Furthermore, we show that His64 exists in both conformations equally, independent of pH. Both conformations display an equal distribution of their two neutral tautomeric states. The life time of each conformation is short and both states display high flexibility within their orientation. Therefore, His64 is never static, but rather poised to change conformation. These findings support an energetic, dynamic and solution ensemble-based framework for the high enzymatic activity of human carbonic anhydrase II.
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Affiliation(s)
- Heiner N Raum
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Suzanne Zoë Fisher
- Department of Biology and Lund Protein Production Platform, Lund University, Sölvegatan 35, 22362, Lund, Sweden
- Scientific Activities Division, European Spallation Source ERIC, P.O. Box 176, 22100, Lund, Sweden
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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2
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Hussain T, Ullah S, Alrokayan S, Alamery S, Mohammed AA, Ejaz SA, Aziz M, Iqbal J. Synthesis, characterization and biological evaluation of pyrazole-based benzene sulfonamides as inhibitors of human carbonic anhydrase II, IX and XII. RSC Adv 2023; 13:18461-18479. [PMID: 37346960 PMCID: PMC10280043 DOI: 10.1039/d3ra03276k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/12/2023] [Indexed: 06/23/2023] Open
Abstract
The aberrant level of the carbonic anhydrase isozymes is linked with various disorders which include glaucoma, epilepsy, altitude sickness and obesity. In the present study, a series of the pyrazole-based benzene sulfonamides derivatives (4a-4l) were designed, synthesized and evaluated as the inhibitors of the three isoforms of human carbonic anhydrases (hCAII, hCAIX and hCAXII). A number of the derivatives were found more active inhibitors than acetazolamide used as a standard against the human hCAII, hCAIX and hCAXII. Among the series, the compound 4k inhibited the hCAII to a submicromolar level presenting the IC50 ± SEM concentration of 0.24 ± 0.18 μM, the inhibitor 4j reduced the activity of the hCAIX to the IC50 ± SEM equals 0.15 ± 0.07 μM, whereas, the molecule 4g blocked the catalytic potential of the isozyme hCAXII with as low as IC50 concentration of 0.12 ± 0.07 μM. In addition, compounds 4e and 4k were screened as the preferential inhibitors of the isoform hCAXII as compared to the hCAIX and hCAXII with half of the maximal concentrations of 0.75 ± 0.13 μM, and 0.24 ± 0.18 μM, respectively. Moreover, the compounds 4k, 4j and 4g were docked inside the active pocket of the crystallographic structure of the isoforms hCAXII, hCAIX and hCAXII, respectively. The docked inhibitors showed the binding interactions with the important amino acid residues such as Leu1198, Thr1199, His1094, and Phe1131 in hCAXII isozyme; residues Val121, Thr200, Pro203, and Gln71 in hCAIX; the amino acids Val119, Leu197, Gln89, and Asn64 in the case of hCAXII. In addition, structural geometries, reactivity descriptors, optimization energy and electronic parameters were calculated to predict the activity of the synthesized compounds.
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Affiliation(s)
- Tajamul Hussain
- Centre of Excellence in Biotechnology Research, King Saud University Riyadh 11451 Saudi Arabia
- Research Chair for Biomedical Application of Nanomaterials, Biochemistry Department, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Saif Ullah
- Centre for Advanced Drug Research, COMSATS University Islamabad Abbottabad Campus Abbottabad 22060 Pakistan +92-992-383441 +92-992-383591-96
| | - Salman Alrokayan
- Research Chair for Biomedical Application of Nanomaterials, Biochemistry Department, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Salman Alamery
- Biochemistry Department, College of Science, King Saud University Riyadh 11451 Saudi Arabia
| | - Arif Ahmed Mohammed
- Centre of Excellence in Biotechnology Research, King Saud University Riyadh 11451 Saudi Arabia
| | - Syeda Abida Ejaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur Bahawalpur 63100 Pakistan
| | - Mubashir Aziz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur Bahawalpur 63100 Pakistan
| | - Jamshed Iqbal
- Centre for Advanced Drug Research, COMSATS University Islamabad Abbottabad Campus Abbottabad 22060 Pakistan +92-992-383441 +92-992-383591-96
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus Abbottabad 22060 Pakistan
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3
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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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4
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Nocentini A, Angeli A, Carta F, Winum JY, Zalubovskis R, Carradori S, Capasso C, Donald WA, Supuran CT. Reconsidering anion inhibitors in the general context of drug design studies of modulators of activity of the classical enzyme carbonic anhydrase. J Enzyme Inhib Med Chem 2021; 36:561-580. [PMID: 33615947 PMCID: PMC7901698 DOI: 10.1080/14756366.2021.1882453] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Inorganic anions inhibit the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1) generally by coordinating to the active site metal ion. Cyanate was reported as a non-coordinating CA inhibitor but those erroneous results were subsequently corrected by another group. We review the anion CA inhibitors (CAIs) in the more general context of drug design studies and the discovery of a large number of inhibitor classes and inhibition mechanisms, including zinc binders (sulphonamides and isosteres, dithiocabamates and isosteres, thiols, selenols, benzoxaboroles, ninhydrins, etc.); inhibitors anchoring to the zinc-coordinated water molecule (phenols, polyamines, sulfocoumarins, thioxocoumarins, catechols); CAIs occluding the entrance to the active site (coumarins and derivatives, lacosamide), as well as compounds that bind outside the active site. All these new chemotypes integrated with a general procedure for obtaining isoform-selective compounds (the tail approach) has resulted, through the guidance of rigorous X-ray crystallography experiments, in the development of highly selective CAIs for all human CA isoforms with many pharmacological applications.
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Affiliation(s)
- Alessio Nocentini
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
| | - Andrea Angeli
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
| | - Fabrizio Carta
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
| | | | - Raivis Zalubovskis
- Latvian Institute of Organic Synthesis, Riga, Latvia.,Institute of Technology of Organic Chemistry, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Riga, Latvia
| | - Simone Carradori
- Department of Pharmacy, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Clemente Capasso
- Institute of Biosciences and Bioresources, National Research Council, Napoli, Italy
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Claudiu T Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Florence, Italy
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5
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Immobilization of carbonic anhydrase for CO2 capture and its industrial implementation: A review. J CO2 UTIL 2021. [DOI: 10.1016/j.jcou.2021.101475] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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6
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Polishchuk OV. Stress-Related Changes in the Expression and Activity of Plant Carbonic Anhydrases. PLANTA 2021; 253:58. [PMID: 33532871 DOI: 10.1007/s00425-020-03553-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/23/2020] [Indexed: 05/17/2023]
Abstract
The data on stress-related changes in the expression and activity of plant carbonic anhydrases (CAs) suggest that they are generally upregulated at moderate stress severity. This indicates probable involvement of CAs in adaptation to drought, high salinity, heat, high light, Ci deficit, and excess bicarbonate. The changes in CA levels under cold stress are less studied and generally represented by the downregulation of CAs excepting βCA2. Excess Cd2+ and deficit of Zn2+ specifically reduce CA activity and reduce its synthesis. Probable roles of βCAs in stress adaptation include stomatal closure, ROS scavenging and partial compensation for decreased mesophyll CO2 conductance. βCAs play contrasting roles in pathogen responses, interacting with phytohormone signaling networks. Their role can be either negative or positive, probably depending on the host-pathogen system, pathogen initial titer, and levels of ·NO and ROS. It is still not clear why CAs are suppressed under severe stress levels. It should be noted, that the role of βCAs in the facilitation of CO2 diffusion and their involvement in redox signaling or ROS detoxication are potentially antagonistic, as they are inactivated by oxidation or nitrosylation. Interestingly, some chloroplastic βCAs may be relocated to the cytoplasm under stress conditions, but the physiological meaning of this effect remains to be studied.
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Affiliation(s)
- O V Polishchuk
- Membranology and Phytochemistry Department, M.G. Kholodny Institute of Botany of NAS of Ukraine, 2 Tereshchenkivska Str, Kyiv, 01004, Ukraine.
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7
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Paul TK, Taraphder S. Coordination Dynamics of Zinc Triggers the Rate Determining Proton Transfer in Human Carbonic Anhydrase II. Chemphyschem 2020; 21:1455-1473. [DOI: 10.1002/cphc.202000177] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/17/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Tanmoy Kumar Paul
- Department of Chemistry Indian Institute of Technology Kharagpur 721302 India
| | - Srabani Taraphder
- Department of Chemistry Indian Institute of Technology Kharagpur 721302 India
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8
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Andring JT, Kim CU, McKenna R. Structure and mechanism of copper-carbonic anhydrase II: a nitrite reductase. IUCRJ 2020; 7:287-293. [PMID: 32148856 PMCID: PMC7055381 DOI: 10.1107/s2052252520000986] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/24/2020] [Indexed: 05/06/2023]
Abstract
Nitric oxide (NO) promotes vasodilation through the activation of guanylate cyclase, resulting in the relaxation of the smooth muscle vasculature and a subsequent decrease in blood pressure. Therefore, its regulation is of interest for the treatment and prevention of heart disease. An example is pulmonary hypertension which is treated by targeting this NO/vasodilation pathway. In bacteria, plants and fungi, nitrite (NO2 -) is utilized as a source of NO through enzymes known as nitrite reductases. These enzymes reduce NO2 - to NO through a catalytic metal ion, often copper. Recently, several studies have shown nitrite reductase activity of mammalian carbonic anhydrase II (CAII), yet the molecular basis for this activity is unknown. Here we report the crystal structure of copper-bound human CAII (Cu-CAII) in complex with NO2 - at 1.2 Å resolution. The structure exhibits Type 1 (T-1) and 2 (T-2) copper centers, analogous to bacterial nitrite reductases, both required for catalysis. The copper-substituted CAII active site is penta-coordinated with a 'side-on' bound NO2 -, resembling a T-2 center. At the N terminus, several residues that are normally disordered form a porphyrin ring-like configuration surrounding a second copper, acting as a T-1 center. A structural comparison with both apo- (without metal) and zinc-bound CAII (Zn-CAII) provides a mechanistic picture of how, in the presence of copper, CAII, with minimal conformational changes, can function as a nitrite reductase.
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Affiliation(s)
- Jacob T. Andring
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610 USA
| | - Chae Un Kim
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610 USA
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9
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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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10
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North ML, Wilcox DE. Shift from Entropic Cu 2+ Binding to Enthalpic Cu + Binding Determines the Reduction Thermodynamics of Blue Copper Proteins. J Am Chem Soc 2019; 141:14329-14339. [PMID: 31433629 DOI: 10.1021/jacs.9b06836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The enthalpic and entropic components of Cu2+ and Cu+ binding to the blue copper protein azurin have been quantified with isothermal titration calorimetry (ITC) measurements and analysis, providing the first such experimental values for Cu+ binding to a protein. The high affinity of azurin for Cu2+ is entirely due to a very favorable binding entropy, while its even higher affinity for Cu+ is due to a favorable binding enthalpy and entropy. The binding thermodynamics provide insight into bond enthalpies at the blue copper site and entropic contributions from desolvation and proton displacement. These values were used in thermodynamic cycles to determine the enthalpic and entropic contributions to the free energy of reduction and thus the reduction potential. The reduction thermodynamics obtained with this method are in good agreement with previous results from temperature-dependent electrochemical measurements. The calorimetry method, however, provides new insight into contributions from the initial (oxidized) and final (reduced) states of the reduction. Since ITC measurements quantify the protons that are displaced upon metal binding, the proton transfer that is coupled with electron transfer is also determined with this method. Preliminary results for Cu2+ and Cu+ binding to the Phe114Pro variant of azurin demonstrate the insight about protein tuning of the reduction potential that is provided by the binding thermodynamics of each metal oxidation state.
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Affiliation(s)
- Molly L North
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
| | - Dean E Wilcox
- Department of Chemistry , Dartmouth College , Hanover , New Hampshire 03755 , United States
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11
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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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12
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Ngo C, Mehta R, Aggarwal K, Fikes AG, Santos IC, Greer SM, Que EL. Pull-Down of Metalloproteins in Their Native States by Using Desthiobiotin-Based Probes. Chembiochem 2019; 20:1003-1007. [PMID: 30520207 PMCID: PMC6530555 DOI: 10.1002/cbic.201800613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Indexed: 11/07/2022]
Abstract
One-third of all proteins are estimated to require metals for structural stability and/or catalytic activity. Desthiobiotin probes containing metal binding groups can be used to capture metalloproteins with exposed active-site metals under mild conditions so as to prevent changes in metallation state. The proof-of-concept was demonstrated with carbonic anhydrase (CA), an open active site, Zn2+ -containing protein. CA was targeted by using sulfonamide derivatives. Linkers of various lengths and structures were screened to determine the optimal structure for capture of the native protein. The optimized probes could selectively pull down CA from red blood cell lysate and other protein mixtures. Pull-down of differently metallated CAs was also investigated.
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Affiliation(s)
- Chinh Ngo
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Radhika Mehta
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Kanchan Aggarwal
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Audrey G. Fikes
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Ines C. Santos
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Sylvester M. Greer
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
| | - Emily L. Que
- Department of Chemistry, University of Texas at Austin, 105 E 24 St Stop A5300, Austin, TX 78712, USA
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13
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Zeisel L, Szimhardt N, Wurzenberger MHH, Klapötke TM, Stierstorfer J. 2-Methyl-substituted monotetrazoles in copper(ii) perchlorate complexes: manipulating coordination chemistry and derived energetic properties. NEW J CHEM 2019. [DOI: 10.1039/c8nj05375h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Several new energetic coordination compounds (ECC) have been prepared using two 2-methyl-substituted tetrazoles. By simply changing the reaction conditions, the coordination sphere of the metal center can be manipulated in order to obtain different complexes with varying energetic properties.
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Affiliation(s)
- Lukas Zeisel
- Department of Chemistry
- Ludwig Maximilian University Munich
- D-81377 Munich
- Germany
| | - Norbert Szimhardt
- Department of Chemistry
- Ludwig Maximilian University Munich
- D-81377 Munich
- Germany
| | | | - Thomas M. Klapötke
- Department of Chemistry
- Ludwig Maximilian University Munich
- D-81377 Munich
- Germany
| | - Jörg Stierstorfer
- Department of Chemistry
- Ludwig Maximilian University Munich
- D-81377 Munich
- Germany
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14
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Sharma A, Sharma D, Verma SK. In silico Study of Iron, Zinc and Copper Binding Proteins of Pseudomonas syringae pv. lapsa: Emphasis on Secreted Metalloproteins. Front Microbiol 2018; 9:1838. [PMID: 30186242 PMCID: PMC6110883 DOI: 10.3389/fmicb.2018.01838] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/23/2018] [Indexed: 11/17/2022] Open
Abstract
The phytopathogenic bacteria, Pseudomonas syringae pv. lapsa (P. syringae pv. lapsa) infects the staple food crop wheat. Metalloproteins play important roles in plant-pathogen interactions. Hence, the present work is aimed to predict and analyze the iron (Fe), zinc (Zn), and copper (Cu) binding proteins of P. syringae pv. lapsa which help in its growth, adaptation, survival and pathogenicity. A total of 232 Fe, 307 Zn, and 38 Cu-binding proteins have been identified. The functional annotation, subcellular localization and gene ontology enriched network analysis revealed their role in wide range of biological activities of the phytopathogen. Among the identified metalloproteins, a total of 29 Fe-binding, 31 Zn-binding, and 5 Cu-binding proteins were found to be secreted in nature. These putative secreted metalloproteins may perform diverse cellular and biological functions ranging from transport, response to oxidative stress, proteolysis, antimicrobial resistance, metabolic processes, protein folding and DNA repair. The observations obtained here may provide initial information required to draft new schemes to control microbial infections of staple food crops and will further help in developing sustainable agriculture.
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Affiliation(s)
- Ankita Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Dixit Sharma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Shailender K Verma
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, India
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15
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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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16
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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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17
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Cerofolini L, Staderini T, Giuntini S, Ravera E, Fragai M, Parigi G, Pierattelli R, Luchinat C. Long-range paramagnetic NMR data can provide a closer look on metal coordination in metalloproteins. J Biol Inorg Chem 2017; 23:71-80. [PMID: 29218635 DOI: 10.1007/s00775-017-1511-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/06/2017] [Indexed: 11/24/2022]
Abstract
Paramagnetic NMR data can be profitably incorporated in structural refinement protocols of metalloproteins or metal-substituted proteins, mostly as distance or angle restraints. However, they could in principle provide much more information, because the magnetic susceptibility of a paramagnetic metal ion is largely determined by its coordination sphere. This information can in turn be used to evaluate changes occurring in the coordination sphere of the metal when ligands (e.g.: inhibitors) are bound to the protein. This gives an experimental handle on the molecular structure in the vicinity of the metal which falls in the so-called blind sphere. The magnetic susceptibility anisotropy tensors of cobalt(II) and nickel(II) ions bound to human carbonic anhydrase II in free and inhibited forms have been determined. The change of the magnetic susceptibility anisotropy is directly linked to the binding mode of different ligands in the active site of the enzyme. Indication about the metal coordination sphere in the presence of an inhibitor in pharmaceutically relevant proteins could be important in the design of selective drugs with a structure-based approach.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Tommaso Staderini
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019, Sesto Fiorentino, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Roberta Pierattelli
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) and Interuniversity Consortium for Magnetic Resonance of Metallo Proteins (CIRMMP), Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
- Department of Chemistry "Ugo Schiff", University of Florence, Via Della Lastruccia 3, 50019, Sesto Fiorentino, Italy.
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18
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Cerofolini L, Giuntini S, Louka A, Ravera E, Fragai M, Luchinat C. High-Resolution Solid-State NMR Characterization of Ligand Binding to a Protein Immobilized in a Silica Matrix. J Phys Chem B 2017; 121:8094-8101. [PMID: 28762736 DOI: 10.1021/acs.jpcb.7b05679] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Solid-state NMR is becoming a powerful tool to detect atomic-level structural features of biomolecules even when they are bound to (or trapped in) solid systems that lack long-range three-dimensional order. We here demonstrate that it is possible to probe protein-ligand interactions from a protein-based perspective also when the protein is entrapped in silica, thus translating into biomolecular solid-state NMR all of the considerations that are usually made to understand the chemical nature of the interaction of a protein with its ligands. This work provides a proof of concept that also immobilized enzymes can be used for protein-based NMR protein-ligand interactions for drug discovery.
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Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Stefano Giuntini
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Alexandra Louka
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy.,GiottoBiotech S.R.L. , Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP) , Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy.,Department of Chemistry "Ugo Schiff", University of Florence , Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
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19
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Henderson KL, Li M, Martinez S, Lewis EA, Hausinger RP, Emerson JP. Global stability of an α-ketoglutarate-dependent dioxygenase (TauD) and its related complexes. Biochim Biophys Acta Gen Subj 2017; 1861:987-994. [PMID: 28214548 PMCID: PMC5453726 DOI: 10.1016/j.bbagen.2017.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/22/2017] [Accepted: 02/14/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND TauD is a nonheme iron(II) and α-ketoglutarate (αKG) dependent dioxygenase, and a member of a broader family of enzymes that oxidatively decarboxylate αKG to succinate and carbon dioxide thereby activating O2 to perform a range of oxidation reactions. However before O2 activation can occur, these enzymes bind both substrate and cofactor in an effective manner. Here the thermodynamics associated with substrate and cofactor binding to FeTauD are explored. METHODS Thermal denaturation of TauD and its enzyme-taurine, enzyme-αKG, and enzyme-taurine-αKG complexes are explored using circular dichroism (CD) spectroscopy and differential scanning calorimetry (DSC). RESULTS Taurine binding is endothermic (+26kcal/mol) and entropically driven that includes burial of hydrophobic surfaces to close the lid domain. Binding of αKG is enthalpically favorable and shows cooperativity with taurine binding, where the change in enthalpy associated with αKG binding (δΔHcal) increases from -30.1kcal/mol when binding to FeTauD to -65.2kcal/mol when binding to the FeTauD-taurine complex. CONCLUSIONS The intermolecular interactions that govern taurine and αKG binding impact the global stability of TauD and its complexes, with clear and dramatic cooperativity between substrate and cofactor. GENERAL SIGNIFICANCE Thermal denaturation of TauD and its enzyme-taurine, enzyme-αKG, and enzyme-taurine-αKG complexes each exhibited increased temperature stability over the free enzyme. Through deconvolution of the energetic profiles for all species studied, a thermodynamic cycle was generated that shows significant cooperativity between substrate and cofactor binding which continues to clarity the events leading up O2 activation.
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Affiliation(s)
- Kate L Henderson
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, United States
| | - Mingjie Li
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, United States
| | - Salette Martinez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, United States
| | - Edwin A Lewis
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, United States
| | - Robert P Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824-4320, United States
| | - Joseph P Emerson
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, United States.
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20
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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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21
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Ash T, Debnath T, Banu T, Das AK. Exploration of Binding Interactions of Cu2+ with d-Penicillamine and its O- and Se- Analogues in Both Gas and Aqueous Phases: A Theoretical Approach. J Phys Chem B 2016; 120:3467-78. [DOI: 10.1021/acs.jpcb.5b11825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tamalika Ash
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Tanay Debnath
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Tahamida Banu
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Abhijit K. Das
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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22
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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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23
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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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