1
|
Baronas D, Knašienė B, Mickevičiūtė A, Jachno J, Naujalis E, Zubrienė A, Matulis D. Inhibitor binding to metal-substituted metalloenzyme: Sulfonamide affinity for carbonic anhydrase IX. J Inorg Biochem 2024; 256:112547. [PMID: 38581802 DOI: 10.1016/j.jinorgbio.2024.112547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/18/2024] [Accepted: 03/30/2024] [Indexed: 04/08/2024]
Abstract
Transition metal ions are structural and catalytic cofactors of many proteins including human carbonic anhydrase (CA), a Zn-dependent hydrolase. Sulfonamide inhibitors of CA recognize and form a coordination bond with the Zn ion located in the active site of the enzyme. The Zn ion may be removed or substituted with other metal ions. Such CA protein retains the structure and could serve as a tool to study metal ion role in the recognition and binding affinity of inhibitor molecules. We measured the affinities of selected divalent transition metal ions, including Mn, Fe, Co, Ni, Cu, Cd, Hg, and Zn to metal-free CA isozymes CA I, CA II, and CAIX by fluorescence-based thermal shift assay, prepared metal-substituted CAs, and determined binding of diverse sulfonamide compounds. Sulfonamide inhibitor binding to metal substituted CA followed a U-shape pH dependence. The binding was dissected to contributing binding-linked reactions and the intrinsic binding reaction affinity was calculated. This value is independent of pH and protonation reactions that occur simultaneously upon binding native CA and as demonstrated here, to metal substituted CA. Sulfonamide inhibitor binding to cancer-associated isozyme CAIX diminished in the order: Zn > Co > Hg > Cu > Cd > Mn > Ni. Energetic contribution of the inhibitor-metal coordination bond was determined for all above metals. The understanding of the principles of metal influence on ligand affinity and selectivity should help design new drugs targeting metalloenzymes.
Collapse
Affiliation(s)
- Denis Baronas
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Birutė Knašienė
- Center for Physical Sciences and Technology, Saulėtekio 3, Vilnius LT-10257, Lithuania
| | - Aurelija Mickevičiūtė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Jelena Jachno
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Evaldas Naujalis
- Center for Physical Sciences and Technology, Saulėtekio 3, Vilnius LT-10257, Lithuania
| | - Asta Zubrienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio 7, Vilnius LT-10257, Lithuania.
| |
Collapse
|
2
|
Cutright AJ, Al Mohanna T, Matthews EL, Aulds JM, Thornton JA, Stokes SL, Emerson JP. Calorimetric analysis of AdcR and its interactions with zinc(II) and DNA. J Inorg Biochem 2023; 247:112305. [PMID: 37441924 DOI: 10.1016/j.jinorgbio.2023.112305] [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: 04/18/2023] [Revised: 06/09/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
Zinc(II) ions play critical roles in all known life as structurally important stabilizing ions in proteins, catalytically active metals in enzymes, and signaling agents impacting physiological changes. To maintain homeostasis, the intracellular concentration of zinc(II) is strictly controlled by a family of metal-regulatory proteins in both prokaryotic and eukaryotic organisms. In S. pneumoniae, there are two proteins that share responsibility for Zn2+ homeostasis, one of them is the Adhesin Competence Repressor (AdcR) and it binds to a specific double-stranded DNA binding domain (dsDNA). AdcR has been structurally characterized containing two zinc(II) metal centers per monomeric unit. Here we report data collected from differential scanning calorimetry (DSC) experiments aimed to measure the structural stability of AdcR, the fully complimented Zn2AdcR complex, and the protein/DNA complex Zn2AdcR/dsDNA. Thermograms collected from DSC experiments yielded endothermic unfolding events for AdcR, Zn2AdcR, and Zn2AdcR/dsDNA complex at 55.6, 70.2, and 56.6 °C, respectively. A non-two state unfolding model best fits the data, giving ΔH terms associated with these thermal unfolding events of 5.1, 7.1, and 4.9 kcal/mol. These data allow for the development of a thermodynamic cycle connecting both zinc(II) and DNA binding to AdcR. Furthermore, pairing this newly reported data with known association constants for zinc(II) and DNA binding allowed for the generation of thermodynamic profiles for both zinc(II) binding to AdcR and Zn2AdcR binding to DNA, which show both are decisively entropy-driven processes.
Collapse
Affiliation(s)
- Alexander J Cutright
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, United States
| | - Thualfeqar Al Mohanna
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, United States
| | - Erin L Matthews
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, United States
| | - James M Aulds
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, United States
| | - Justin A Thornton
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, United States
| | - Sean L Stokes
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, United States
| | - Joseph P Emerson
- Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, United States.
| |
Collapse
|
3
|
Dürr SL, Levy A, Rothlisberger U. Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins. Nat Commun 2023; 14:2713. [PMID: 37169763 PMCID: PMC10175565 DOI: 10.1038/s41467-023-37870-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/29/2023] [Indexed: 05/13/2023] Open
Abstract
Metal ions are essential cofactors for many proteins and play a crucial role in many applications such as enzyme design or design of protein-protein interactions because they are biologically abundant, tether to the protein using strong interactions, and have favorable catalytic properties. Computational design of metalloproteins is however hampered by the complex electronic structure of many biologically relevant metals such as zinc . In this work, we develop two tools - Metal3D (based on 3D convolutional neural networks) and Metal1D (solely based on geometric criteria) to improve the location prediction of zinc ions in protein structures. Comparison with other currently available tools shows that Metal3D is the most accurate zinc ion location predictor to date with predictions within 0.70 ± 0.64 Å of experimental locations. Metal3D outputs a confidence metric for each predicted site and works on proteins with few homologes in the protein data bank. Metal3D predicts a global zinc density that can be used for annotation of computationally predicted structures and a per residue zinc density that can be used in protein design workflows. Currently trained on zinc, the framework of Metal3D is readily extensible to other metals by modifying the training data.
Collapse
Affiliation(s)
- Simon L Dürr
- Laboratory of Computational Chemistry and Biochemistry,Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Andrea Levy
- Laboratory of Computational Chemistry and Biochemistry,Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry,Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
| |
Collapse
|
4
|
Gao S, Campbell JX, Oas TG, Franz KJ. Multiple Modes of Zinc Binding to Histatin 5 Revealed by Buffer-Independent Thermodynamics. Inorg Chem 2023; 62:7087-7096. [PMID: 37083393 DOI: 10.1021/acs.inorgchem.3c00608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Histatin 5 (Hist5) is an antimicrobial peptide found in human saliva as part of the innate immune system. Hist5 can bind several metal ions in vitro, and Zn2+ has been shown to function as an inhibitory switch to regulate the peptide's biological activity against the opportunistic fungal pathogen Candida albicans in cell culture. Here, we studied Zn2+ binding to Hist5 at four temperatures from 15 to 37 °C using isothermal titration calorimetry to obtain thermodynamic parameters that were corrected for competing buffer effects. Hist5 bound Zn2+ with a buffer-dependent association constant of ∼105 M-1 and a buffer-independent association constant of ∼6 × 106 M-1 at pH 7.4 and at all temperatures tested. Zn2+ binding was both enthalpically and entropically favorable, with larger entropic contributions at 15 °C and larger enthalpic contributions at 37 °C. Additionally, the Zn:Hist5 binding stoichiometry increased from 1:1 to 2:1 as temperature increased. The enthalpy-entropy compensation and the variable stoichiometry lead us to propose a model in which the Zn-Hist5 complex exists in an equilibrium between two distinct binding modes with different Zn:Hist5 stoichiometries. The in-depth thermodynamic analysis presented herein may help illuminate the biophysical basis for Zn-dependent changes in the antifungal activity of Hist5.
Collapse
Affiliation(s)
- Sean Gao
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Joanna X Campbell
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Terrence G Oas
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Katherine J Franz
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| |
Collapse
|
5
|
Xu JX, Alom MS, Yadav R, Fitzkee NC. Predicting protein function and orientation on a gold nanoparticle surface using a residue-based affinity scale. Nat Commun 2022; 13:7313. [PMID: 36437251 PMCID: PMC9701677 DOI: 10.1038/s41467-022-34749-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/07/2022] [Indexed: 11/28/2022] Open
Abstract
The orientation adopted by proteins on nanoparticle surfaces determines the nanoparticle's bioactivity and its interactions with living systems. Here, we present a residue-based affinity scale for predicting protein orientation on citrate-gold nanoparticles (AuNPs). Competitive binding between protein variants accounts for thermodynamic and kinetic aspects of adsorption in this scale. For hydrophobic residues, the steric considerations dominate, whereas electrostatic interactions are critical for hydrophilic residues. The scale rationalizes the well-defined binding orientation of the small GB3 protein, and it subsequently predicts the orientation and active site accessibility of two enzymes on AuNPs. Additionally, our approach accounts for the AuNP-bound activity of five out of six additional enzymes from the literature. The model developed here enables high-throughput predictions of protein behavior on nanoparticles, and it enhances our understanding of protein orientation in the biomolecular corona, which should greatly enhance the performance and safety of nanomedicines used in vivo.
Collapse
Affiliation(s)
- Joanna Xiuzhu Xu
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Md Siddik Alom
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Rahul Yadav
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Paul TK, Taraphder S. Molecular modelling of two coordination states of Zn(II) ion at the active site of human carbonic anhydrase II. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
8
|
Effendi SSW, Tan SI, Ting WW, Ng IS. Genetic design of co-expressed Mesorhizobium loti carbonic anhydrase and chaperone GroELS to enhancing carbon dioxide sequestration. Int J Biol Macromol 2020; 167:326-334. [PMID: 33275972 DOI: 10.1016/j.ijbiomac.2020.11.189] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/20/2020] [Accepted: 11/27/2020] [Indexed: 12/18/2022]
Abstract
Mesorhizobium loti carbonic anhydrase (MlCA), an intrinsically high catalytic enzyme, has been employed for carbon dioxide capture and sequestration. However, recombinant expression of MlCA in Escherichia coli often forms inclusion bodies. Hence, protein partners such as fusion-tags and molecular chaperones are involved in regarding reduce the harshness of protein folding. TrxA-tag and GroELS have been chosen to co-express with MlCA in E. coli under an inducible T7 promoter or a constitutive J23100 promoter to compare productivity and activity. The results possessed that coupling protein partners effectively increased soluble MlCA up to 2.9-folds under T7 promoter, thus enhancing the CA activity by 120% and achieving a 5.2-folds turnover rate. Besides, it has also shifted the optimum temperature from 40 °C to 50 °C, promoted stability in the broad pH range (4.5 to 9.5) and the presence of various metal ions. Based on the in vitro assay and isothermal titration calorimetry (ITC) analysis, GroELS enhancing CA activity was due to change the intrinsic thermodynamic properties of the enzyme from endothermic to exothermic reaction (i.e., ∆H = 89.8 to -121.8 kJ/mol). Therefore, the collaboration of TrxA-MlCA with GroELS successfully augmented CO2 biomineralization.
Collapse
Affiliation(s)
- Sefli Sri Wahyu Effendi
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Shih-I Tan
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - Wan-Wen Ting
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan, ROC.
| |
Collapse
|
9
|
Zoppi C, Nocentini A, Supuran CT, Pratesi A, Messori L. Native mass spectrometry of human carbonic anhydrase I and its inhibitor complexes. J Biol Inorg Chem 2020; 25:979-993. [PMID: 32926233 PMCID: PMC7584553 DOI: 10.1007/s00775-020-01818-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/30/2020] [Indexed: 02/03/2023]
Abstract
Abstract Native mass spectrometry is a potent technique to study and characterize biomacromolecules in their native state. Here, we have applied this method to explore the solution chemistry of human carbonic anhydrase I (hCA I) and its interactions with four different inhibitors, namely three sulfonamide inhibitors (AAZ, MZA, SLC-0111) and the dithiocarbamate derivative of morpholine (DTC). Through high-resolution ESI-Q-TOF measurements, the native state of hCA I and the binding of the above inhibitors were characterized in the molecular detail. Native mass spectrometry was also exploited to assess the direct competition in solution among the various inhibitors in relation to their affinity constants. Additional studies were conducted on the interaction of hCA I with the metallodrug auranofin, under various solution and instrumental conditions. Auranofin is a selective reagent for solvent-accessible free cysteine residues, and its reactivity was analyzed also in the presence of CA inhibitors. Overall, our investigation reveals that native mass spectrometry represents an excellent tool to characterize the solution behavior of carbonic anhydrase. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-020-01818-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Carlotta Zoppi
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - Alessio Nocentini
- Department of Neurofarba, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via U. Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Claudiu T Supuran
- Department of Neurofarba, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via U. Schiff 6, 50019, Sesto Fiorentino, Italy
| | - Alessandro Pratesi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy.
| | - Luigi Messori
- Laboratory of Metals in Medicine (MetMed), Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy.
| |
Collapse
|
10
|
Kim Y, Hwang SW, Kim S, Lee YS, Kim TY, Lee SH, Kim SJ, Yoo HJ, Kim EN, Kweon MN. Dietary cellulose prevents gut inflammation by modulating lipid metabolism and gut microbiota. Gut Microbes 2020; 11:944-961. [PMID: 32138587 PMCID: PMC7524403 DOI: 10.1080/19490976.2020.1730149] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A Western diet comprising high fat, high carbohydrate, and low fiber content has been suggested to contribute to an increased prevalence of colitis. To clarify the effect of dietary cellulose (an insoluble fiber) on gut homeostasis, for 3 months mice were fed a high-cellulose diet (HCD) or a low-cellulose diet (LCD) based on the AIN-93G formulation. Histologic evaluation showed crypt atrophy and goblet cell depletion in the colons of LCD-fed mice. RNA-sequencing analysis showed a higher expression of genes associated with immune system processes, especially those of chemokines and their receptors, in the colon tissues of LCD-fed mice than in those of HCD-fed mice. The HCD was protective against dextran sodium sulfate-induced colitis in mice, while LCD exacerbated gut inflammation; however, the depletion of gut microbiota by antibiotic treatment diminished both beneficial and non-beneficial effects of the HCD and LCD on colitis, respectively. A comparative analysis of the cecal contents of mice fed the HCD or the LCD showed that the LCD did not influence the diversity of gut microbiota, but it resulted in a higher and lower abundance of Oscillibacter and Akkermansia organisms, respectively. Additionally, linoleic acid, nicotinate, and nicotinamide pathways were most affected by cellulose intake, while the levels of short-chain fatty acids were comparable in HCD- and LCD-fed mice. Finally, oral administration of Akkermansia muciniphila to LCD-fed mice elevated crypt length, increased goblet cells, and ameliorated colitis. These results suggest that dietary cellulose plays a beneficial role in maintaining gut homeostasis through the alteration of gut microbiota and metabolites.
Collapse
Affiliation(s)
- Yeji Kim
- Mucosal Immunology Laboratory, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea
| | - Sung Wook Hwang
- Mucosal Immunology Laboratory, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea,Department of Gastroenterology, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea
| | - Seungil Kim
- Mucosal Immunology Laboratory, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea
| | - Yong-Soo Lee
- Mucosal Immunology Laboratory, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea
| | - Tae-Young Kim
- Mucosal Immunology Laboratory, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea
| | - Su-Hyun Lee
- Mucosal Immunology Laboratory, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea
| | - Su Jung Kim
- Department of Convergence Medicine, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea
| | - Hyun Ju Yoo
- Department of Convergence Medicine, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea
| | - Eun Na Kim
- Department of Pathology, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea
| | - Mi-Na Kweon
- Mucosal Immunology Laboratory, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea,CONTACT Mi-Na Kweon Mucosal Immunology Laboratory, Department of Convergence Medicine, University of Ulsan College of Medicine/Asan Medical Center, Seoul, Republic of Korea
| |
Collapse
|
11
|
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.
Collapse
Affiliation(s)
- Danuta Witkowska
- Public Higher Medical Professional School in Opole, Katowicka 68, 45060 Opole, Poland.
| | | |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
Li M, Martinez S, Hausinger RP, Emerson JP. Thermodynamics of Iron(II) and Substrate Binding to the Ethylene-Forming Enzyme. Biochemistry 2018; 57:5696-5705. [PMID: 30183265 PMCID: PMC7199160 DOI: 10.1021/acs.biochem.8b00730] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ethylene-forming enzyme (EFE), like many other 2-oxoglutarate (2OG)-dependent nonheme iron(II) oxygenases, catalyzes the oxidative decarboxylation of 2OG to succinate and CO2 to generate a highly reactive iron species that hydroxylates a specific alkane C-H bond, in this case targeting l-arginine (Arg) for hydroxylation. However, the prominently observed reactivity of EFE is the transformation of 2OG into ethylene and three molecules of CO2. Crystallographic and biochemical studies have led to several proposed mechanisms for this 2-fold reactivity, but the detailed reaction steps are still obscure. Here, the thermodynamics associated with iron(II), 2OG, and Arg binding to EFE are studied using calorimetry (isothermal titration calorimetry and differential scanning calorimetry) to gain insight into how these binding equilibria organize the active site of EFE, which may have an impact on the O2 activation pathways observed in this system. Calorimetric data show that the addition of iron(II), Arg, and 2OG increases the stability over that of the apoenzyme, and there is distinctive cooperativity between substrate and cofactor binding. The energetics of binding of 2OG to Fe·EFE are consistent with a unique monodentate binding mode, which is different than the prototypical 2OG coordination mode in other 2OG-dependent oxygenases. This difference in the pre-O2 activation equilibria may be important for supporting the alternative ethylene-forming chemistry of EFE.
Collapse
Affiliation(s)
- Mingjie Li
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Salette Martinez
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, United States
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824-4320, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-4320, United States
| | - Joseph P. Emerson
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| |
Collapse
|
14
|
The Irving-Williams series and the 2-His-1-carboxylate facial triad: a thermodynamic study of Mn 2+, Fe 2+, and Co 2+ binding to taurine/α-ketoglutarate dioxygenase (TauD). J Biol Inorg Chem 2018; 23:785-793. [PMID: 29923040 DOI: 10.1007/s00775-018-1574-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/20/2018] [Indexed: 12/30/2022]
Abstract
Taurine/α-ketoglutarate (αKG) dioxygenase (TauD) is an E. coli nonheme Fe2+- and αKG-dependent metalloenzyme that catalyzes the hydroxylation of taurine, leading to the production of sulfite. The metal-dependent active site in TauD is formed by two histidine and one aspartate that coordinating to one face of an octahedral coordination geometry, known as the 2-His-1-carboxylate facial triad. This motif is found in many nonheme Fe2+ proteins, but there is limited information on the thermodynamic parameters that govern metal-ion binding to this site. Here, we report data from calorimetry and related biophysical techniques to generate complete thermodynamic profiles of Mn2+ and Co2+ binding to TauD, and these values are compared to the Fe2+ data reported earlier Henderson et al. (Inorg Chem 54: 2278-2283, 2015). The buffer-independent binding constants (K) were measured to be 1.6 × 106, 2.4 × 107, and 1.7 × 109, for Mn2+, Fe2+, and Co2+, respectively. The corresponding ΔG° values were calculated to be - 8.4, - 10.1, and - 12.5 kcal/mol, respectively. The metal-binding enthalpy changes (ΔH) for these binding events are - 11.1 (± 0.1), - 12.2 (± 0.1), and - 16.0 (± 0.6) kcal/mol, respectively. These data are fully consistent with the Irving-Williams series, which show an increasing affinity for transition metal ions across the periodic table. It appears that the periodic increase in affinity, however, is a result of a complicated summation of enthalpy terms (including favorable metal-ion coordination processes and unfavorable ionization events) and related entropy terms.
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
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]
|
17
|
Kalyanavenkataraman S, Nanjan P, Banerji A, Nair BG, Kumar GB. Discovery of arjunolic acid as a novel non-zinc binding carbonic anhydrase II inhibitor. Bioorg Chem 2016; 66:72-9. [PMID: 27038848 DOI: 10.1016/j.bioorg.2016.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/04/2016] [Accepted: 03/23/2016] [Indexed: 11/29/2022]
Abstract
Elevated levels of carbonic anhydrase II (CA II) have been shown to be associated with cardiac hypertrophy and heart failure. Although arjunolic acid (AA) has a diverse range of therapeutic applications including cardio-protection, there have been no reports on the effect of AA on CA II. The present study describes for the first time, the novel zinc independent inhibition of CA II by AA. The molecular docking studies of AA indicated that the hydroxyl group at C2 of the A-ring, which hydrogen bonds with the catalytic site residues (His64, Asn62 and Asn67), along with the gem-dimethyl group at C20 of the E-ring, greatly influences the inhibitory activity, independent of the catalytic zinc, unlike the inhibition observed with most CA II inhibitors. Among the triterpenoids tested viz. arjunolic acid, arjunic acid, asiatic acid, oleanolic acid and ursolic acid, AA was the most potent in inhibiting CA II in vitro with an IC50 of 9μM. It was interesting to note, that in spite of exhibiting very little differences in their structures, these triterpenoids exhibited vast differences in their inhibitory activities, with IC50 values ranging from 9μM to as high as 333μM. Furthermore, AA also inhibited the cytosolic activity of CA in H9c2 cardiomyocytes, as reflected by the decrease in acidification of the intracellular pH (pHi). The decreased acidification reduced the intracellular calcium levels, which further prevented the mitochondrial membrane depolarization. Thus, these studies provide a better understanding for establishing the novel molecular mechanism involved in CA II inhibition by the non-zinc binding inhibitor AA.
Collapse
Affiliation(s)
| | - Pandurangan Nanjan
- Amrita School of Biotechnology, Amrita University, Amritapuri Campus, Clappana P.O., Kollam 690 525, Kerala, India
| | - Asoke Banerji
- Amrita School of Biotechnology, Amrita University, Amritapuri Campus, Clappana P.O., Kollam 690 525, Kerala, India
| | - Bipin G Nair
- Amrita School of Biotechnology, Amrita University, Amritapuri Campus, Clappana P.O., Kollam 690 525, Kerala, India
| | - Geetha B Kumar
- Amrita School of Biotechnology, Amrita University, Amritapuri Campus, Clappana P.O., Kollam 690 525, Kerala, India.
| |
Collapse
|
18
|
Siek S, Dixon NA, Kumar M, Kraus JS, Wells KR, Rowe BW, Kelley SP, Zeller M, Yap GPA, Papish ET. Synthesis of Biomimetic Zinc Complexes for CO2 Activation and the Influence of Steric Changes in the Ttz Ligands [Ttz = Tris(triazolyl)borate]. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500819] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sopheavy Siek
- Department of ChemistryThe University of AlabamaBox 87033635487‐0336TuscaloosaAlabamaUSA
| | - Natalie A. Dixon
- Department of ChemistryDrexel University3141 Chestnut St.19104PhiladelphiaPAUSA
| | - Mukesh Kumar
- Department of ChemistryDrexel University3141 Chestnut St.19104PhiladelphiaPAUSA
| | - Jodi S. Kraus
- Department of ChemistryDrexel University3141 Chestnut St.19104PhiladelphiaPAUSA
| | - Kirsten R. Wells
- Department of ChemistrySalisbury University1101 Camden Ave.21801SalisburyMDUSA
| | - Brittany W. Rowe
- Department of ChemistrySalisbury University1101 Camden Ave.21801SalisburyMDUSA
| | - Steven P. Kelley
- Department of ChemistryThe University of AlabamaBox 87033635487‐0336TuscaloosaAlabamaUSA
| | - Matthias Zeller
- Department of ChemistryYoungstown State UniversityOne University Plaza44555YoungstownOHUSA
| | - Glenn P. A. Yap
- Department of Chemistry and BiochemistryUniversity of Delaware102 Brown Laboratory19716NewarkDEUSA
| | - Elizabeth T. Papish
- Department of ChemistryThe University of AlabamaBox 87033635487‐0336TuscaloosaAlabamaUSA
| |
Collapse
|
19
|
Bou-Abdallah F, Giffune TR. The thermodynamics of protein interactions with essential first row transition metals. Biochim Biophys Acta Gen Subj 2015; 1860:879-891. [PMID: 26569121 DOI: 10.1016/j.bbagen.2015.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/27/2015] [Accepted: 11/01/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND The binding of metal ions to proteins is a crucial process required for their catalytic activity, structural stability and/or functional regulation. Isothermal titration calorimetry provides a wealth of fundamental information which when combined with structural data allow for a much deeper understanding of the underlying molecular mechanism. SCOPE OF REVIEW A rigorous understanding of any molecular interaction requires in part an in-depth quantification of its thermodynamic properties. Here, we provide an overview of recent studies that have used ITC to quantify the interaction of essential first row transition metals with relevant proteins and highlight major findings from these thermodynamic studies. GENERAL SIGNIFICANCE The thermodynamic characterization of metal ion-protein interactions is one important step to understanding the role that metal ions play in living systems. Such characterization has important implications not only to elucidating proteins' structure-function relationships and biological properties but also in the biotechnology sector, medicine and drug design particularly since a number of metal ions are involved in several neurodegenerative diseases. MAJOR CONCLUSIONS Isothermal titration calorimetry measurements can provide complete thermodynamic profiles of any molecular interaction through the simultaneous determination of the reaction binding stoichiometry, binding affinity as well as the enthalpic and entropic contributions to the free energy change thus enabling a more in-depth understanding of the nature of these interactions.
Collapse
Affiliation(s)
- Fadi Bou-Abdallah
- State University of New York at Potsdam, Potsdam, NY 13676, United States.
| | - Thomas R Giffune
- State University of New York at Potsdam, Potsdam, NY 13676, United States
| |
Collapse
|
20
|
Johnson RA, Manley OM, Spuches AM, Grossoehme NE. Dissecting ITC data of metal ions binding to ligands and proteins. Biochim Biophys Acta Gen Subj 2015; 1860:892-901. [PMID: 26327285 DOI: 10.1016/j.bbagen.2015.08.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/19/2015] [Accepted: 08/25/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND ITC is a powerful technique that can reliably assess the thermodynamic underpinnings of a wide range of binding events. When metal ions are involved, complications arise in evaluating the data due to unavoidable solution chemistry that includes metal speciation and a variety of linked equilibria. SCOPE OF REVIEW This paper identifies these concerns, provides recommendations to avoid common mistakes, and guides the reader through the mathematical treatment of ITC data to arrive at a set of thermodynamic state functions that describe identical chemical events and, ideally, are independent of solution conditions. Further, common metal chromophores used in biological metal sensing studies are proposed as a robust system to determine unknown solution competition. MAJOR CONCLUSIONS Metal ions present several complications in ITC experiments. This review presents strategies to avoid these pitfalls and proposes and experimentally validates mathematical approaches to deconvolute complex equilibria that exist in these systems. GENERAL SIGNIFICANCE This review discusses the wide range of complications that exists in metal-based ITC experiments. It provides a starting point for scientists new to this field and articulates concerns that will help experienced researchers troubleshoot experiments.
Collapse
Affiliation(s)
- Rachel A Johnson
- Department of Chemistry, East Carolina University, Greenville, NC 27858, United States
| | - Olivia M Manley
- Department of Chemistry, Physics and Geology, Winthrop University, Rock Hill, SC 29730, United States
| | - Anne M Spuches
- Department of Chemistry, East Carolina University, Greenville, NC 27858, United States.
| | - Nicholas E Grossoehme
- Department of Chemistry, Physics and Geology, Winthrop University, Rock Hill, SC 29730, United States.
| |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Henderson KL, Müller TA, Hausinger RP, Emerson JP. Calorimetric assessment of Fe(2+) binding to α-ketoglutarate/taurine dioxygenase: ironing out the energetics of metal coordination by the 2-His-1-carboxylate facial triad. Inorg Chem 2015; 54:2278-83. [PMID: 25668068 DOI: 10.1021/ic502881q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The thermodynamic properties of Fe(2+) binding to the 2-His-1-carboxylate facial triad in α-ketoglutarate/taurine dioxygenase (TauD) were explored using isothermal titration calorimetry. Direct titrations of Fe(2+) into TauD and chelation experiments involving the titration of ethylenediaminetetraacetic acid into Fe(2+)-TauD were performed under an anaerobic environment to yield a binding equilibrium of 2.4 (±0.1) × 10(7) (Kd = 43 nM) and a ΔG° value of -10.1 (±0.03) kcal/mol. Further analysis of the enthalpy/entropy contributions indicates a highly enthalpic binding event, where ΔH = -11.6 (±0.3) kcal/mol. Investigations into the unfavorable entropy term led to the observation of water molecules becoming organized within the Fe(2+)-TauD structure.
Collapse
Affiliation(s)
- Kate L Henderson
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
| | | | | | | |
Collapse
|
23
|
Plegaria JS, Pecoraro VL. Sculpting Metal-binding Environments in De Novo Designed Three-helix Bundles. Isr J Chem 2015; 55:85-95. [PMID: 29353917 PMCID: PMC5771423 DOI: 10.1002/ijch.201400146] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
De novo protein design is a biologically relevant approach used to study the active centers of native metalloproteins. In this review, we will first discuss the design process in achieving α3D, a de novo designed three-helix bundle peptide with a well-defined fold. We will then cover our recent work in functionalizing the α3D framework by incorporating a tris(cysteine) and tris(histidine) motif. Our first design contains the thiol-rich sites found in metalloregulatory proteins that control the levels of toxic metal ions (Hg, Cd, and Pb). The latter design recapitulates the catalytic site and activity of a natural metalloenzyme carbonic anhydrase. The review will conclude with future design goals aimed at introducing an asymmetric metal-binding site in the α3D framework.
Collapse
Affiliation(s)
- Jefferson S Plegaria
- 930 North University Ave, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 (USA)
| | - Vincent L Pecoraro
- 930 North University Ave, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 (USA)
| |
Collapse
|
24
|
Falcón‐León MP, Tapia‐Benavides AR, Tlahuext H, Galán‐Vidal C, Suarez‐Castillo OR, Tlahuextl M. The Effect of Zn
II
Coordination on the Addition of 2‐(Aminomethyl)benzimidazole to Acrylonitrile. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Martha P. Falcón‐León
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, Carr. Pachuca‐Tulancingo km 4.5, Hidalgo, México CP 42184, http://www.uaeh.edu.mx
| | - Antonio R. Tapia‐Benavides
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, Carr. Pachuca‐Tulancingo km 4.5, Hidalgo, México CP 42184, http://www.uaeh.edu.mx
| | - Hugo Tlahuext
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Morelos, Mexico CP 62209
| | - Carlos Galán‐Vidal
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, Carr. Pachuca‐Tulancingo km 4.5, Hidalgo, México CP 42184, http://www.uaeh.edu.mx
| | - Oscar R. Suarez‐Castillo
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, Carr. Pachuca‐Tulancingo km 4.5, Hidalgo, México CP 42184, http://www.uaeh.edu.mx
| | - Margarita Tlahuextl
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Hidalgo, Carr. Pachuca‐Tulancingo km 4.5, Hidalgo, México CP 42184, http://www.uaeh.edu.mx
| |
Collapse
|
25
|
Cangelosi VM, Deb A, Penner-Hahn JE, Pecoraro VL. A De Novo Designed Metalloenzyme for the Hydration of CO2. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404925] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
26
|
Cangelosi VM, Deb A, Penner-Hahn JE, Pecoraro VL. A de novo designed metalloenzyme for the hydration of CO2. Angew Chem Int Ed Engl 2014; 53:7900-3. [PMID: 24943466 DOI: 10.1002/anie.201404925] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Indexed: 11/07/2022]
Abstract
Protein design will ultimately allow for the creation of artificial enzymes with novel functions and unprecedented stability. To test our current mastery of nature's approach to catalysis, a Zn(II) metalloenzyme was prepared using de novo design. α3DH3 folds into a stable single-stranded three-helix bundle and binds Zn(II) with high affinity using His3 O coordination. The resulting metalloenzyme catalyzes the hydration of CO2 better than any small molecule model of carbonic anhydrase and with an efficiency within 1400-fold of the fastest carbonic anhydrase isoform, CAII, and 11-fold of CAIII.
Collapse
|
27
|
Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | |
Collapse
|
28
|
Syntheses and structural studies of hexa- and pentacoordinated Zn complexes derived from 2-(aminomethyl)benzimidazole and water. Struct Chem 2014. [DOI: 10.1007/s11224-014-0416-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
29
|
Zastrow M, Pecoraro VL. Designing hydrolytic zinc metalloenzymes. Biochemistry 2014; 53:957-78. [PMID: 24506795 PMCID: PMC3985962 DOI: 10.1021/bi4016617] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 01/23/2014] [Indexed: 12/15/2022]
Abstract
Zinc is an essential element required for the function of more than 300 enzymes spanning all classes. Despite years of dedicated study, questions regarding the connections between primary and secondary metal ligands and protein structure and function remain unanswered, despite numerous mechanistic, structural, biochemical, and synthetic model studies. Protein design is a powerful strategy for reproducing native metal sites that may be applied to answering some of these questions and subsequently generating novel zinc enzymes. From examination of the earliest design studies introducing simple Zn(II)-binding sites into de novo and natural protein scaffolds to current studies involving the preparation of efficient hydrolytic zinc sites, it is increasingly likely that protein design will achieve reaction rates previously thought possible only for native enzymes. This Current Topic will review the design and redesign of Zn(II)-binding sites in de novo-designed proteins and native protein scaffolds toward the preparation of catalytic hydrolytic sites. After discussing the preparation of Zn(II)-binding sites in various scaffolds, we will describe relevant examples for reengineering existing zinc sites to generate new or altered catalytic activities. Then, we will describe our work on the preparation of a de novo-designed hydrolytic zinc site in detail and present comparisons to related designed zinc sites. Collectively, these studies demonstrate the significant progress being made toward building zinc metalloenzymes from the bottom up.
Collapse
Affiliation(s)
| | - Vincent L. Pecoraro
- Department of Chemistry, University
of Michigan, Ann Arbor, Michigan 48109, United
States
| |
Collapse
|
30
|
Lauria A, Bonsignore R, Terenzi A, Spinello A, Giannici F, Longo A, Almerico AM, Barone G. Nickel(ii), copper(ii) and zinc(ii) metallo-intercalators: structural details of the DNA-binding by a combined experimental and computational investigation. Dalton Trans 2014; 43:6108-19. [DOI: 10.1039/c3dt53066c] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
31
|
Building reactive copper centers in human carbonic anhydrase II. J Biol Inorg Chem 2013; 18:595-8. [PMID: 23744511 DOI: 10.1007/s00775-013-1009-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/14/2013] [Indexed: 10/26/2022]
Abstract
Reengineering metalloproteins to generate new biologically relevant metal centers is an effective a way to test our understanding of the structural and mechanistic features that steer chemical transformations in biological systems. Here, we report thermodynamic data characterizing the formation of two type-2 copper sites in carbonic anhydrase and experimental evidence showing one of these new, copper centers has characteristics similar to a variety of well-characterized copper centers in synthetic models and enzymatic systems. Human carbonic anhydrase II is known to bind two Cu(2+) ions; these binding events were explored using modern isothermal titration calorimetry techniques that have become a proven method to accurately measure metal-binding thermodynamic parameters. The two Cu(2+)-binding events have different affinities (K a approximately 5 × 10(12) and 1 × 10(10)), and both are enthalpically driven processes. Reconstituting these Cu(2+) sites under a range of conditions has allowed us to assign the Cu(2+)-binding event to the three-histidine, native, metal-binding site. Our initial efforts to characterize these Cu(2+) sites have yielded data that show distinctive (and noncoupled) EPR signals associated with each copper-binding site and that this reconstituted enzyme can activate hydrogen peroxide to catalyze the oxidation of 2-aminophenol.
Collapse
|
32
|
Zastrow ML, Pecoraro VL. Influence of active site location on catalytic activity in de novo-designed zinc metalloenzymes. J Am Chem Soc 2013; 135:5895-903. [PMID: 23516959 DOI: 10.1021/ja401537t] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
While metalloprotein design has now yielded a number of successful metal-bound and even catalytically active constructs, the question of where to put a metal site along a linear, repetitive sequence has not been thoroughly addressed. Often several possibilities in a given sequence may exist that would appear equivalent but may in fact differ for metal affinity, substrate access, or protein dynamics. We present a systematic variation of active site location for a hydrolytically active ZnHis3O site contained within a de novo-designed three-stranded coiled coil. We find that the maximal rate, substrate access, and metal-binding affinity are dependent on the selected position, while catalytic efficiency for p-nitrophenyl acetate hydrolysis can be retained regardless of the location of the active site. This achievement demonstrates how efficient, tailor-made enzymes which control rate, pKa, substrate and solvent access (and selectivity), and metal-binding affinity may be realized. These findings may be applied to the more advanced de novo design of constructs containing secondary interactions, such as hydrogen-bonding channels. We are now confident that changes to location for accommodating such channels can be achieved without location-dependent loss of catalytic efficiency. These findings bring us closer to our ultimate goal of incorporating the secondary interactions we believe will be necessary in order to improve both active site properties and the catalytic efficiency to be competitive with the native enzyme, carbonic anhydrase.
Collapse
Affiliation(s)
- Melissa L Zastrow
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | |
Collapse
|