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Eade L, Sullivan MP, Allison TM, Goldstone DC, Hartinger CG. Not All Binding Sites Are Equal: Site Determination and Folding State Analysis of Gas-Phase Protein-Metallodrug Adducts. Chemistry 2024:e202400268. [PMID: 38472116 DOI: 10.1002/chem.202400268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
Modern approaches in metallodrug research focus on compounds that bind protein targets rather than DNA. However, the identification of protein targets and binding sites is challenging. Using intact mass spectrometry and proteomics, we investigated the binding of the antimetastatic agent RAPTA-C to the model proteins ubiquitin, cytochrome c, lysozyme, and myoglobin. Binding to cytochrome c and lysozyme was negligible. However, ubiquitin bound up to three Ru moieties, two of which were localized at Met1 and His68 as [Ru(cym)], and [Ru(cym)] or [Ru(cym)(PTA)] adducts, respectively. Myoglobin bound up to four [Ru(cym)(PTA)] moieties and five sites were identified at His24, His36, His64, His81/82 and His113. Collision-induced unfolding (CIU) studies via ion-mobility mass spectrometry allowed measuring protein folding as a function of collisional activation. CIU of protein-RAPTA-C adducts showed binding of [Ru(cym)] to Met1 caused a significant compaction of ubiquitin, likely from N-terminal S-Ru-N chelation, while binding of [Ru(cym)(PTA)] to His residues of ubiquitin or myoglobin induced a smaller effect. Interestingly, the folded state of ubiquitin formed by His functionalization was more stable than Met1 metalation. The data suggests that selective metalation of amino acids at different positions on the protein impacts the conformation and potentially the biological activity of anticancer compounds.
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Affiliation(s)
- Liam Eade
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Matthew P Sullivan
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Timothy M Allison
- Biomolecular Interaction Centre, School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - David C Goldstone
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Christian G Hartinger
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
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2
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Sharma S, Takkella D, Vishwakarma J, Gavvala K. Spectroscopy and dynamics of beta-lactoglobulin complexed with rifampicin. J Biomol Struct Dyn 2023:1-14. [PMID: 37904335 DOI: 10.1080/07391102.2023.2275191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023]
Abstract
In this paper, we report the binding interaction of milk protein, beta-lactoglobulin (BLG), with an antibiotic against tuberculosis, rifampicin (RIF). BLG intrinsic fluorescence from tryptophan (Trp) amino acids was monitored to understand protein-drug interactions. Binding parameters and stoichiometry were estimated with the help of fluorescence spectral changes. Synchronous fluorescence spectroscopy was employed to exclusively monitor the Trp and Tyrosine (Tyr) environment in the presence of RIF. With the help of steady state fluorescence at different temperatures supported by time-resolved fluorescence, we confirmed that the protein forms a static complex with RIF. Thermodynamic parameters, ΔH and ΔS values, showed the involvement of hydrophobic forces between the RIF and BLG. Competitive displacement assay with ANS confirmed the BLG calyx as the binding site for RIF. Energy transfer mechanism from Trp to RIF was attributed to the fluorescence changes in protein upon complexation. The Förster resonance energy transfer (FRET) was used to find distance, energy transfer efficiency and rate of energy transfer between donor (BLG) and acceptor (RIF). Fourier-transform infrared (FTIR) spectroscopy was utilized for estimating changes in the secondary structure of BLG induced by RIF. Molecular docking was used to visualise the binding location of RIF on BLG. Molecular dynamics (MD) simulation studies showed a consistent binding interactions between BLG and RIF during the 100 ns simulation period and this well supported the increased beta sheet content in FTIR. Overall our results establish the potential of intrinsic fluorescence of BLG in combination with biophysical tools to rationalize drug-protein interactions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sudhanshu Sharma
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, India
| | - Dineshbabu Takkella
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, India
| | - Jyoti Vishwakarma
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, India
| | - Krishna Gavvala
- Department of Chemistry, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, India
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Bonarek P, Mularczyk D, Loch JI, Kurpiewska K, Dziedzicka-Wasylewska M. β-Lactoglobulin variants as potential carriers of pramoxine: Comprehensive structural and biophysical studies. J Mol Recognit 2023; 36:e3052. [PMID: 37610054 DOI: 10.1002/jmr.3052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
β-Lactoglobulin (BLG) is a member of the lipocalin family. As other proteins from this group, BLG can be modified to bind specifically compounds of medical interests. The aim of this study was to evaluate the role of two mutations, L39Y and L58F, in the binding of topical anesthetic pramoxine (PRM) to β-lactoglobulin. Circular dichroism spectroscopy, isothermal titration calorimetry (ITC), and X-ray crystallography were used to understand the mechanisms of BLG-PRM interactions. Studies were performed for three new BLG mutants: L39Y, L58F, and L39Y/L58F. ITC measurements indicated a significant increase in the affinity to the PRM of variants L58F and L39Y. Measurements taken for the double mutant L39Y/L58F showed the additivity of two mutations leading to about 80-fold increase in the affinity to PRM in comparison to natural protein BLG from bovine milk. The determined crystal structures revealed that pramoxine is accommodated in the β-barrel interior of BLG mutants and stabilized by hydrophobic interactions. The observed additive effect of two mutations on drug binding opens the possibility for further designing of new BLG variants with high affinity to selected drugs.
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Affiliation(s)
- Piotr Bonarek
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
| | - Dorota Mularczyk
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
| | - Joanna I Loch
- Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Jagiellonian University, Kraków, Poland
| | - Katarzyna Kurpiewska
- Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Jagiellonian University, Kraków, Poland
| | - Marta Dziedzicka-Wasylewska
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Kraków, Poland
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Wang B, Yan C, Lou S, Emani P, Li B, Xu M, Kong X, Meyerson W, Yang YT, Lee D, Gerstein M. Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions. Structure 2019; 27:1469-1481.e3. [PMID: 31279629 DOI: 10.1016/j.str.2019.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 02/14/2019] [Accepted: 06/03/2019] [Indexed: 11/17/2022]
Abstract
A key issue in drug design is how population variation affects drug efficacy by altering binding affinity (BA) in different individuals, an essential consideration for government regulators. Ideally, we would like to evaluate the BA perturbations of millions of single-nucleotide variants (SNVs). However, only hundreds of protein-drug complexes with SNVs have experimentally characterized BAs, constituting too small a gold standard for straightforward statistical model training. Thus, we take a hybrid approach: using physically based calculations to bootstrap the parameterization of a full model. In particular, we do 3D structure-based docking on ∼10,000 SNVs modifying known protein-drug complexes to construct a pseudo gold standard. Then we use this augmented set of BAs to train a statistical model combining structure, ligand and sequence features and illustrate how it can be applied to millions of SNVs. Finally, we show that our model has good cross-validated performance (97% AUROC) and can also be validated by orthogonal ligand-binding data.
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Affiliation(s)
- Bo Wang
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Chengfei Yan
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Shaoke Lou
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Prashant Emani
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Bian Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Min Xu
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Xiangmeng Kong
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - William Meyerson
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Yale School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Yucheng T Yang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Donghoon Lee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA.
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Hernandez Maganhi S, Jensen P, Caracelli I, Zukerman Schpector J, Fröhling S, Friedman R. Palbociclib can overcome mutations in cyclin dependent kinase 6 that break hydrogen bonds between the drug and the protein. Protein Sci 2017; 26:870-879. [PMID: 28168755 PMCID: PMC5368058 DOI: 10.1002/pro.3135] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 12/27/2016] [Accepted: 01/29/2017] [Indexed: 01/04/2023]
Abstract
Inhibition of cyclin dependent kinases (CDKs) 4 and 6 prevent cells from entering the synthesis phase of the cell cycle. CDK4 and 6 are therefore important drug targets in various cancers. The selective CDK4/6 inhibitor palbociclib is approved for the treatment of breast cancer and has shown activity in a cellular model of mixed lineage leukaemia (MLL)‐rearranged acute myeloid leukaemia (AML). We studied the interactions of palbociclib and CDK6 using molecular dynamics simulations. Analysis of the simulations suggested several interactions that stabilized the drug in its binding site and that were not observed in the crystal structure of the protein‐drug complex. These included a hydrogen bond to His 100 that was hitherto not reported and several hydrophobic contacts. Evolutionary‐based bioinformatic analysis was used to suggest two mutants, D163G and H100L that would potentially yield drug resistance, as they lead to loss of important protein–drug interactions without hindering the viability of the protein. One of the mutants involved a change in the glycine of the well‐conserved DFG motif of the kinase. Interestingly, CDK6‐dependent human AML cells stably expressing either mutant retained sensitivity to palbociclib, indicating that the protein‐drug interactions are not affected by these. Furthermore, the cells were proliferative in the absence of palbociclib, indicating that the Asp to Gly mutation in the DFG motif did not interfere with the catalytic activity of the protein. PDB Code(s): 2EUF
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Affiliation(s)
| | - Patrizia Jensen
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ignez Caracelli
- Department of Physics, Federal University of São Carlos, São Carlos, Brazil
| | | | - Stefan Fröhling
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden.,Centre of Excellence "Biomaterials Chemistry", Linnaeus University, 391 82 Kalmar, Sweden
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Georgieva ER, Borbat PP, Grushin K, Stoilova-McPhie S, Kulkarni NJ, Liang Z, Freed JH. Conformational Response of Influenza A M2 Transmembrane Domain to Amantadine Drug Binding at Low pH (pH 5.5). Front Physiol 2016; 7:317. [PMID: 27524969 PMCID: PMC4965473 DOI: 10.3389/fphys.2016.00317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/13/2016] [Indexed: 12/27/2022] Open
Abstract
The M2 protein from influenza A plays important roles in its viral cycle. It contains a single transmembrane helix, which oligomerizes into a homotetrameric proton channel that conducts in the low-pH environment of the host-cell endosome and Golgi apparatus, leading to virion uncoating at an early stage of infection. We studied conformational rearrangements that occur in the M2 core transmembrane domain residing on the lipid bilayer, flanked by juxtamembrane residues (M2TMD21-49 fragment), upon its interaction with amantadine drug at pH 5.5 when M2 is conductive. We also tested the role of specific mutation and lipid chain length. Electron spin resonance (ESR) spectroscopy and electron microscopy were applied to M2TMD21-49, labeled at the residue L46C with either nitroxide spin-label or Nanogold® reagent, respectively. Electron microscopy confirmed that M2TMD21-49 reconstituted into DOPC/POPS at 1:10,000 peptide-to-lipid molar ratio (P/L) either with or without amantadine, is an admixture of monomers, dimers, and tetramers, confirming our model based on a dimer intermediate in the assembly of M2TMD21-49. As reported by double electron-electron resonance (DEER), in DOPC/POPS membranes amantadine shifts oligomer equilibrium to favor tetramers, as evidenced by an increase in DEER modulation depth for P/L's ranging from 1:18,000 to 1:160. Furthermore, amantadine binding shortens the inter-spin distances (for nitroxide labels) by 5-8 Å, indicating drug induced channel closure on the C-terminal side. No such effect was observed for the thinner membrane of DLPC/DLPS, emphasizing the role of bilayer thickness. The analysis of continuous wave (cw) ESR spectra of spin-labeled L46C residue provides additional support to a more compact helix bundle in amantadine-bound M2TMD 21-49 through increased motional ordering. In contrast to wild-type M2TMD21-49, the amantadine-bound form does not exhibit noticeable conformational changes in the case of G34A mutation found in certain drug-resistant influenza strains. Thus, the inhibited M2TMD21-49 channel is a stable tetramer with a closed C-terminal exit pore. This work is aimed at contributing to the development of structure-based anti-influenza pharmaceuticals.
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Affiliation(s)
- Elka R Georgieva
- Department of Chemistry and Chemical Biology, Cornell UniversityIthaca, NY, USA; National Biomedical Center for Advanced ESR TechnologyIthaca, NY, USA
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell UniversityIthaca, NY, USA; National Biomedical Center for Advanced ESR TechnologyIthaca, NY, USA
| | - Kirill Grushin
- Department of Neuroscience and Cell Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston Galveston, TX, USA
| | - Svetla Stoilova-McPhie
- Department of Neuroscience and Cell Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch at Galveston Galveston, TX, USA
| | | | - Zhichun Liang
- Department of Chemistry and Chemical Biology, Cornell UniversityIthaca, NY, USA; National Biomedical Center for Advanced ESR TechnologyIthaca, NY, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell UniversityIthaca, NY, USA; National Biomedical Center for Advanced ESR TechnologyIthaca, NY, USA
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7
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Seckler JM, Leioatts N, Miao H, Grossfield A. The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures. Proteins 2013; 81:1792-801. [PMID: 23720322 DOI: 10.1002/prot.24325] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 04/12/2013] [Accepted: 04/19/2013] [Indexed: 11/07/2022]
Abstract
HIV-1 reverse transcriptase (RT) is a critical drug target for HIV treatment, and understanding the exact mechanisms of its function and inhibition would significantly accelerate the development of new anti-HIV drugs. It is well known that structure plays a critical role in protein function, but for RT, structural information has proven to be insufficient-despite enormous effort-to explain the mechanism of inhibition and drug resistance of non-nucleoside RT inhibitors. We hypothesize that the missing link is dynamics, information about the motions of the system. However, many of the techniques that give the best information about dynamics, such as solution nuclear magnetic resonance and molecular dynamics simulations, cannot be easily applied to a protein as large as RT. As an alternative, we combine elastic network modeling with simultaneous hierarchical clustering of structural and dynamic data. We present an extensive survey of the dynamics of RT bound to a variety of ligands and with a number of mutations, revealing a novel mechanism for drug resistance to non-nucleoside RT inhibitors. Hydrophobic core mutations restore active-state motion to multiple functionally significant regions of HIV-1 RT. This model arises out of a combination of structural and dynamic information, rather than exclusively from one or the other.
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Affiliation(s)
- James M Seckler
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, New York
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8
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Yanagawa M, Yamashita T, Shichida Y. Glutamate acts as a partial inverse agonist to metabotropic glutamate receptor with a single amino acid mutation in the transmembrane domain. J Biol Chem 2013; 288:9593-9601. [PMID: 23420844 PMCID: PMC3617263 DOI: 10.1074/jbc.m112.437780] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/15/2013] [Indexed: 11/06/2022] Open
Abstract
Metabotropic glutamate receptor (mGluR), a prototypical family 3 G protein-coupled receptor (GPCR), has served as a model for studying GPCR dimerization, and growing evidence has revealed that a glutamate-induced dimeric rearrangement promotes activation of the receptor. However, structural information of the seven-transmembrane domain is severely limited, in contrast to the well studied family 1 GPCRs including rhodopsins and adrenergic receptors. Homology modeling of mGluR8 transmembrane domain with rhodopsin as a template suggested the presence of a conserved water-mediated hydrogen-bonding network between helices VI and VII, which presumably constrains the receptor in an inactive conformation. We therefore conducted a mutational analysis to assess structural similarities between mGluR and family 1 GPCRs. Mutational experiments confirmed that the disruption of the hydrogen-bonding network by T789Y(6.43) mutation induced high constitutive activity. Unexpectedly, this high constitutive activity was suppressed by glutamate, the natural agonist ligand, indicating that glutamate acts as a partial inverse agonist to this mutant. Fluorescence energy transfer analysis of T789Y(6.43) suggested that the glutamate-induced reduction of the activity originated not from the dimeric rearrangement but from conformational changes within each protomer. Double mutational analysis showed that the specific interaction between Tyr-789(6.43) and Gly-831(7.45) in T789Y(6.43) mutant was important for this phenotype. Therefore, the present study is consistent with the notion that the metabotropic glutamate receptor shares a common activation mechanism with family 1 GPCRs, where rearrangement between helices VI and VII causes the active state formation.
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Affiliation(s)
- Masataka Yanagawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Takahiro Yamashita
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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Kimura T, Yeliseev AA, Vukoti K, Rhodes SD, Cheng K, Rice KC, Gawrisch K. Recombinant cannabinoid type 2 receptor in liposome model activates g protein in response to anionic lipid constituents. J Biol Chem 2012; 287:4076-87. [PMID: 22134924 PMCID: PMC3281699 DOI: 10.1074/jbc.m111.268425] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 11/29/2011] [Indexed: 11/06/2022] Open
Abstract
Human cannabinoid type 2 (CB(2)) receptor expressed in Escherichia coli was purified and successfully reconstituted in the functional form into lipid bilayers composed of POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS), and cholesteryl hemisuccinate (CHS). Reconstitution was performed by detergent removal from the protein/lipid/detergent mixed micelles either on an adsorbent column, or by rapid dilution to below the critical micelle concentration of detergent followed by removal of detergent monomers on a concentrator. Proteoliposomes prepared at a protein/phospholipid/CHS molar ratio of 1/620-650/210-220 are free of detergent as shown by (1)H NMR, have a homogeneous protein/lipid ratio shown by isopycnic gradient ultracentrifugation, and are small in size with a mean diameter of 150-200 nm as measured by dynamic light scattering. Functional integrity of the reconstituted receptor was confirmed by quantitative binding of (2)H-labeled agonist CP-55,940-d(6) measured by (2)H magic angle spinning NMR, as well as by activation of G protein. The efficiency of G protein activation by agonist-bound CB(2) receptor was affected by negative electric surface potentials of proteoliposomes controlled by the content of anionic CHS or POPS. The activation was highest at an anionic lipid content of about 50 mol %. There was no correlation between the efficiency of G protein activation and an increase of hydrocarbon chain order induced by CHS or cholesterol. The results suggest the importance of anionic lipids in regulating signal transduction by CB(2) receptor and other class A GPCR. The successful reconstitution of milligram quantities of pure, functional CB(2) receptor enables a wide variety of structural studies.
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Affiliation(s)
- Tomohiro Kimura
- From the Laboratory of Membrane Biochemistry and Biophysics, NIAAA, and
| | | | - Krishna Vukoti
- From the Laboratory of Membrane Biochemistry and Biophysics, NIAAA, and
| | - Steven D. Rhodes
- From the Laboratory of Membrane Biochemistry and Biophysics, NIAAA, and
| | - Kejun Cheng
- the Chemical Biology Research Branch, NIDA and NIAAA, National Institutes of Health, Bethesda, Maryland 20852
| | - Kenner C. Rice
- the Chemical Biology Research Branch, NIDA and NIAAA, National Institutes of Health, Bethesda, Maryland 20852
| | - Klaus Gawrisch
- From the Laboratory of Membrane Biochemistry and Biophysics, NIAAA, and
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Pantoom S, Vetter IR, Prinz H, Suginta W. Potent family-18 chitinase inhibitors: x-ray structures, affinities, and binding mechanisms. J Biol Chem 2011; 286:24312-23. [PMID: 21531720 PMCID: PMC3129211 DOI: 10.1074/jbc.m110.183376] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 03/20/2011] [Indexed: 11/06/2022] Open
Abstract
Six novel inhibitors of Vibrio harveyi chitinase A (VhChiA), a family-18 chitinase homolog, were identified by in vitro screening of a library of pharmacologically active compounds. Unlike the previously identified inhibitors that mimicked the reaction intermediates, crystallographic evidence from 14 VhChiA-inhibitor complexes showed that all of the inhibitor molecules occupied the outer part of the substrate-binding cleft at two hydrophobic areas. The interactions at the aglycone location are well defined and tightly associated with Trp-397 and Trp-275, whereas the interactions at the glycone location are patchy, indicating lower affinity and a loose interaction with two consensus residues, Trp-168 and Val-205. When Trp-275 was substituted with glycine (W275G), the binding affinity toward all of the inhibitors dramatically decreased, and in most structures two inhibitor molecules were found to stack against Trp-397 at the aglycone site. Such results indicate that hydrophobic interactions are important for binding of the newly identified inhibitors by the chitinase. X-ray data and isothermal microcalorimetry showed that the inhibitors occupied the active site of VhChiA in three different binding modes, including single-site binding, independent two-site binding, and sequential two-site binding. The inhibitory effect of dequalinium in the low nanomolar range makes this compound an extremely attractive lead compound for plausible development of therapeutics against human diseases involving chitinase-mediated pathologies.
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Affiliation(s)
- Supansa Pantoom
- From the Biochemistry-Electrochemistry Research Unit, Schools of Chemistry and Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand and
| | - Ingrid R. Vetter
- the Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Heino Prinz
- the Max Planck Institute for Molecular Physiology, 44227 Dortmund, Germany
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, Schools of Chemistry and Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand and
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Aertgeerts K, Skene R, Yano J, Sang BC, Zou H, Snell G, Jennings A, Iwamoto K, Habuka N, Hirokawa A, Ishikawa T, Tanaka T, Miki H, Ohta Y, Sogabe S. Structural analysis of the mechanism of inhibition and allosteric activation of the kinase domain of HER2 protein. J Biol Chem 2011; 286:18756-65. [PMID: 21454582 PMCID: PMC3099692 DOI: 10.1074/jbc.m110.206193] [Citation(s) in RCA: 232] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 03/09/2011] [Indexed: 11/06/2022] Open
Abstract
Aberrant signaling of ErbB family members human epidermal growth factor 2 (HER2) and epidermal growth factor receptor (EGFR) is implicated in many human cancers, and HER2 expression is predictive of human disease recurrence and prognosis. Small molecule kinase inhibitors of EGFR and of both HER2 and EGFR have received approval for the treatment of cancer. We present the first high resolution crystal structure of the kinase domain of HER2 in complex with a selective inhibitor to understand protein activation, inhibition, and function at the molecular level. HER2 kinase domain crystallizes as a dimer and suggests evidence for an allosteric mechanism of activation comparable with previously reported activation mechanisms for EGFR and HER4. A unique Gly-rich region in HER2 following the α-helix C is responsible for increased conformational flexibility within the active site and could explain the low intrinsic catalytic activity previously reported for HER2. In addition, we solved the crystal structure of the kinase domain of EGFR in complex with a HER2/EGFR dual inhibitor (TAK-285). Comparison with previously reported inactive and active EGFR kinase domain structures gave insight into the mechanism of HER2 and EGFR inhibition and may help guide the design and development of new cancer drugs with improved potency and selectivity.
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Affiliation(s)
- Kathleen Aertgeerts
- Takeda San Diego Inc, 10410 Science Center Drive, San Diego, California 92121, USA.
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12
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Lemke CT, Goudreau N, Zhao S, Hucke O, Thibeault D, Llinàs-Brunet M, White PW. Combined X-ray, NMR, and kinetic analyses reveal uncommon binding characteristics of the hepatitis C virus NS3-NS4A protease inhibitor BI 201335. J Biol Chem 2011; 286:11434-43. [PMID: 21270126 PMCID: PMC3064199 DOI: 10.1074/jbc.m110.211417] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 01/17/2011] [Indexed: 11/06/2022] Open
Abstract
Hepatitis C virus infection, a major cause of liver disease worldwide, is curable, but currently approved therapies have suboptimal efficacy. Supplementing these therapies with direct-acting antiviral agents has the potential to considerably improve treatment prospects for hepatitis C virus-infected patients. The critical role played by the viral NS3 protease makes it an attractive target, and despite its shallow, solvent-exposed active site, several potent NS3 protease inhibitors are currently in the clinic. BI 201335, which is progressing through Phase IIb trials, contains a unique C-terminal carboxylic acid that binds noncovalently to the active site and a bromo-quinoline substitution on its proline residue that provides significant potency. In this work we have used stopped flow kinetics, x-ray crystallography, and NMR to characterize these distinctive features. Key findings include: slow association and dissociation rates within a single-step binding mechanism; the critical involvement of water molecules in acid binding; and protein side chain rearrangements, a bromine-oxygen halogen bond, and profound pK(a) changes within the catalytic triad associated with binding of the bromo-quinoline moiety.
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Affiliation(s)
- Christopher T Lemke
- Boehringer Ingelheim (Canada) Ltd., Research and Development, Laval, Quebec, Canada.
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13
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Giorgetti S, Raimondi S, Pagano K, Relini A, Bucciantini M, Corazza A, Fogolari F, Codutti L, Salmona M, Mangione P, Colombo L, De Luigi A, Porcari R, Gliozzi A, Stefani M, Esposito G, Bellotti V, Stoppini M. Effect of tetracyclines on the dynamics of formation and destructuration of beta2-microglobulin amyloid fibrils. J Biol Chem 2011; 286:2121-31. [PMID: 21068391 PMCID: PMC3023509 DOI: 10.1074/jbc.m110.178376] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 11/03/2010] [Indexed: 12/31/2022] Open
Abstract
The discovery of methods suitable for the conversion in vitro of native proteins into amyloid fibrils has shed light on the molecular basis of amyloidosis and has provided fundamental tools for drug discovery. We have studied the capacity of a small library of tetracycline analogues to modulate the formation or destructuration of β2-microglobulin fibrils. The inhibition of fibrillogenesis of the wild type protein was first established in the presence of 20% trifluoroethanol and confirmed under a more physiologic environment including heparin and collagen. The latter conditions were also used to study the highly amyloidogenic variant, P32G. The NMR analysis showed that doxycycline inhibits β2-microglobulin self-association and stabilizes the native-like species through fast exchange interactions involving specific regions of the protein. Cell viability assays demonstrated that the drug abolishes the natural cytotoxic activity of soluble β2-microglobulin, further strengthening a possible in vivo therapeutic exploitation of this drug. Doxycycline can disassemble preformed fibrils, but the IC(50) is 5-fold higher than that necessary for the inhibition of fibrillogenesis. Fibril destructuration is a dynamic and time-dependent process characterized by the early formation of cytotoxic protein aggregates that, in a few hours, convert into non-toxic insoluble material. The efficacy of doxycycline as a drug against dialysis-related amyloidosis would benefit from the ability of the drug to accumulate just in the skeletal system where amyloid is formed. In these tissues, the doxycycline concentration reaches values several folds higher than those resulting in inhibition of amyloidogenesis and amyloid destructuration in vitro.
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Affiliation(s)
- Sofia Giorgetti
- From the Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia
| | - Sara Raimondi
- From the Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia
| | - Katiuscia Pagano
- the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine
| | - Annalisa Relini
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
- the Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa
| | - Monica Bucciantini
- the Department of Biochemical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence
| | - Alessandra Corazza
- the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
| | - Federico Fogolari
- the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
| | - Luca Codutti
- the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine
| | - Mario Salmona
- the Department of Molecular Biochemistry and Pharmacology, Mario Negri Institute for Pharmacological Research, Via La Masa, 19, 20156 Milan, and
| | - Palma Mangione
- From the Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia
| | - Lino Colombo
- the Department of Pharmaceutical Chemistry, University of Pavia, via Taramelli 12, 27100 Pavia, Italy
| | - Ada De Luigi
- the Department of Molecular Biochemistry and Pharmacology, Mario Negri Institute for Pharmacological Research, Via La Masa, 19, 20156 Milan, and
| | - Riccardo Porcari
- From the Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia
| | - Alessandra Gliozzi
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
- the Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa
| | - Massimo Stefani
- the Department of Biochemical Sciences, University of Florence, Viale Morgagni 50, 50134 Florence
| | - Gennaro Esposito
- the Department of Biomedical Sciences and Technologies, University of Udine, Piazzale Kolbe 4, 33100 Udine
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
| | - Vittorio Bellotti
- From the Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
| | - Monica Stoppini
- From the Department of Biochemistry, University of Pavia, via Taramelli 3b, 27100 Pavia
- the National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro 305, 00136 Rome
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14
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Zhang H, Zhou R, Li L, Chen J, Chen L, Li C, Ding H, Yu L, Hu L, Jiang H, Shen X. Danthron functions as a retinoic X receptor antagonist by stabilizing tetramers of the receptor. J Biol Chem 2011; 286:1868-75. [PMID: 21084305 PMCID: PMC3023482 DOI: 10.1074/jbc.m110.166215] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 11/05/2010] [Indexed: 12/11/2022] Open
Abstract
Retinoic X receptor (RXR) is a promising target for drug discovery against cancer and metabolic syndromes. Here, we identified a specific RXRα antagonist, danthron, from the traditional Chinese medicine rhubarb. Danthron repressed all tested RXRα-involved response element transcription, including the RXRE, PPRE, FXRE, and LXRE. Results from native PAGE and isothermal titration calorimetry (ITC)-based assays indicated that danthron bound to the tetrameric RXRα-LBD in a specific stoichimetric ratio, and such a binding could influence the corepressor SMRT affinity to the receptor. Additionally, a unique tetrameric structure of the apo-RXRα ligand-binding domain (LBD) was determined, which exhibited a larger tetramer interface and different ligand-binding pocket size compared with the one previously reported. Together with the biochemical and biophysical results, the determined crystal structure of danthron-soaked RXRα-LBD suggested a new mechanism for danthron antagonism to tetrameric RXRα. Moreover, the in vivo efficient improvement of insulin sensitivity by danthron was observed in diet-induced obese (DIO) mice. Thus, our findings were expected to supply new insights into the structural basis of RXRα antagonist for its further potential therapeutic application.
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Affiliation(s)
- Haitao Zhang
- From the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203
| | - Rong Zhou
- the East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, and
| | - Li Li
- the East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, and
| | - Jing Chen
- From the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203
| | - Lili Chen
- From the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203
| | - Chenjing Li
- From the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203
| | - Hong Ding
- From the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203
| | - Liang Yu
- From the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203
| | - Lihong Hu
- From the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203
| | - Hualiang Jiang
- From the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203
| | - Xu Shen
- From the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203
- the East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, and
- the E-Institutes of Shanghai Municipal Education Commission, Shanghai Jiaotong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
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15
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Subbotina J, Yarov-Yarovoy V, Lees-Miller J, Durdagi S, Guo J, Duff HJ, Noskov SY. Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations. Proteins 2010; 78:2922-34. [PMID: 20740484 PMCID: PMC2939218 DOI: 10.1002/prot.22815] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The hERG1 gene (Kv11.1) encodes a voltage-gated potassium channel. Mutations in this gene lead to one form of the Long QT Syndrome (LQTS) in humans. Promiscuous binding of drugs to hERG1 is known to alter the structure/function of the channel leading to an acquired form of the LQTS. Expectably, creation and validation of reliable 3D model of the channel have been a key target in molecular cardiology and pharmacology for the last decade. Although many models were built, they all were limited to pore domain. In this work, a full model of the hERG1 channel is developed which includes all transmembrane segments. We tested a template-driven de-novo design with ROSETTA-membrane modeling using side-chain placements optimized by subsequent molecular dynamics (MD) simulations. Although backbone templates for the homology modeled parts of the pore and voltage sensors were based on the available structures of KvAP, Kv1.2 and Kv1.2-Kv2.1 chimera channels, the missing parts are modeled de-novo. The impact of several alignments on the structure of the S4 helix in the voltage-sensing domain was also tested. Herein, final models are evaluated for consistency to the reported structural elements discovered mainly on the basis of mutagenesis and electrophysiology. These structural elements include salt bridges and close contacts in the voltage-sensor domain; and the topology of the extracellular S5-pore linker compared with that established by toxin foot-printing and nuclear magnetic resonance studies. Implications of the refined hERG1 model to binding of blockers and channels activators (potent new ligands for channel activations) are discussed.
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Affiliation(s)
- Julia Subbotina
- Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | | | - James Lees-Miller
- Libin Cardiovascular Institute of Alberta, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Serdar Durdagi
- Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Jiqing Guo
- Libin Cardiovascular Institute of Alberta, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Henry J. Duff
- Libin Cardiovascular Institute of Alberta, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Sergei Yu. Noskov
- Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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