1
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Mao A, Chen C, Portillo-Ledesma S, Schlick T. Effect of Single-Residue Mutations on CTCF Binding to DNA: Insights from Molecular Dynamics Simulations. Int J Mol Sci 2023; 24:ijms24076395. [PMID: 37047368 PMCID: PMC10094706 DOI: 10.3390/ijms24076395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023] Open
Abstract
In humans and other eukaryotes, DNA is condensed into chromatin fibers that are further wound into chromosomes. This organization allows regulatory elements in the genome, often distant from each other in the linear DNA, to interact and facilitate gene expression through regions known as topologically associating domains (TADs). CCCTC–binding factor (CTCF) is one of the major components of TAD formation and is responsible for recruiting a partner protein, cohesin, to perform loop extrusion and facilitate proper gene expression within TADs. Because single-residue CTCF mutations have been linked to the development of a variety of cancers in humans, we aim to better understand how these mutations affect the CTCF structure and its interaction with DNA. To this end, we compare all-atom molecular dynamics simulations of a wildtype CTCF–DNA complex to those of eight different cancer-linked CTCF mutant sequences. We find that most mutants have lower binding energies compared to the wildtype protein, leading to the formation of less stable complexes. Depending on the type and position of the mutation, this loss of stability can be attributed to major changes in the electrostatic potential, loss of hydrogen bonds between the CTCF and DNA, and/or destabilization of specific zinc fingers. Interestingly, certain mutations in specific fingers can affect the interaction with the DNA of other fingers, explaining why mere single mutations can impair CTCF function. Overall, these results shed mechanistic insights into experimental observations and further underscore CTCF’s importance in the regulation of chromatin architecture and gene expression.
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Affiliation(s)
- Albert Mao
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; (A.M.); (C.C.); (S.P.-L.)
| | - Carrie Chen
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; (A.M.); (C.C.); (S.P.-L.)
| | - Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; (A.M.); (C.C.); (S.P.-L.)
| | - Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; (A.M.); (C.C.); (S.P.-L.)
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USA
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China
- Simons Center for Computational Physical Chemistry, New York University, 24 Waverly Place, Silver Building, New York, NY 10003, USA
- Correspondence:
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2
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Ha JH, Prela O, Carpizo DR, Loh SN. p53 and Zinc: A Malleable Relationship. Front Mol Biosci 2022; 9:895887. [PMID: 35495631 PMCID: PMC9043292 DOI: 10.3389/fmolb.2022.895887] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 03/30/2022] [Indexed: 12/14/2022] Open
Abstract
A large percentage of transcription factors require zinc to bind DNA. In this review, we discuss what makes p53 unique among zinc-dependent transcription factors. The conformation of p53 is unusually malleable: p53 binds zinc extremely tightly when folded, but is intrinsically unstable in the absence of zinc at 37°C. Whether the wild-type protein folds in the cell is largely determined by the concentration of available zinc. Consequently, zinc dysregulation in the cell as well as a large percentage of tumorigenic p53 mutations can cause p53 to lose zinc, misfold, and forfeit its tumor suppressing activity. We highlight p53’s noteworthy biophysical properties that give rise to its malleability and how proper zinc binding can be restored by synthetic metallochaperones to reactivate mutant p53. The activity and mechanism of metallochaperones are compared to those of other mutant p53-targeted drugs with an emphasis on those that have reached the clinical trial stage.
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Affiliation(s)
- Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States
| | - Orjola Prela
- Division of Surgical Oncology, Department of Surgery, Wilmot Cancer Center, University of Rochester, Rochester, NY, United States
| | - Darren R Carpizo
- Division of Surgical Oncology, Department of Surgery, Wilmot Cancer Center, University of Rochester, Rochester, NY, United States
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States
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3
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Padjasek M, Kocyła A, Kluska K, Kerber O, Tran JB, Krężel A. Structural zinc binding sites shaped for greater works: Structure-function relations in classical zinc finger, hook and clasp domains. J Inorg Biochem 2020; 204:110955. [DOI: 10.1016/j.jinorgbio.2019.110955] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/08/2019] [Accepted: 12/01/2019] [Indexed: 12/12/2022]
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4
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Yousef EN, Angel LA. Comparison of the pH-dependent formation of His and Cys heptapeptide complexes of nickel(II), copper(II), and zinc(II) as determined by ion mobility-mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4489. [PMID: 31881105 DOI: 10.1002/jms.4489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/05/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
The analog methanobactin (amb) peptide with the sequence ac-His1 -Cys2 -Gly3 -Pro4 -Tyr5 -His6 -Cys7 (amb5A ) will bind the metal ions of zinc, nickel, and copper. To further understand how amb5A binds these metals, we have undertaken a series of studies of structurally related heptapeptides where one or two of the potential His or Cys binding sites have been replaced by Gly, or the C-terminus has been blocked by amidation. The studies were designed to compare how these metals bind to these sequences in different pH solutions of pH 4.2 to 10 and utilized native electrospray ionization (ESI) with ion mobility-mass spectrometry (IM-MS) which allows for the quantitative analysis of the charged species produced during the reactions. The native ESI conditions were chosen to conserve as much of the solution-phase behavior of the amb peptides as possible and an analysis of how the IM-MS results compare with the expected solution-phase behavior is discussed. The oligopeptides studied here have applications for tag-based protein purification methods, as therapeutics for diseases caused by elevated metal ion levels or as inhibitors for metal-protein enzymes such as matrix metalloproteinases.
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Affiliation(s)
- Enas N Yousef
- Department of Chemistry, Texas A&M University-Commerce, Commerce, Texas, 75428, USA
| | - Laurence A Angel
- Department of Chemistry, Texas A&M University-Commerce, Commerce, Texas, 75428, USA
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5
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Designing heterotropically activated allosteric conformational switches using supercharging. Proc Natl Acad Sci U S A 2020; 117:5291-5297. [PMID: 32098845 DOI: 10.1073/pnas.1916046117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterotropic allosteric activation of protein function, in which binding of one ligand thermodynamically activates the binding of another, different ligand or substrate, is a fundamental control mechanism in metabolism and as such has been a long-aspired capability in protein design. Here we show that greatly increasing the magnitude of a protein's net charge using surface supercharging transforms that protein into an allosteric ligand- and counterion-gated conformational molecular switch. To demonstrate this we first modified the designed helical bundle hemoprotein H4, creating a highly charged protein which both unfolds reversibly at low ionic strength and undergoes the ligand-induced folding transition commonly observed in signal transduction by intrinsically disordered proteins in biology. As a result of the high surface-charge density, ligand binding to this protein is allosterically activated up to 1,300-fold by low concentrations of divalent cations and the polyamine spermine. To extend this process further using a natural protein, we similarly modified Escherichia coli cytochrome b 562 and the resulting protein behaves in a like manner. These simple model systems not only establish a set of general engineering principles which can be used to convert natural and designed soluble proteins into allosteric molecular switches useful in biodesign, sensing, and synthetic biology, the behavior we have demonstrated--functional activation of supercharged intrinsically disordered proteins by low concentrations of multivalent ions--may be a control mechanism utilized by Nature which has yet to be appreciated.
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6
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Malik A, Angel LA, Spezia R, Hase WL. Collisional dynamics simulations revealing fragmentation properties of Zn(ii)-bound poly-peptide. Phys Chem Chem Phys 2020; 22:14551-14559. [DOI: 10.1039/d0cp02463e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Collisional simulations show how peptide fragmentation is modified by the presence of Zn(ii).
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Affiliation(s)
- Abdul Malik
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
| | | | - Riccardo Spezia
- Laboratoire de Chimie Théorique
- Sorbonne Université
- UMR 7616 CNRS
- 75005 Paris
- France
| | - William L. Hase
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock
- USA
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7
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Zheng S, Yuan S, Hou Z, Li G, Chen Y, Pan Y, Liu Y, Huang G. Charge-dependent modulation of specific and nonspecific protein-metal ion interactions in nanoelectrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1502-1511. [PMID: 31151135 DOI: 10.1002/rcm.8493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Previous studies found that charge state could affect both specific and nonspecific binding of protein-metal ion interactions in nanoelectrospray ionization mass spectrometry (nESI-MS). However, the two kinds of interactions have been studied individually in spite of the problem that they often coexist in the same system. Thus, it is necessary to study the effects of charge state on specific and nonspecific protein-metal ion interactions in one system to reveal more accurate binding state. METHODS The HIV-1 nucleocapsid protein (NCp7(31-55)) which can bind specifically and nonspecifically to Zn2+ served as the model to show the charge-dependent protein-metal ion interactions. Hydrogen/deuterium exchange (HDX) and photodissociation (PD) were used to demonstrate that specific binding state was correlated with protein structure. In addition to NCp7(31-55), three other model proteins were used to investigate the reason for the charge-dependent nonspecific binding. RESULTS For specific binding, we proposed that protein ions with different charge states had different conformations. The HDX results showed that labile protons in the NCp7(31-55)-Zn complex were exchanged in a charge-state-dependent way. The PD experiments revealed differential fragment yields for different charge states. For nonspecific binding, higher charge states had more Zn2+ additions, but less SO4 2- additions. The effects of charge states on nonspecific binding levels were entirely the opposite for Zn2+ and SO4 2- . These results could reveal that the nonspecific binding was caused by electrostatic interaction. CONCLUSIONS For specific binding, NCp7(31-55) with lower charge states have folding and undenatured structures. The binding states of lower charge states can better reflect more native binding states. For nonspecific binding, when multiple metal ions adduct to proteins, the proteins have more net positive charges, which tend to generate higher charge ions during electrospray.
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Affiliation(s)
- Shihui Zheng
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Siming Yuan
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Zhuanghao Hou
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Gongyu Li
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Yuting Chen
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Yang Pan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, 230029, P. R. China
| | - Yangzhong Liu
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Guangming Huang
- Department of Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, 230029, P. R. China
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8
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Macchiagodena M, Pagliai M, Andreini C, Rosato A, Procacci P. Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands. J Chem Inf Model 2019; 59:3803-3816. [PMID: 31385702 DOI: 10.1021/acs.jcim.9b00407] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We developed and validated a novel force field in the context of the AMBER parameterization for the simulation of zinc(II)-binding proteins. The proposed force field assumes nonbonded spherical interactions between the central zinc(II) and the coordinating residues. A crucial innovative aspect of our approach is to account for the polarization effects of the cation by redefining the atomic charges of the coordinating residues and an adjustment of Lennard-Jones parameters of Zn-interacting atoms to reproduce mean distance distributions. The optimal transferable parametrization was obtained by performing accurate quantum mechanical calculations on a training set of high-quality protein structures, encompassing the most common folds of zinc(II) sites. The addressed sites contain a zinc(II) ion tetra-coordinated by histidine and cysteine residues and represent about 70% of all physiologically relevant zinc(II) sites in the Protein Data Bank. Molecular dynamics simulations with explicit solvent, carried out on several zinc(II)-binding proteins not included in the training set, show that our model for zinc(II) sites preserves the tetra-coordination of the metal site with remarkable stability, yielding zinc(II)-X mean distances similar to experimental data. Finally, the model was tested by evaluating the zinc(II)-binding affinities, using the alchemical free energy perturbation approach. The calculated dissociation constants correlate satisfactorily with the experimental counterpart demonstrating the validity and transferability of the proposed parameterization for zinc(II)-binding proteins.
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Affiliation(s)
- Marina Macchiagodena
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
| | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
| | - Claudia Andreini
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy.,Magnetic Resonance Center (CERM)-Università degli Studi di Firenze , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy
| | - Antonio Rosato
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy.,Magnetic Resonance Center (CERM)-Università degli Studi di Firenze , Via L. Sacconi 6 , 50019 Sesto Fiorentino , Italy
| | - Piero Procacci
- Dipartimento di Chimica "Ugo Schiff" , Università degli Studi di Firenze , Via della Lastruccia 3 , 50019 Sesto Fiorentino , Italy
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9
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Zhu M, Song D, Liu N, Wang K, Su J, Xiong M, Zhang X, Xu Y, Gao E. Isomeric Effect on the anticancer Behavior of two Zinc (II) complexes based on 3,5‐bis(1‐imidazoly) pyridine: Experimental and Theoretical Approach. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Mingchang Zhu
- The key Laboratory of the Inorganic Molecule‐Based Chemistry of Liaoning Province, Laboratory of Coordination ChemistryShenyang University of Chemical Technology Shenyang 110142 China
| | - Da Song
- The key Laboratory of the Inorganic Molecule‐Based Chemistry of Liaoning Province, Laboratory of Coordination ChemistryShenyang University of Chemical Technology Shenyang 110142 China
| | - Ning Liu
- Liaoning Institute for Food Control (Liaoning Institute of Pharmaceutical Research) Shenyang 110015 China
| | - Kehua Wang
- School of Chemistry and Life ScienceAnshan Normal University Anshan China
| | - Junqi Su
- The key Laboratory of the Inorganic Molecule‐Based Chemistry of Liaoning Province, Laboratory of Coordination ChemistryShenyang University of Chemical Technology Shenyang 110142 China
| | - Meng Xiong
- The key Laboratory of the Inorganic Molecule‐Based Chemistry of Liaoning Province, Laboratory of Coordination ChemistryShenyang University of Chemical Technology Shenyang 110142 China
| | - Xi Zhang
- The key Laboratory of the Inorganic Molecule‐Based Chemistry of Liaoning Province, Laboratory of Coordination ChemistryShenyang University of Chemical Technology Shenyang 110142 China
| | - Yuang Xu
- The key Laboratory of the Inorganic Molecule‐Based Chemistry of Liaoning Province, Laboratory of Coordination ChemistryShenyang University of Chemical Technology Shenyang 110142 China
| | - Enjun Gao
- The key Laboratory of the Inorganic Molecule‐Based Chemistry of Liaoning Province, Laboratory of Coordination ChemistryShenyang University of Chemical Technology Shenyang 110142 China
- School of Chemical EngineeringUniversity of Science and Technology Liaoning Anshan 114051 China
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10
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Kluska K, Adamczyk J, Krężel A. Metal binding properties of zinc fingers with a naturally altered metal binding site. Metallomics 2019; 10:248-263. [PMID: 29230465 DOI: 10.1039/c7mt00256d] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Zinc fingers (ZFs) are among the most abundant motifs found in proteins, and are commonly known for their structural role. Classical ZFs (CCHH) are part of the transcription factors that participate in DNA binding. Although biochemical studies of classical ZFs have a long history, there is limited knowledge about the sequential and structural diversity of ZFs. We have found that classical ZFs, with metal binding sites consisting of amino acids other than conserved Cys or His residues, are frequently encoded in the human genome, and we refer to these peptides as ZFs with a naturally altered metal binding site. The biological role of the altered ZFs remains undiscovered. In this study, we characterized nine natural XCHH, CXHH, CCXH and CCHX ZFs in terms of their Zn(ii) and Co(ii) binding properties, such as complex stoichiometry, spectroscopic properties and metal-to-peptide affinity. We revealed that XCHH and CXHH ZFs form ML complexes that are 4-5 orders of magnitude weaker in comparison to CCHH ZFs. Nevertheless, spectroscopic studies demonstrate that, depending on the altered position, they may adopt an open coordination geometry with one or two water molecules bound to a central metal ion, which has not been demonstrated in natural ZFs before. Stability data show that both CCXH and CCHX peptides have high Zn(ii) affinity (with a Kd of 10-9 to 10-11 M), suggesting their potential biological function. This study is a comprehensive overview of the relationship between the sequence, structure, and stability of ZFs.
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Affiliation(s)
- Katarzyna Kluska
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383 Wrocław, Poland.
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11
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Klamt A, Nagarathinam K, Tanabe M, Kumar A, Balbach J. Hyperbolic Pressure-Temperature Phase Diagram of the Zinc-Finger Protein apoKti11 Detected by NMR Spectroscopy. J Phys Chem B 2019; 123:792-801. [PMID: 30608169 DOI: 10.1021/acs.jpcb.8b11019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For a comprehensive understanding of the thermodynamic state functions describing the stability of a protein, the influence of the intensive properties of temperature and pressure has to be known. With the zinc-finger-containing Kti11, we found a suitable protein for this purpose because folding and unfolding transitions occur at an experimentally accessible temperature (280-330 °K) and pressure (0.1-240 MPa) range. We solved the crystal structure of the apo form of Kti11 to reveal two disulfide bonds at the metal-binding site, which seals off a cavity in the β-barrel part of the protein. From a generally applicable proton NMR approach, we could determine the populations of folded and unfolded chains under all conditions, leading to a hyperbolic pressure-temperature phase diagram rarely observed for proteins. A global fit of a two-state model to all derived populations disclosed reliable values for the change in Gibbs free energy, volume, entropy, heat capacity, compressibility, and thermal expansion upon unfolding. The unfolded state of apoKti11 has a lower compressibility compared to the native state and a smaller volume at ambient pressure. Therefore, a pressure increase up to 200 MPa reduces the population of the native state, and above this value, the native population increases again. Pressure-induced chemical-shift changes in two-dimensional 1H-15N NMR spectra could be employed for a molecular interpretation of the thermodynamic properties of apoKti11.
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Affiliation(s)
- Andi Klamt
- Institute of Physics, Biophysics , Martin-Luther University Halle-Wittenberg , Betty-Heimann Street 7 , 06120 Halle , Germany
| | - Kumar Nagarathinam
- HALOmem, Membrane Protein Biochemistry , Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Street 3 , 06120 Halle (Saale) , Germany.,Institute of Virology , Hannover Medical School , Carl-Neuberg-Straße 1 , D-30625 Hannover , Germany
| | - Mikio Tanabe
- HALOmem, Membrane Protein Biochemistry , Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Street 3 , 06120 Halle (Saale) , Germany.,Structural Biology Research Center, Institute of Materials Structure Science , KEK/High Energy Accelerator Research Organization , 1-1 Oho , Tsukuba , Ibaraki , 305-0801 , Japan
| | - Amit Kumar
- Institute of Physics, Biophysics , Martin-Luther University Halle-Wittenberg , Betty-Heimann Street 7 , 06120 Halle , Germany.,Department of Diabetes, Faculty of Lifesciences and Medicine , King's College London , Great Maze Pond , London SE1 1UL , U.K
| | - Jochen Balbach
- Institute of Physics, Biophysics , Martin-Luther University Halle-Wittenberg , Betty-Heimann Street 7 , 06120 Halle , Germany.,HALOmem, Membrane Protein Biochemistry , Martin-Luther-University Halle-Wittenberg , Kurt-Mothes-Street 3 , 06120 Halle (Saale) , Germany
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12
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Kluska K, Adamczyk J, Krężel A. Metal binding properties, stability and reactivity of zinc fingers. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.04.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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13
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Belmonte L, Mansy SS. Patterns of Ligands Coordinated to Metallocofactors Extracted from the Protein Data Bank. J Chem Inf Model 2017; 57:3162-3171. [PMID: 29116779 DOI: 10.1021/acs.jcim.7b00468] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A new R tool is described that rapidly identifies, ranks, and clusters sequence patterns coordinated to metallocofactors. This tool, PdPDB, fills a void because, unlike currently available tools, PdPDB searches through sequences with metal coordination as the primary determinant and can identify patterns consisting of amino acids, nucleotides, and small molecule ligands at once. PdPDB was tested by analyzing structures that coordinate Fe2+/3+, [2Fe-2S], [4Fe-4S], Zn2+, and Mg2+ cofactors. PdPDB confirmed previously identified sequence motifs and revealed which residues are enriched (e.g., glycine) and are under-represented (e.g., glutamine) near ligands to metal centers. The data show the similarities and differences between different metal-binding sites. The patterns that coordinate metallocofactors vary, depending upon whether the metal ions play a structural or catalytic role, with catalytic metal centers exhibiting partial coordination by small molecule ligands. PdPDB 2.0.1 is freely available as a CRAN package.
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Affiliation(s)
- Luca Belmonte
- CIBIO, University of Trento , Via Sommarive 9, 38123 Povo, Italy
| | - Sheref S Mansy
- CIBIO, University of Trento , Via Sommarive 9, 38123 Povo, Italy
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14
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Wagoner SM, Deeconda M, Cumpian KL, Ortiz R, Chinthala S, Angel LA. The multiple conformational charge states of zinc(II) coordination by 2His-2Cys oligopeptide investigated by ion mobility-mass spectrometry, density functional theory and theoretical collision cross sections. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:1120-1129. [PMID: 27594546 DOI: 10.1002/jms.3846] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/28/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Whether traveling wave ion mobility-mass spectrometry (IM-MS), B3LYP/LanL2DZ density functional theory, and ion size scaled Lennard-Jones (LJ) collision cross sections (CCS) from the B3LYP optimized structures could be used to determine the type of Zn(II) coordination by the oligopeptide acetyl-His1 -Cys2 -Gly3 -Pro4 -Tyr5 -His6 -Cys7 (amb5 ) was investigated. The IM-MS analyses of a pH titration of molar equivalents of Zn(II):amb5 showed that both negatively and positively charged complexes formed and coordination of Zn(II) increased as the His and Cys deprotonated near their pKa values. The B3LYP method was used to generate a series of alternative coordination structures to compare with the experimental results. The method predicted that the single negatively charged complex coordinated Zn(II) in a distorted tetrahedral geometry via the 2His-2Cys substituent groups, whereas, the double negatively charged and positively charged complexes coordinated Zn(II) via His, carbonyl oxygens and the C-terminus. The CCS of the B3LYP complexes were calculated using the LJ method and compared with those measured by IM-MS for the various charge state complexes. The LJ method provided CCS that agreed with five of the alternative distorted tetrahedral and trigonal bipyramidal coordinations for the doubly charged complexes, but provided CCS that were 15 to 31 Å2 larger than those measured by IM-MS for the singly charged complexes. Collision-induced dissociation of the Zn(II) complexes and a further pH titration study of amb5B , which included amidation of the C-terminus, suggested that the 2His-2Cys coordination was more significant than coordinations that included the C-terminus. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Stephanie M Wagoner
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX, 75428, USA
| | - Manogna Deeconda
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX, 75428, USA
| | - Kayleah L Cumpian
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX, 75428, USA
| | - Rafael Ortiz
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX, 75428, USA
| | - Swetha Chinthala
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX, 75428, USA
| | - Laurence A Angel
- Department of Chemistry, Texas A&M University-Commerce, Commerce, TX, 75428, USA
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15
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Synthesis, structures, molecular docking, cytotoxicity and bioimaging studies of two novel Zn(II) complexes. Eur J Med Chem 2016; 121:1-11. [DOI: 10.1016/j.ejmech.2016.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/11/2016] [Accepted: 05/05/2016] [Indexed: 01/24/2023]
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16
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Besold AN, Widger LR, Namuswe F, Michalek JL, Michel SLJ, Goldberg DP. Revisiting and re-engineering the classical zinc finger peptide: consensus peptide-1 (CP-1). MOLECULAR BIOSYSTEMS 2016; 12:1183-93. [PMID: 26936488 DOI: 10.1039/c5mb00796h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Zinc plays key structural and catalytic roles in biology. Structural zinc sites are often referred to as zinc finger (ZF) sites, and the classical ZF contains a Cys2His2 motif that is involved in coordinating Zn(II). An optimized Cys2His2 ZF, named consensus peptide 1 (CP-1), was identified more than 20 years ago using a limited set of sequenced proteins. We have reexamined the CP-1 sequence, using our current, much larger database of sequenced proteins that have been identified from high-throughput sequencing methods, and found the sequence to be largely unchanged. The CCHH ligand set of CP-1 was then altered to a CAHH motif to impart hydrolytic activity. This ligand set mimics the His2Cys ligand set of peptide deformylase (PDF), a hydrolytically active M(II)-centered (M = Zn or Fe) protein. The resultant peptide [CP-1(CAHH)] was evaluated for its ability to coordinate Zn(II) and Co(II) ions, adopt secondary structure, and promote hydrolysis. CP-1(CAHH) was found to coordinate Co(II) and Zn(II) and a pentacoordinate geometry for Co(II)-CP-1(CAHH) was implicated from UV-vis data. This suggests a His2Cys(H2O)2 environment at the metal center. The Zn(II)-bound CP-1(CAHH) was shown to adopt partial secondary structure by 1-D (1)H NMR spectroscopy. Both Zn(II)-CP-1(CAHH) and Co(II)-CP-1(CAHH) show good hydrolytic activity toward the test substrate 4-nitrophenyl acetate, exhibiting faster rates than most active synthetic Zn(II) complexes.
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Affiliation(s)
- Angelique N Besold
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA.
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17
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Kocyła A, Pomorski A, Krężel A. Molar absorption coefficients and stability constants of metal complexes of 4-(2-pyridylazo)resorcinol (PAR): Revisiting common chelating probe for the study of metalloproteins. J Inorg Biochem 2015; 152:82-92. [PMID: 26364130 DOI: 10.1016/j.jinorgbio.2015.08.024] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/25/2015] [Accepted: 08/26/2015] [Indexed: 01/14/2023]
Abstract
4-(2-Pyridylazo)resorcinol (PAR) is one of the most popular chromogenic chelator used in the determination of the concentrations of various metal ions from the d, p and f blocks and their affinities for metal ion-binding biomolecules. The most important characteristics of such a sensor are the molar absorption coefficient and the metal-ligand complex dissociation constant. However, it must be remembered that these values are dependent on the specific experimental conditions (e.g. pH, solvent components, and reactant ratios). If one uses these values to process data obtained in different conditions, the final result can be under- or overestimated. We aimed to establish the spectral properties and the stability of PAR and its complexes accurately with Zn(2+), Cd(2+), Hg(2+), Co(2+), Ni(2+), Cu(2+), Mn(2+) and Pb(2+) at a multiple pH values. The obtained results account for the presence of different species of metal-PAR complexes in the physiological pH range of 5 to 8 and have been frequently neglected in previous studies. The effective molar absorption coefficient at 492 nm for the ZnHx(PAR)2 complex at pH7.4 in buffered water solution is 71,500 M(-1) cm(-1), and the dissociation constant of the complex in these conditions is 7.08×10(-13) M(2). To confirm these values and estimate the range of the dissociation constants of zinc-binding biomolecules that can be measured using PAR, we performed several titrations of zinc finger peptides and zinc chelators. Taken together, our results provide the updated parameters that are applicable to any experiment conducted using inexpensive and commercially available PAR.
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Affiliation(s)
- Anna Kocyła
- Laboratory of Chemical Biology, University of Wrocław, ul. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Adam Pomorski
- Laboratory of Chemical Biology, University of Wrocław, ul. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Artur Krężel
- Laboratory of Chemical Biology, University of Wrocław, ul. Joliot-Curie 14a, 50-383 Wrocław, Poland.
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18
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Deng S, Zhang T, Ji X, Wan Y, Xin P, Shan D, Zhang X. Detection of zinc finger protein (EGR1) based on electrogenerated chemiluminescence from singlet oxygen produced in a nanoclay-supported porphyrin environment. Anal Chem 2015; 87:9155-62. [PMID: 26301820 DOI: 10.1021/acs.analchem.5b01318] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Early growth response protein 1 (EGR1), as a characteristic example of zinc finger proteins, acts as a transcription factor in eukaryotic cells, mediating protein-protein interactions. Here, a novel electrochemiluminescence (ECL)-based protocol for EGR1 assay was developed with a new eco-friendly emitter: singlet oxygen produced in the vicinity of nanoclay-supported zinc proto-porphyrin IX (ZnPPIX). Its electrochemical reduction stimulates an intense monochromic CL irradiation at 644 nm from the dissolved oxygen as endogenous coreactant in the aqueous solution. This ECL derivation was rationalized via hyphenated spectroscopy and theoretical calculation. To promote hydrophilicity and solid-state immobilization of porphyrins, the lamellar artificial laponite was employed as a nanocarrier owning to its large specific area without the blackbody effect. The facile exfoliation of laponite produced quality monolayered nanosheets and facilitated the adsorption and flattening of PPIX upon the surface, resulting in a highly efficient ECL emission. Based on the release of Zn(2+) in zinc finger domains of EGR1 upon contact with the ECL-inactive PPIX, which was monitored by circular dichroism and UV-absorption, a sensitive Zn(2+)-selective electrode for the "signal-on" detection of EGR1 was prepared with a detection limit down to 0.48 pg mL(-1) and a linearity over 6 orders of magnitude. The proposed porphyrin-based ECL system thus infused fresh blood into the traditional ECL family, showing great promise in bioassays of structural Zn(II) proteins and zinc finger-binding nucleotides.
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Affiliation(s)
- Shengyuan Deng
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Tingting Zhang
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Xubo Ji
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Ying Wan
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China.,Intelligent Microsystem Technology and Engineering Center, School of Mechanical Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Peng Xin
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Dan Shan
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
| | - Xueji Zhang
- Sino-French Laboratory of Biomaterials and Bioanalytical Chemistry, School of Environmental and Biological Engineering, Nanjing University of Science and Technology , Nanjing 210094, P. R. China
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19
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Reddi AR, Pawlowska M, Gibney BR. Evaluation of the Intrinsic Zn(II) Affinity of a Cys3His1 Site in the Absence of Protein Folding Effects. Inorg Chem 2015; 54:5942-8. [DOI: 10.1021/acs.inorgchem.5b00718] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amit R. Reddi
- Department of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Malgorzata Pawlowska
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, United States
| | - Brian R. Gibney
- Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program
in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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20
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Kochańczyk T, Drozd A, Krężel A. Relationship between the architecture of zinc coordination and zinc binding affinity in proteins – insights into zinc regulation. Metallomics 2015; 7:244-57. [DOI: 10.1039/c4mt00094c] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Relationship between the architecture and stability of zinc proteins.
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Affiliation(s)
- Tomasz Kochańczyk
- Laboratory of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław, Poland
| | - Agnieszka Drozd
- Laboratory of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław, Poland
| | - Artur Krężel
- Laboratory of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław, Poland
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21
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Khrenova M, Savitsky AP, Topol IA, Nemukhin AV. Exploration of the zinc finger motif in controlling activity of matrix metalloproteinases. J Phys Chem B 2014; 118:13505-12. [PMID: 25375834 PMCID: PMC4254000 DOI: 10.1021/jp5088702] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/05/2014] [Indexed: 12/19/2022]
Abstract
Discovering ways to control the activity of matrix metalloproteinases (MMPs), zinc-dependent enzymes capable of degrading extracellular matrix proteins, is an important field of cancer research. We report here a novel strategy for assembling MMP inhibitors on the basis of oligopeptide ligands by exploring the pattern known as the zinc finger motif. Advanced molecular modeling tools were used to characterize the structural binding motifs of experimentally tested MMP inhibitors, as well as those of newly proposed peptidomimetics, in their zinc-containing active sites. The results of simulations based on the quantum mechanics/molecular mechanics (QM/MM) approach and Car-Parrinello molecular dynamics with QM/MM potentials demonstrate that, upon binding of Regasepin1, a known MMP-9 inhibitor, the Zn(2+)(His3) structural element is rearranged to the Zn(2+)(Cys2His2) zinc finger motif, in which two Cys residues are borrowed from the ligand. Following consideration of the crystal structure of MMP-2 with its inhibitor, the oligopeptide APP-IP, we proposed a new peptidomimetic with two replacements in the substrate, Tyr3Cys and Asp6Cys. Simulations show that this peptide variant blocks an enzyme active site by the Zn(2+)(Cys2His2) zinc finger construct. Similarly, a natural substrate of MMP-2, Ace-Gln-Gly ∼ Ile-Ala-Gly-Nme, can be converted to an inhibiting compound by two replacements, Ile by Cys and Gly by the d isomer of Cys, favoring formation of the zinc finger motif.
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Affiliation(s)
- Maria
G. Khrenova
- A.N. Bach Institute
of Biochemistry of the Russian Academy of Science, Leninsky Prospect, 33, Moscow 119071, Russian Federation
- Chemistry
Department, M.V. Lomonosov Moscow State
University, Leninskie
Gory 1/3, Moscow, 119991, Russian Federation
| | - Alexander P. Savitsky
- A.N. Bach Institute
of Biochemistry of the Russian Academy of Science, Leninsky Prospect, 33, Moscow 119071, Russian Federation
| | - Igor A. Topol
- Advanced
Biomedical Computing Center, Information Systems Program, Leidos Biomedical
Research Inc., Frederick National Laboratory
for Cancer Research, Frederick, Maryland 21702, United States
| | - Alexander V. Nemukhin
- Chemistry
Department, M.V. Lomonosov Moscow State
University, Leninskie
Gory 1/3, Moscow, 119991, Russian Federation
- N.M.
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation
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