1
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Lahiri D, Agrawal R, Chandravanshi K, Rajput P, Agrawal A, Dwivedi A, Makde RD, Jha SN, Garg N. Assessing the prospect of XAFS experiments of metalloproteins under in vivo conditions at Indus-2 synchrotron facility, India. JOURNAL OF SYNCHROTRON RADIATION 2023; 30:449-456. [PMID: 36891859 PMCID: PMC10000809 DOI: 10.1107/s1600577522011791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/10/2022] [Indexed: 06/18/2023]
Abstract
The feasibility of X-ray absorption fine-structure (XAFS) experiments of ultra-dilute metalloproteins under in vivo conditions (T = 300 K, pH = 7) at the BL-9 bending-magnet beamline (Indus-2) is reported, using as an example analogous synthetic Zn (0.1 mM) M1dr solution. The (Zn K-edge) XAFS of M1dr solution was measured with a four-element silicon drift detector. The first-shell fit was tested and found to be robust against statistical noise, generating reliable nearest-neighbor bond results. The results are found to be invariant between physiological and non-physiological conditions, which confirms the robust coordination chemistry of Zn with important biological implications. The scope of improving spectral quality for accommodation of higher-shell analysis is addressed.
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Affiliation(s)
- Debdutta Lahiri
- High Pressure and Synchrotron Radiation Physics, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Richa Agrawal
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
| | | | - Parasmani Rajput
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Ankur Agrawal
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Ashutosh Dwivedi
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Ravindra D. Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - S. N. Jha
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Nandini Garg
- High Pressure and Synchrotron Radiation Physics, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
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2
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A rigorous theory of valence. Struct Chem 2023. [DOI: 10.1007/s11224-023-02128-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
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3
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Relations between Structure and Zn(II) Binding Affinity Shed Light on the Mechanisms of Rad50 Hook Domain Functioning and Its Phosphorylation. Int J Mol Sci 2022; 23:ijms231911140. [PMID: 36232441 PMCID: PMC9569753 DOI: 10.3390/ijms231911140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
The metal binding at protein–protein interfaces is still uncharted territory in intermolecular interactions. To date, only a few protein complexes binding Zn(II) in an intermolecular manner have been deeply investigated. The most notable example of such interfaces is located in the highly conserved Rad50 protein, part of the Mre11-Rad50-Nbs1 (MRN) complex, where Zn(II) is required for homodimerization (Zn(Rad50)2). The high stability of Zn(Rad50)2 is conserved not only for the protein derived from the thermophilic archaeon Pyrococcus furiosus (logK12 = 20.95 for 130-amino-acid-long fragment), which was the first one studied, but also for the human paralog studied here (logK12 = 19.52 for a 183-amino-acid-long fragment). As we reported previously, the extremely high stability results from the metal-coupled folding process where particular Rad50 protein fragments play a critical role. The sequence–structure–stability analysis based on human Rad50 presented here separates the individual structural components that increase the stability of the complex, pointing to amino acid residues far away from the Zn(II) binding site as being largely responsible for the complex stabilization. The influence of the individual components is very well reflected by the previously published crystal structure of the human Rad50 zinc hook (PDB: 5GOX). In addition, we hereby report the effect of phosphorylation of the zinc hook domain, which exerts a destabilizing effect on the domain. This study identifies factors governing the stability of metal-mediated protein–protein interactions and illuminates their molecular basis.
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4
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Dokania A, Ould-Chikh S, Ramirez A, Cerrillo JL, Aguilar A, Russkikh A, Alkhalaf A, Hita I, Bavykina A, Shterk G, Wehbe N, Prat A, Lahera E, Castaño P, Fonda E, Hazemann JL, Gascon J. Designing a Multifunctional Catalyst for the Direct Production of Gasoline-Range Isoparaffins from CO 2. JACS AU 2021; 1:1961-1974. [PMID: 34841412 PMCID: PMC8611669 DOI: 10.1021/jacsau.1c00317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The production of carbon-neutral fuels from CO2 presents an avenue for causing an appreciable effect in terms of volume toward the mitigation of global carbon emissions. To that end, the production of isoparaffin-rich fuels is highly desirable. Here, we demonstrate the potential of a multifunctional catalyst combination, consisting of a methanol producer (InCo) and a Zn-modified zeolite beta, which produces a mostly isoparaffinic hydrocarbon mixture from CO2 (up to ∼85% isoparaffin selectivity among hydrocarbons) at a CO2 conversion of >15%. The catalyst combination was thoroughly characterized via an extensive complement of techniques. Specifically, operando X-ray absorption spectroscopy (XAS) reveals that Zn (which plays a crucial role of providing a hydrogenating function, improving the stability of the overall catalyst combination and isomerization performance) is likely present in the form of Zn6O6 clusters within the zeolite component, in contrast to previously reported estimations.
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Affiliation(s)
- Abhay Dokania
- King
Abdullah University of Science and Technology, KAUST Catalysis Center (KCC), Thuwal 23955, Saudi Arabia
| | - Samy Ould-Chikh
- King
Abdullah University of Science and Technology, KAUST Catalysis Center (KCC), Thuwal 23955, Saudi Arabia
| | - Adrian Ramirez
- King
Abdullah University of Science and Technology, KAUST Catalysis Center (KCC), Thuwal 23955, Saudi Arabia
| | - Jose Luis Cerrillo
- King
Abdullah University of Science and Technology, KAUST Catalysis Center (KCC), Thuwal 23955, Saudi Arabia
| | - Antonio Aguilar
- Institut
Neel, UPR 2940 CNRS-Université Grenoble Alpes, F-38000 Grenoble, France
| | - Artem Russkikh
- King
Abdullah University of Science and Technology, KAUST Catalysis Center (KCC), Thuwal 23955, Saudi Arabia
| | - Ahmed Alkhalaf
- King
Abdullah University of Science and Technology, KAUST Catalysis Center (KCC), Thuwal 23955, Saudi Arabia
| | - Idoia Hita
- King
Abdullah University of Science and Technology, KAUST Catalysis Center (KCC), Thuwal 23955, Saudi Arabia
| | - Anastasiya Bavykina
- King
Abdullah University of Science and Technology, KAUST Catalysis Center (KCC), Thuwal 23955, Saudi Arabia
| | - Genrikh Shterk
- King
Abdullah University of Science and Technology, KAUST Catalysis Center (KCC), Thuwal 23955, Saudi Arabia
| | - Nimer Wehbe
- King
Abdullah University of Science and Technology, Imaging and Characterization Core Laboratories, Thuwal 23955, Saudi Arabia
| | - Alain Prat
- Institut
Neel, UPR 2940 CNRS-Université Grenoble Alpes, F-38000 Grenoble, France
| | - Eric Lahera
- OSUG,
UMS 832 CNRS-Université Grenoble Alpes, F-38041 Grenoble, France
| | - Pedro Castaño
- King
Abdullah University of Science and Technology, KAUST Catalysis Center (KCC), Thuwal 23955, Saudi Arabia
| | - Emiliano Fonda
- Synchrotron
SOLEIL, L’orme des Merisiers, BP 48 Saint Aubin, 91192 Gif-sur-Yvette, France
| | - Jean-Louis Hazemann
- Institut
Neel, UPR 2940 CNRS-Université Grenoble Alpes, F-38000 Grenoble, France
| | - Jorge Gascon
- King
Abdullah University of Science and Technology, KAUST Catalysis Center (KCC), Thuwal 23955, Saudi Arabia
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5
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Sterbinsky GE, Heald SM. A simple method for mitigating error in the fixed-offset of a double-crystal monochromator. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1737-1746. [PMID: 34738927 DOI: 10.1107/s1600577521008626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
In order to maintain a constant monochromatic synchrotron X-ray beam height for all energies, the separation between the crystals of a double-crystal monochromator is typically adjusted, via translation of the second crystal, while X-ray energy is varied, via rotation of the crystal pair. The ability to accurately translate the second crystal requires precise knowledge of the separation between the two crystals and, when present, crystal miscuts. Here, a simple method for calibrating the crystal gap from measured variation in the X-ray beam height that eliminates error in the fixed beam offset is provided.
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Affiliation(s)
- George E Sterbinsky
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Steve M Heald
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
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6
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Hollings AL, Lam V, Takechi R, Mamo JCL, Reinhardt J, de Jonge MD, Kappen P, Hackett MJ. Revealing differences in the chemical form of zinc in brain tissue using K-edge X-ray absorption near-edge structure spectroscopy. Metallomics 2020; 12:2134-2144. [PMID: 33300524 DOI: 10.1039/d0mt00198h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Zinc is a prominent trace metal required for normal memory function. Memory loss and cognitive decline during natural ageing and neurodegenerative disease have been associated with altered brain-Zn homeostasis. Yet, the exact chemical pathways through which Zn influences memory function during health, natural ageing, or neurodegenerative disease remain unknown. The gap in the literature may in part be due to the difficulty to simultaneously image, and therefore, study the different chemical forms of Zn within the brain (or biological samples in general). To this extent, we have begun developing and optimising protocols that incorporate X-ray absorption near-edge structure (XANES) spectroscopic analysis of tissue at the Zn K-edge as an analytical tool to study Zn speciation in the brain. XANES is ideally suited for this task as all chemical forms of Zn are detected, the technique requires minimal sample preparation that may otherwise redistribute or alter the chemical form of Zn, and the Zn K-edge has known sensitivity to coordination geometry and ligand type. Herein, we report our initial results where we fit K-edge spectra collected from micro-dissected flash-frozen brain tissue, to a spectral library prepared from standard solutions, to demonstrate differences in the chemical form of Zn that exist between two brain regions, the hippocampus and cerebellum. Lastly, we have used an X-ray microprobe to demonstrate differences in Zn speciation within sub-regions of thin air-dried sections of the murine hippocampus; but, the corresponding results highlight that the chemical form of Zn is easily perturbed by sample preparation such as tissue sectioning or air-drying, which must be a critical consideration for future work.
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Affiliation(s)
- Ashley L Hollings
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia.
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7
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McCubbin Stepanic O, Ward J, Penner-Hahn JE, Deb A, Bergmann U, DeBeer S. Probing a Silent Metal: A Combined X-ray Absorption and Emission Spectroscopic Study of Biologically Relevant Zinc Complexes. Inorg Chem 2020; 59:13551-13560. [PMID: 32893611 PMCID: PMC7509839 DOI: 10.1021/acs.inorgchem.0c01931] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
As the second most common transition metal in the human body, zinc is of great interest to research but has few viable routes for its direct structural study in biological systems. Herein, Zn valence-to-core X-ray emission spectroscopy (VtC XES) and Zn K-edge X-ray absorption spectroscopy (XAS) are presented as a means to understand the local structure of zinc in biological systems through the application of these methods to a series of biologically relevant molecular model complexes. Taken together, the Zn K-edge XAS and VtC XES provide a means to establish the ligand identity, local geometry, and metal-ligand bond lengths. Experimental results are supported by correlation with density-functional-theory-based calculations. Combining these theoretical and experimental approaches will enable future applications to protein systems in a predictive manner.
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Affiliation(s)
- Olivia McCubbin Stepanic
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Jesse Ward
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James E Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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8
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Pritts JD, Hursey MS, Michalek JL, Batelu S, Stemmler TL, Michel SLJ. Unraveling the RNA Binding Properties of the Iron-Sulfur Zinc Finger Protein CPSF30. Biochemistry 2020; 59:970-982. [PMID: 32027124 DOI: 10.1021/acs.biochem.9b01065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cleavage and polyadenylation specificity factor 30 (CPSF30) is a "zinc finger" protein that plays a crucial role in the transition of pre-mRNA to RNA. CPSF30 contains five conserved CCCH domains and a CCHC "zinc knuckle" domain. CPSF30 activity is critical for pre-mRNA processing. A truncated form of the protein, in which only the CCCH domains are present, has been shown to specifically bind AU-rich pre-mRNA targets; however, the RNA binding and recognition properties of full-length CPSF30 are not known. Herein, we report the isolation and biochemical characterization of full-length CPSF30. We report that CPSF30 contains one 2Fe-2S cluster in addition to five zinc ions, as measured by inductively coupled plasma mass spectrometry, ultraviolet-visible spectroscopy, and X-ray absorption spectroscopy. Utilizing fluorescence anisotropy RNA binding assays, we show that full-length CPSF30 has high binding affinity for two types of pre-mRNA targets, AAUAAA and polyU, both of which are conserved sequence motifs present in the majority of pre-mRNAs. Binding to the AAUAAA motif requires that the five CCCH domains of CPSF30 be present, whereas binding to polyU sequences requires the entire, full-length CPSF30. These findings implicate the CCHC "zinc knuckle" present in the full-length protein as being critical for mediating polyU binding. We also report that truncated forms of the protein, containing either just two CCCH domains (ZF2 and ZF3) or the CCHC "zinc knuckle" domain, do not exhibit any RNA binding, indicating that CPSF30/RNA binding requires several ZF (and/or Fe-S cluster) domains working in concert to mediate RNA recognition.
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Affiliation(s)
- Jordan D Pritts
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Matthew S Hursey
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Jamie L Michalek
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Sharon Batelu
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201, United States
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201, United States
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
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9
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Thomas SA, Mishra B, Myneni SCB. High Energy Resolution-X-ray Absorption Near Edge Structure Spectroscopy Reveals Zn Ligation in Whole Cell Bacteria. J Phys Chem Lett 2019; 10:2585-2592. [PMID: 31039606 DOI: 10.1021/acs.jpclett.9b01186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Identifying the zinc (Zn) ligation and coordination environment in complex biological and environmental systems is crucial to understand the role of Zn as a biologically essential but sometimes toxic metal. Most studies on Zn coordination in biological or environmental samples rely on the extended X-ray absorption fine structure (EXAFS) region of a Zn K-edge X-ray absorption spectroscopy (XAS) spectrum. However, EXAFS analysis cannot identify unique nearest neighbors with similar atomic number (i.e., O versus N) and provides little information on Zn ligation. Herein, we demonstrate that high energy resolution-X-ray absorption near edge structure (HR-XANES) spectroscopy enables the direct determination of Zn ligation in whole cell bacteria, providing additional insights lost from EXAFS analysis at a fraction of the scan time and Zn concentration. HR-XANES is a relatively new technique that has improved our understanding of trace metals (e.g., Hg, Cu, and Ce) in dilute systems. This study is the first to show that HR-XANES can unambiguously detect Zn coordination to carboxyl, phosphoryl, imidazole, and/or thiol moieties in model microorganisms.
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Affiliation(s)
- Sara A Thomas
- Department of Geosciences , Princeton University , Guyot Hall, Princeton , New Jersey 08544 , United States
| | - Bhoopesh Mishra
- School of Chemical and Process Engineering , University of Leeds , Leeds LS2 9JT , United Kingdom
| | - Satish C B Myneni
- Department of Geosciences , Princeton University , Guyot Hall, Princeton , New Jersey 08544 , United States
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10
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Pinilla-Herrero I, Borfecchia E, Holzinger J, Mentzel UV, Joensen F, Lomachenko KA, Bordiga S, Lamberti C, Berlier G, Olsbye U, Svelle S, Skibsted J, Beato P. High Zn/Al ratios enhance dehydrogenation vs hydrogen transfer reactions of Zn-ZSM-5 catalytic systems in methanol conversion to aromatics. J Catal 2018. [DOI: 10.1016/j.jcat.2018.03.032] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Blahut M, Dzul S, Wang S, Kandegedara A, Grossoehme NE, Stemmler T, Outten FW. Conserved cysteine residues are necessary for nickel-induced allosteric regulation of the metalloregulatory protein YqjI (NfeR) in E. coli. J Inorg Biochem 2018; 184:123-133. [PMID: 29723740 DOI: 10.1016/j.jinorgbio.2018.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 04/19/2018] [Accepted: 04/22/2018] [Indexed: 11/28/2022]
Abstract
Transition metal homeostasis is necessary to sustain life. First row transition metals act as cofactors within the cell, performing vital functions ranging from DNA repair to respiration. However, intracellular metal concentrations exceeding physiological requirements may be toxic. In E. coli, the YqjH flavoprotein is thought to play a role in iron homeostasis. YqjH is transcriptionally regulated by the ferric uptake regulator and a newly discovered regulator encoded by yqjI. The apo-form of YqjI is a transcriptional repressor of both the yqjH and yqjI genes. YqjI repressor function is disrupted upon binding of nickel. The YqjI N-terminus is homologous to nickel-binding proteins, implicating this region as a nickel-binding domain. Based on function, yqjI and yqjH should be renamed Ni-responsive Fe-uptake regulator (nfeR) and Ni-responsive Fe-uptake flavoprotein (nfeF), respectively. X-ray Absorption Spectroscopy was employed to characterize the nickel binding site(s) within YqjI. Putative nickel binding ligands were targeted by site-directed mutagenesis and resulting variants were analyzed in vivo for repressor function. Isothermal titration calorimetry and competitive binding assays were used to further quantify nickel interactions with wild-type YqjI and its mutant derivatives. Results indicate plasticity in the nickel binding domain of YqjI. Residues C42 and C43 were found to be required for in vivo response of YqjI to nickel stress, though these residues are not required for in vitro nickel binding. We propose that YqjI may contain a vicinal disulfide bond between C42 and C43 that is important for nickel-responsive allosteric interactions between YqjI domains.
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Affiliation(s)
- Matthew Blahut
- University of South Carolina, Department of Chemistry and Biochemistry, Columbia, SC 29208, USA
| | - Stephen Dzul
- Wayne State University, Department of Pharmaceutical Sciences, Detroit, MI 48201, USA
| | - Suning Wang
- University of South Carolina, Department of Chemistry and Biochemistry, Columbia, SC 29208, USA
| | - Ashoka Kandegedara
- Wayne State University, Department of Pharmaceutical Sciences, Detroit, MI 48201, USA
| | - Nicholas E Grossoehme
- Winthrop University, Department of Chemistry, Physics, and Geology, Rock Hill, SC 29733, USA
| | - Timothy Stemmler
- Wayne State University, Department of Pharmaceutical Sciences, Detroit, MI 48201, USA
| | - F Wayne Outten
- University of South Carolina, Department of Chemistry and Biochemistry, Columbia, SC 29208, USA.
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12
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Khorasani-Motlagh M, Lacasse MJ, Zamble DB. High-affinity metal binding by the Escherichia coli [NiFe]-hydrogenase accessory protein HypB is selectively modulated by SlyD. Metallomics 2018; 9:482-493. [PMID: 28352890 DOI: 10.1039/c7mt00037e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
[NiFe]-hydrogenase, which catalyzes the reversible conversion between hydrogen gas and protons, is a vital component of the metabolism of many pathogens. Maturation of [NiFe]-hydrogenase requires selective nickel insertion that is completed, in part, by the metallochaperones SlyD and HypB. Escherichia coli HypB binds nickel with sub-picomolar affinity, and the formation of the HypB-SlyD complex activates nickel release from the high-affinity site (HAS) of HypB. In this study, the metal selectivity of this process was investigated. Biochemical experiments revealed that the HAS of full length HypB can bind stoichiometric zinc. Moreover, in contrast to the acceleration of metal release observed with nickel-loaded HypB, SlyD blocks the release of zinc from the HypB HAS. X-ray absorption spectroscopy (XAS) demonstrated that SlyD does not impact the primary coordination sphere of nickel or zinc bound to the HAS of HypB. Instead, computational modeling and XAS of HypB loaded with nickel or zinc indicated that zinc binds to HypB with a different coordination sphere than nickel. The data suggested that Glu9, which is not a nickel ligand, directly coordinates zinc. These results were confirmed through the characterization of E9A-HypB, which afforded weakened zinc affinity compared to wild-type HypB but similar nickel affinity. This mutant HypB fully supports the production of [NiFe]-hydrogenase in E. coli. Altogether, these results are consistent with the model that the HAS of HypB functions as a nickel site during [NiFe]-hydrogenase enzyme maturation and that the metal selectivity is controlled by activation of metal release by SlyD.
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13
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Glauninger H, Zhang Y, Higgins KA, Jacobs AD, Martin JE, Fu Y, Coyne Rd HJ, Bruce KE, Maroney MJ, Clemmer DE, Capdevila DA, Giedroc DP. Metal-dependent allosteric activation and inhibition on the same molecular scaffold: the copper sensor CopY from Streptococcus pneumoniae. Chem Sci 2018; 9:105-118. [PMID: 29399317 PMCID: PMC5772342 DOI: 10.1039/c7sc04396a] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/08/2017] [Indexed: 11/21/2022] Open
Abstract
Resistance to copper (Cu) toxicity in the respiratory pathogen Streptococcus pneumoniae is regulated by the Cu-specific metallosensor CopY. CopY is structurally related to the antibiotic-resistance regulatory proteins MecI and BlaI from Staphylococcus aureus, but is otherwise poorly characterized. Here we employ a multi-pronged experimental strategy to define the Spn CopY coordination chemistry and the unique mechanism of allosteric activation by Zn(ii) and allosteric inhibition by Cu(i) of cop promoter DNA binding. We show that Zn(ii) is coordinated by a subunit-bridging 3S 1H2O complex formed by the same residues that coordinate Cu(i), as determined by X-ray absorption spectroscopy and ratiometric pulsed alkylation-mass spectrometry (rPA-MS). Apo- and Zn-bound CopY are homodimers by small angle X-ray scattering (SAXS); however, Zn stabilizes the dimer, narrows the conformational ensemble of the apo-state as revealed by ion mobility-mass spectroscopy (IM-MS), and activates DNA binding in vitro and in cells. In contrast, Cu(i) employs the same Cys pair to form a subunit-bridging, kinetically stable, multi-metallic Cu·S cluster (KCu ≈ 1016 M-1) that induces oligomerization beyond the dimer as revealed by SAXS, rPA-MS and NMR spectroscopy, leading to inhibition of DNA binding. These studies suggest that CopY employs conformational selection to drive Zn-activation of DNA binding, and a novel Cu(i)-mediated assembly mechanism that dissociates CopY from the DNA via ligand exchange-catalyzed metal substitution, leading to expression of Cu resistance genes. Mechanistic parallels to antibiotic resistance repressors MecI and BlaI are discussed.
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Affiliation(s)
- Hendrik Glauninger
- Department of Chemistry , Indiana University , Bloomington , IN 47405-7102 , USA . ; ; Tel: +1-812-856-3178 ; Tel: +1-812-856-6398
| | - Yifan Zhang
- Department of Chemistry , Indiana University , Bloomington , IN 47405-7102 , USA . ; ; Tel: +1-812-856-3178 ; Tel: +1-812-856-6398
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA
| | - Khadine A Higgins
- Department of Chemistry , Indiana University , Bloomington , IN 47405-7102 , USA . ; ; Tel: +1-812-856-3178 ; Tel: +1-812-856-6398
- Department of Chemistry , Salve Regina University , Newport , RI 02840 , USA
| | - Alexander D Jacobs
- Department of Chemistry , Indiana University , Bloomington , IN 47405-7102 , USA . ; ; Tel: +1-812-856-3178 ; Tel: +1-812-856-6398
| | - Julia E Martin
- Department of Chemistry , Indiana University , Bloomington , IN 47405-7102 , USA . ; ; Tel: +1-812-856-3178 ; Tel: +1-812-856-6398
| | - Yue Fu
- Department of Chemistry , Indiana University , Bloomington , IN 47405-7102 , USA . ; ; Tel: +1-812-856-3178 ; Tel: +1-812-856-6398
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA
| | - H Jerome Coyne Rd
- Department of Chemistry , Indiana University , Bloomington , IN 47405-7102 , USA . ; ; Tel: +1-812-856-3178 ; Tel: +1-812-856-6398
| | - Kevin E Bruce
- Department of Biology , Indiana University , Bloomington , IN 47405 , USA
| | - Michael J Maroney
- Department of Chemistry , University of Massachusetts , Amherst , MA 01003 , USA
| | - David E Clemmer
- Department of Chemistry , Indiana University , Bloomington , IN 47405-7102 , USA . ; ; Tel: +1-812-856-3178 ; Tel: +1-812-856-6398
| | - Daiana A Capdevila
- Department of Chemistry , Indiana University , Bloomington , IN 47405-7102 , USA . ; ; Tel: +1-812-856-3178 ; Tel: +1-812-856-6398
| | - David P Giedroc
- Department of Chemistry , Indiana University , Bloomington , IN 47405-7102 , USA . ; ; Tel: +1-812-856-3178 ; Tel: +1-812-856-6398
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , IN 47405 , USA
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14
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Cabral ACS, Jakovleska J, Deb A, Penner-Hahn JE, Pecoraro VL, Freisinger E. Further insights into the metal ion binding abilities and the metalation pathway of a plant metallothionein from Musa acuminata. J Biol Inorg Chem 2018; 23:91-107. [PMID: 29218632 PMCID: PMC5756683 DOI: 10.1007/s00775-017-1513-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
The superfamily of metallothioneins (MTs) combines a diverse group of metalloproteins, sharing the characteristics of rather low molecular weight and high cysteine content. The latter provides MTs with the capability to coordinate thiophilic metal ions, in particular those with a d 10 electron configuration. The sub-family of plant MT3 proteins is only poorly characterized and there is a complete lack of three-dimensional structure information. Building upon our previous results on the Musa acuminata MT3 (musMT3) protein, the focus of the present work is to understand the metal cluster formation process, the role of the single histidine residue present in musMT3, and the metal ion binding affinity. We concentrate our efforts on the coordination of ZnII and CdII ions, using CoII as a spectroscopic probe for ZnII binding. The overall protein-fold is analysed with a combination of limited proteolytic digestion, mass spectrometry, and dynamic light scattering. Histidine coordination of metal ions is probed with extended X-ray absorption fine structure spectroscopy and CoII titration experiments. Initial experiments with isothermal titration calorimetry provide insights into the thermodynamics of metal ion binding.
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Affiliation(s)
- Augusto C S Cabral
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jovana Jakovleska
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109, USA
| | - James E Penner-Hahn
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109, USA
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109, USA
| | - Eva Freisinger
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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15
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Incorporation of second coordination sphere D-amino acids alters Cd(II) geometries in designed thiolate-rich proteins. J Biol Inorg Chem 2017; 23:123-135. [PMID: 29218636 DOI: 10.1007/s00775-017-1515-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
We use a de Novo protein design strategy to demonstrate that the second coordination sphere of a metal site plays a key role in controlling coordination geometries of Cd(II)-tris-thiolate complexes. Specifically, we show that alteration of chirality within the core hydrophobic packing region of a three-stranded coiled coil (3SCC) can control the coordination number of Cd(II) by limiting steric encumbrance to the metal center. Within a specific class of 3SCCs [Ac-G-(LKALEEK) n -G-NH2], where n = 4 is TRI and n = 5 is GRAND, one L-Leu may be substituted by L-Cys to generate a planar tris-thiolate array capable of metal binding. In the native peptide containing only the L-configuration of leucine, the three-Cys ligand site leads to a mixture of 3- and 4-coordinate Cd(II). When the L-Leu above (toward the N-terminus) the tris-Cys site is substituted with D-Leu, solely a 3-coordinate structure [Cd(II)S3] was obtained. When D-Leu is located below (toward the C-terminus), a mixture of two coordination geometries, presumably Cd(II)S3O and Cd(II)S3O2, is observed, while substitution with D-Leu both above and below the tris-Cys plane yields a higher percentage of 4-coordinate Cd(II)S3O species. Thus, the use of D-amino acids around a metal's coordination sphere provides a powerful tool for controlling the properties of future designed metalloproteins.
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16
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Truong PT, Gale EM, Dzul SP, Stemmler TL, Harrop TC. Steric Enforcement about One Thiolate Donor Leads to New Oxidation Chemistry in a NiSOD Model Complex. Inorg Chem 2017; 56:7761-7780. [PMID: 28459242 DOI: 10.1021/acs.inorgchem.7b00485] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ni-containing superoxide dismutase (NiSOD) represents an unusual member of the SOD family due to the presence of oxygen-sensitive Ni-SCys bonds at its active site. Reported in this account is the synthesis and properties of the NiII complex of the N3S2 ligand [N3S2Me2]3- ([N3S2Me2]3- = deprotonated form of 2-((2-mercapto-2-methylpropyl)(pyridin-2-ylmethyl)amino)-N-(2-mercaptoethyl)acetamide), namely Na[Ni(N3S2Me2)] (2), as a NiSOD model that features sterically robust gem-(CH3)2 groups on the thiolate α-C positioned trans to the carboxamide. The crystal structure of 2, coupled with spectroscopic measurements from 1H NMR, X-ray absorption, IR, UV-vis, and mass spectrometry (MS), reveal a planar NiII (S = 0) ion coordinated by only the N2S2 basal donors of the N3S2 ligand. While the structure and spectroscopic properties of 2 resemble those of NiSODred and other models, the asymmetric S ligands open up new reaction paths upon chemical oxidation. One unusual oxidation product is the planar NiII-N3S complex [Ni(Lox)] (5; Lox = 2-(5,5-dimethyl-2-(pyridin-2-yl)thiazolidin-3-yl)-N-(2-mercaptoethyl)acetamide), where two-electron oxidation takes place at the substituted thiolate and py-CH2 carbon to generate a thiazolidine heterocycle. Electrochemical measurements of 2 reveal irreversible events wholly consistent with thiolate redox, which were identified by comparison to the ZnII complex Na[Zn(N3S2Me2)] (3). Although no reaction is observed between 2 and azide, reaction of 2 with superoxide produces multiple products on the basis of UV-vis and MS data, one of which is 5. Density functional theory (DFT) computations suggest that the HOMO in 2 is π* with primary contributions from Ni-dπ/S-pπ orbitals. These contributions can be modulated and biased toward Ni when electron-withdrawing groups are placed on the thiolate α-C. Analysis of the oxidized five-coordinate species 2ox* by DFT reveal a singly occupied spin-up (α) MO that is largely thiolate based, which supports the proposed NiIII-thiolate/NiII-thiyl radical intermediates that ultimately yield 5 and other products.
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Affiliation(s)
- Phan T Truong
- Department of Chemistry and Center for Metalloenzyme Studies, The University of Georgia , 140 Cedar Street, Athens, Georgia 30602, United States
| | - Eric M Gale
- Department of Chemistry and Center for Metalloenzyme Studies, The University of Georgia , 140 Cedar Street, Athens, Georgia 30602, United States
| | - Stephen P Dzul
- Departments of Pharmaceutical Sciences, Biochemistry and Molecular Biology, Wayne State University , Detroit, Michigan 48201, United States
| | - Timothy L Stemmler
- Departments of Pharmaceutical Sciences, Biochemistry and Molecular Biology, Wayne State University , Detroit, Michigan 48201, United States
| | - Todd C Harrop
- Department of Chemistry and Center for Metalloenzyme Studies, The University of Georgia , 140 Cedar Street, Athens, Georgia 30602, United States
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17
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Carr CE, Musiani F, Huang HT, Chivers PT, Ciurli S, Maroney MJ. Glutamate Ligation in the Ni(II)- and Co(II)-Responsive Escherichia coli Transcriptional Regulator, RcnR. Inorg Chem 2017; 56:6459-6476. [PMID: 28517938 DOI: 10.1021/acs.inorgchem.7b00527] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Escherichia coli RcnR (resistance to cobalt and nickel regulator, EcRcnR) is a metal-responsive repressor of the genes encoding the Ni(II) and Co(II) exporter proteins RcnAB by binding to PRcnAB. The DNA binding affinity is weakened when the cognate ions Ni(II) and Co(II) bind to EcRcnR in a six-coordinate site that features a (N/O)5S ligand donor-atom set in distinct sites: while both metal ions are bound by the N terminus, Cys35, and His64, Co(II) is additionally bound by His3. On the other hand, the noncognate Zn(II) and Cu(I) ions feature a lower coordination number, have a solvent-accessible binding site, and coordinate protein ligands that do not include the N-terminal amine. A molecular model of apo-EcRcnR suggested potential roles for Glu34 and Glu63 in binding Ni(II) and Co(II) to EcRcnR. The roles of Glu34 and Glu63 in metal binding, metal selectivity, and function were therefore investigated using a structure/function approach. X-ray absorption spectroscopy was used to assess the structural changes in the Ni(II), Co(II), and Zn(II) binding sites of Glu → Ala and Glu → Cys variants at both positions. The effect of these structural alterations on the regulation of PrcnA by EcRcnR in response to metal binding was explored using LacZ reporter assays. These combined studies indicate that while Glu63 is a ligand for both metal ions, Glu34 is a ligand for Co(II) but possibly not for Ni(II). The Glu34 variants affect the structure of the cognate metal sites, but they have no effect on the transcriptional response. In contrast, the Glu63 variants affect both the structure and transcriptional response, although they do not completely abolish the function of EcRcnR. The structure of the Zn(II) site is not significantly perturbed by any of the glutamic acid variations. The spectroscopic and functional data obtained on the mutants were used to calculate models of the metal-site structures of EcRcnR bound to Ni(II), Co(II), and Zn(II). The results are interpreted in terms of a switch mechanism, in which a subset of the metal-binding ligands is responsible for the allosteric response required for DNA release.
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Affiliation(s)
- Carolyn E Carr
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna , Bologna 40126, Italy
| | - Hsin-Ting Huang
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Peter T Chivers
- Departments of Biosciences and Chemistry, Durham University , Durham DH1 3LE, United Kingdom
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna , Bologna 40126, Italy
| | - Michael J Maroney
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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18
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Steiner RA, Dzul SP, Stemmler TL, Harrop TC. Synthesis and Speciation-Dependent Properties of a Multimetallic Model Complex of NiSOD That Exhibits Unique Hydrogen-Bonding. Inorg Chem 2017; 56:2849-2862. [PMID: 28212040 DOI: 10.1021/acs.inorgchem.6b02997] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The complex Na3[{NiII(nmp)}3S3BTAalk)] (1) (nmp2- = deprotonated form of N-(2-mercaptoethyl)picolinamide; H3S3BTAalk = N1,N3,N5-tris(2-mercaptoethyl)benzene-1,3,5-tricarboxamide, where H = dissociable protons), supported by the thiolate-benzenetricarboxamide scaffold (S3BTAalk), has been synthesized as a trimetallic model of nickel-containing superoxide dismutase (NiSOD). X-ray absorption spectroscopy (XAS) and 1H NMR measurements on 1 indicate that the NiII centers are square-planar with N2S2 coordination, and Ni-N and Ni-S distances of 1.95 and 2.16 Å, respectively. Additional evidence from IR indicates the presence of H-bonds in 1 from the approximately -200 cm-1 shift in νNH from free ligand. The presence of H-bonds allows for speciation that is temperature-, concentration-, and solvent-dependent. In unbuffered water and at low temperature, a dimeric complex (1A; λ = 410 nm) that aggregates through intermolecular NH···O═C bonds of BTA units is observed. Dissolution of 1 in pH 7.4 buffer or in unbuffered water at temperatures above 50 °C results in monomeric complex (1M; λ = 367 nm) linked through intramolecular NH···S bonds. DFT computations indicate a low energy barrier between 1A and 1M with nearly identical frontier MOs and Ni-ligand metrics. Notably, 1A and 1M exhibit remarkable stability in protic solvents such as MeOH and H2O, in stark contrast to monometallic [NiII(nmp)(SR)]- complexes. The reactivity of 1 with excess O2, H2O2, and O2•- is species-dependent. IR and UV-vis reveal that 1A in MeOH reacts with excess O2 to yield an S-bound sulfinate, but does not react with O2•-. In contrast, 1M is stable to O2 in pH 7.4 buffer, but reacts with O2•- to yield a putative [NiII(nmp)(O2)]- complex from release of the BTA-thiolate based on EPR.
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Affiliation(s)
- Ramsey A Steiner
- Department of Chemistry and Center for Metalloenzyme Studies, The University of Georgia , 140 Cedar St, Athens, Georgia 30602, United States
| | - Stephen P Dzul
- Departments of Pharmaceutical Sciences, and Biochemistry and Molecular Biology, Wayne State University , Detroit, Michigan 48201, United States
| | - Timothy L Stemmler
- Departments of Pharmaceutical Sciences, and Biochemistry and Molecular Biology, Wayne State University , Detroit, Michigan 48201, United States
| | - Todd C Harrop
- Department of Chemistry and Center for Metalloenzyme Studies, The University of Georgia , 140 Cedar St, Athens, Georgia 30602, United States
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19
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Alies B, Conte-Daban A, Sayen S, Collin F, Kieffer I, Guillon E, Faller P, Hureau C. Zinc(II) Binding Site to the Amyloid-β Peptide: Insights from Spectroscopic Studies with a Wide Series of Modified Peptides. Inorg Chem 2016; 55:10499-10509. [PMID: 27665863 PMCID: PMC5069684 DOI: 10.1021/acs.inorgchem.6b01733] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The Zn(II) ion has been linked to Alzheimer's disease (AD) due to its ability to modulate the aggregating properties of the amyloid-β (Aβ) peptide, where Aβ aggregation is a central event in the etiology of the disease. Delineating Zn(II) binding properties to Aβ is thus a prerequisite to better grasp its potential role in AD. Because of (i) the flexibility of the Aβ peptide, (ii) the multiplicity of anchoring sites, and (iii) the silent nature of the Zn(II) ion in most classical spectroscopies, this is a difficult task. To overcome these difficulties, we have investigated the impact of peptide alterations (mutations, N-terminal acetylation) on the Zn(Aβ) X-ray absorption spectroscopy fingerprint and on the Zn(II)-induced modifications of the Aβ peptides' NMR signatures. We propose a tetrahedrally bound Zn(II) ion, in which the coordination sphere is made by two His residues and two carboxylate side chains. Equilibria between equivalent ligands for one Zn(II) binding position have also been observed, the predominant site being made by the side chains of His6, His13 or His14, Glu11, and Asp1 or Glu3 or Asp7, with a slight preference for Asp1.
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Affiliation(s)
- Bruno Alies
- CNRS, LCC (Laboratoire de Chimie de Coordination) , 205 Route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France.,Université de Toulouse , UPS, INPT, F-31077 Toulouse Cedex 4, France
| | - Amandine Conte-Daban
- CNRS, LCC (Laboratoire de Chimie de Coordination) , 205 Route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France.,Université de Toulouse , UPS, INPT, F-31077 Toulouse Cedex 4, France
| | - Stéphanie Sayen
- Université Reims Champagne Ardenne , Institut de Chimie Moléculaire de Reims (ICMR), UMR 7312 CNRS-URCA, Moulin de la Housse, BP 1039, 51687 Reims Cedex 2, France
| | - Fabrice Collin
- CNRS, LCC (Laboratoire de Chimie de Coordination) , 205 Route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France.,Université de Toulouse , UPS, INPT, F-31077 Toulouse Cedex 4, France.,Université de Toulouse , UPS, UMR 152 PHARMA-DEV, Université Toulouse 3, and Institut de Recherche pour le Développement (IRD), UMR 152 PHARMA-DEV, F-31062 Toulouse Cedex 09, France
| | - Isabelle Kieffer
- Observatoire des Sciences de l'Univers de Grenoble (OSUG) , CNRS UMS 832, 414 Rue de la Piscine, 38400 Saint Martin d'Hères, France.,BM30B/FAME, ESRF, The European Synchrotron , 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Emmanuel Guillon
- Université Reims Champagne Ardenne , Institut de Chimie Moléculaire de Reims (ICMR), UMR 7312 CNRS-URCA, Moulin de la Housse, BP 1039, 51687 Reims Cedex 2, France
| | - Peter Faller
- CNRS, LCC (Laboratoire de Chimie de Coordination) , 205 Route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France.,Université de Toulouse , UPS, INPT, F-31077 Toulouse Cedex 4, France
| | - Christelle Hureau
- CNRS, LCC (Laboratoire de Chimie de Coordination) , 205 Route de Narbonne, BP 44099, F-31077 Toulouse Cedex 4, France.,Université de Toulouse , UPS, INPT, F-31077 Toulouse Cedex 4, France
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20
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Nakashige TG, Stephan JR, Cunden LS, Brophy MB, Wommack AJ, Keegan BC, Shearer JM, Nolan EM. The Hexahistidine Motif of Host-Defense Protein Human Calprotectin Contributes to Zinc Withholding and Its Functional Versatility. J Am Chem Soc 2016; 138:12243-51. [PMID: 27541598 PMCID: PMC5038136 DOI: 10.1021/jacs.6b06845] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Human calprotectin (CP, S100A8/S100A9 oligomer, MRP-8/MRP-14 oligomer) is an abundant host-defense protein that is involved in the metal-withholding innate immune response. CP coordinates a variety of divalent first-row transition metal ions, which is implicated in its antimicrobial function, and its ability to sequester nutrient Zn(II) ions from microbial pathogens has been recognized for over two decades. CP has two distinct transition-metal-binding sites formed at the S100A8/S100A9 dimer interface, including a histidine-rich site composed of S100A8 residues His17 and His27 and S100A9 residues His91 and His95. In this study, we report that CP binds Zn(II) at this site using a hexahistidine motif, completed by His103 and His105 of the S100A9 C-terminal tail and previously identified as the high-affinity Mn(II) and Fe(II) coordination site. Zn(II) binding at this unique site shields the S100A9 C-terminal tail from proteolytic degradation by proteinase K. X-ray absorption spectroscopy and Zn(II) competition titrations support the formation of a Zn(II)-His6 motif. Microbial growth studies indicate that the hexahistidine motif is important for preventing microbial Zn(II) acquisition from CP by the probiotic Lactobacillus plantarum and the opportunistic human pathogen Candida albicans. The Zn(II)-His6 site of CP expands the known biological coordination chemistry of Zn(II) and provides new insight into how the human innate immune system starves microbes of essential metal nutrients.
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Affiliation(s)
- Toshiki G. Nakashige
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Jules R. Stephan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Lisa S. Cunden
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Megan Brunjes Brophy
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Andrew J. Wommack
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | | | - Elizabeth M. Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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21
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Cleavage and polyadenylation specificity factor 30: An RNA-binding zinc-finger protein with an unexpected 2Fe-2S cluster. Proc Natl Acad Sci U S A 2016; 113:4700-5. [PMID: 27071088 DOI: 10.1073/pnas.1517620113] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cleavage and polyadenylation specificity factor 30 (CPSF30) is a key protein involved in pre-mRNA processing. CPSF30 contains five Cys3His domains (annotated as "zinc-finger" domains). Using inductively coupled plasma mass spectrometry, X-ray absorption spectroscopy, and UV-visible spectroscopy, we report that CPSF30 is isolated with iron, in addition to zinc. Iron is present in CPSF30 as a 2Fe-2S cluster and uses one of the Cys3His domains; 2Fe-2S clusters with a Cys3His ligand set are rare and notably have also been identified in MitoNEET, a protein that was also annotated as a zinc finger. These findings support a role for iron in some zinc-finger proteins. Using electrophoretic mobility shift assays and fluorescence anisotropy, we report that CPSF30 selectively recognizes the AU-rich hexamer (AAUAAA) sequence present in pre-mRNA, providing the first molecular-based evidence to our knowledge for CPSF30/RNA binding. Removal of zinc, or both zinc and iron, abrogates binding, whereas removal of just iron significantly lessens binding. From these data we propose a model for RNA recognition that involves a metal-dependent cooperative binding mechanism.
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22
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Lebrun V, Tron A, Lebrun C, Latour J, McClenaghan ND, Sénèque O. Reactivity of a Zn(Cys)
2
(His)
2
Zinc Finger with Singlet Oxygen: Oxidation Directed toward Cysteines but not Histidines. Chemistry 2015; 21:14002-10. [DOI: 10.1002/chem.201501749] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Vincent Lebrun
- Univ. Grenoble Alpes, LCBM/PMB and CEA, IRTSV/CBM/PMB and CNRS, LCBM UMR 5249, PMB, 38000 Grenoble (France)
| | - Arnaud Tron
- Univ. Bordeaux and CNRS, ISM, 33405 Talence (France)
| | - Colette Lebrun
- Univ. Grenoble Alpes and CEA, INAC/SCIB/RICC, 38000 Grenoble (France)
| | - Jean‐Marc Latour
- Univ. Grenoble Alpes, LCBM/PMB and CEA, IRTSV/CBM/PMB and CNRS, LCBM UMR 5249, PMB, 38000 Grenoble (France)
| | | | - Olivier Sénèque
- Univ. Grenoble Alpes, LCBM/PMB and CEA, IRTSV/CBM/PMB and CNRS, LCBM UMR 5249, PMB, 38000 Grenoble (France)
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23
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Kuhn PS, Cremer L, Gavriluta A, Jovanović KK, Filipović L, Hummer AA, Büchel GE, Dojčinović BP, Meier SM, Rompel A, Radulović S, Tommasino JB, Luneau D, Arion VB. Heteropentanuclear Oxalato-Bridged nd-4f (n=4, 5) Metal Complexes with NO Ligand: Synthesis, Crystal Structures, Aqueous Stability and Antiproliferative Activity. Chemistry 2015; 21:13703-13. [PMID: 26260662 PMCID: PMC4583781 DOI: 10.1002/chem.201502026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Indexed: 11/29/2022]
Abstract
A series of heteropentanuclear oxalate-bridged Ru(NO)-Ln (4d–4f) metal complexes of the general formula (nBu4N)5[Ln{RuCl3(μ-ox)(NO)}4], where Ln=Y (2), Gd (3), Tb (4), Dy (5) and ox=oxalate anion, were obtained by treatment of (nBu4N)2[RuCl3(ox)(NO)] (1) with the respective lanthanide salt in 4:1 molar ratio. The compounds were characterized by elemental analysis, IR spectroscopy, electrospray ionization (ESI) mass spectrometry, while 1, 2, and 5 were in addition analyzed by X-ray crystallography, 1 by Ru K-edge XAS and 1 and 2 by 13C NMR spectroscopy. X-ray diffraction showed that in 2 and 5 four complex anions [RuCl3(ox)(NO)]2− are coordinated to YIII and DyIII, respectively, with formation of [Ln{RuCl3(μ-ox)(NO)}4]5− (Ln=Y, Dy). While YIII is eight-coordinate in 2, DyIII is nine-coordinate in 5, with an additional coordination of an EtOH molecule. The negative charge is counterbalanced by five nBu4N+ ions present in the crystal structure. The stability of complexes 2 and 5 in aqueous medium was monitored by UV/Vis spectroscopy. The antiproliferative activity of ruthenium-lanthanide complexes 2–5 were assayed in two human cancer cell lines (HeLa and A549) and in a noncancerous cell line (MRC-5) and compared with those obtained for the previously reported Os(NO)-Ln (5d–4f) analogues (nBu4N)5[Ln{OsCl3(ox)(NO)}4] (Ln=Y (6), Gd (7), Tb (8), Dy (9)). Complexes 2–5 were found to be slightly more active than 1 in inhibiting the proliferation of HeLa and A549 cells, and significantly more cytotoxic than 5d–4f metal complexes 6–9 in terms of IC50 values. The highest antiproliferative activity with IC50 values of 20.0 and 22.4 μM was found for 4 in HeLa and A549 cell lines, respectively. These cytotoxicity results are in accord with the presented ICP-MS data, indicating five- to eightfold greater accumulation of ruthenium versus osmium in human A549 cancer cells.
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Affiliation(s)
- Paul-Steffen Kuhn
- University of Vienna, Faculty of Chemistry, Institute of Inorganic Chemistry, Währinger Strasse 42, 1090 Vienna (Austria)
| | - Laura Cremer
- University of Vienna, Faculty of Chemistry, Institute of Inorganic Chemistry, Währinger Strasse 42, 1090 Vienna (Austria)
| | - Anatolie Gavriluta
- Université Claude Bernard Lyon 1, Laboratoire des Multimatériaux et Interfaces (UMR 5615), Campus de la Doua, 69622 Villeurbanne cedex (France)
| | - Katarina K Jovanović
- Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade (Serbia)
| | - Lana Filipović
- Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade (Serbia)
| | - Alfred A Hummer
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090 Wien (Austria)
| | - Gabriel E Büchel
- University of Vienna, Faculty of Chemistry, Institute of Inorganic Chemistry, Währinger Strasse 42, 1090 Vienna (Austria).,Present address: Division for Physical Sciences and Engineering and KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal (Saudi Arabia)
| | - Biljana P Dojčinović
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, Center of Chemistry, Studentski trg 12-16, Belgrade (Serbia)
| | - Samuel M Meier
- Faculty of Chemistry, Institute of Analytical Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna (Austria)
| | - Annette Rompel
- Universität Wien, Fakultät für Chemie, Institut für Biophysikalische Chemie, Althanstraße 14, 1090 Wien (Austria)
| | - Siniša Radulović
- Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade (Serbia)
| | - Jean Bernard Tommasino
- Université Claude Bernard Lyon 1, Laboratoire des Multimatériaux et Interfaces (UMR 5615), Campus de la Doua, 69622 Villeurbanne cedex (France)
| | - Dominique Luneau
- Université Claude Bernard Lyon 1, Laboratoire des Multimatériaux et Interfaces (UMR 5615), Campus de la Doua, 69622 Villeurbanne cedex (France).
| | - Vladimir B Arion
- University of Vienna, Faculty of Chemistry, Institute of Inorganic Chemistry, Währinger Strasse 42, 1090 Vienna (Austria).
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Chan KL, Bakman I, Marts AR, Batir Y, Dowd TL, Tierney D, Gibney BR. Characterization of the Zn(II) binding properties of the human Wilms' tumor suppressor protein C-terminal zinc finger peptide. Inorg Chem 2014; 53:6309-20. [PMID: 24893204 PMCID: PMC4066921 DOI: 10.1021/ic500862b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Indexed: 12/19/2022]
Abstract
Zinc finger proteins that bind Zn(II) using a Cys2His2 coordination motif within a ββα protein fold are the most abundant DNA binding transcription factor domains in eukaryotic systems. These classic zinc fingers are typically unfolded in the apo state and spontaneously fold into their functional ββα folds upon incorporation of Zn(II). These metal-induced protein folding events obscure the free energy cost of protein folding by coupling the protein folding and metal-ion binding thermodynamics. Herein, we determine the formation constant of a Cys2His2/ββα zinc finger domain, the C-terminal finger of the Wilms' tumor suppressor protein (WT1-4), for the purposes of determining its free energy cost of protein folding. Measurements of individual conditional dissociation constants, Kd values, at pH values from 5 to 9 were determined using fluorescence spectroscopy by direct or competition titration. Potentiometric titrations of apo-WT1-4 followed by NMR spectroscopy provided the intrinsic pKa values of the Cys2His2 residues, and corresponding potentiometric titrations of Zn(II)-WT1-4 followed by fluorescence spectroscopy yielded the effective pKa(eff) values of the Cys2His2 ligands bound to Zn(II). The Kd, pKa, and pKa(eff) values were combined in a minimal, complete equilibrium model to yield the pH-independent formation constant value for Zn(II)-WT1-4, Kf(ML) value of 7.5 × 10(12) M(-1), with a limiting Kd value of 133 fM. This shows that Zn(II) binding to the Cys2His2 site in WT1-4 provides at least -17.6 kcal/mol in driving force to fold the protein scaffold. A comparison of the conditional dissociation constants of Zn(II)-WT1-4 to those from the model peptide Zn(II)-GGG-Cys2His2 over the pH range 5.0 to 9.0 and a comparison of their pH-independent Kf(ML) values demonstrates that the free energy cost of protein folding in WT1-4 is less than +2.1 kcal/mol. These results validate our GGG model system for determining the cost of protein folding in natural zinc finger proteins and support the conclusion that the cost of protein folding in most zinc finger proteins is ≤+4.2 kcal/mol, a value that pales in comparison to the free energy contribution of Zn(II) binding, -17.6 kcal/mol.
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Affiliation(s)
- Ka Lam Chan
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
| | - Inna Bakman
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program in Biochemistry, The City
University of New York, New York, New York 10016, United States
| | - Amy R. Marts
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Yuksel Batir
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
| | - Terry L. Dowd
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program in Biochemistry, The City
University of New York, New York, New York 10016, United States
| | - David
L. Tierney
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Brian R. Gibney
- Department of Chemistry, Brooklyn
College, 2900 Bedford
Avenue, Brooklyn, New York 11210, United States
- Ph.D. Program in Biochemistry, The City
University of New York, New York, New York 10016, United States
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25
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The solution structure of the copper clioquinol complex. J Inorg Biochem 2014; 133:50-6. [PMID: 24503514 DOI: 10.1016/j.jinorgbio.2014.01.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/01/2013] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
Clioquinol (5-chloro-7-iodo-8-hydroxyquinoline) recently has shown promising results in the treatment of Alzheimer's disease and in cancer therapy, both of which also are thought to be due to clioquinol's ability as a lipophilic copper chelator. Previously, clioquinol was used as an anti-fungal and anti-protozoal drug that was responsible for an epidemic of subacute myelo-optic neuropathy (SMON) in Japan during the 1960s, probably a myeloneuropathy arising from a clioquinol-induced copper deficiency. Previous X-ray absorption spectroscopy of solutions of copper chelates of clioquinol suggested unusual coordination chemistry. Here we use a combination of electron paramagnetic, UV-visible and X-ray absorption spectroscopies to provide clarification of the chelation chemistry between clioquinol and copper. We find that the solution structures for the copper complexes formed with stoichiometric and excess clioquinol are conventional 8-hydroxyquinolate chelates. Thus, the promise of clioquinol in new treatments for Alzheimer's disease and in cancer therapy is not likely to be due to any novel chelation chemistry, but rather due to other factors including the high lipophilicity of the free ligand and chelate complexes.
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Abstract
Metalloproteins are enormously important in biology. While a variety of techniques exist for studying metals in biology, X-ray absorption spectroscopy is particularly useful in that it can determine the local electronic and physical structure around the metal center, and is one of the few avenues for studying "spectroscopically silent" metal ions like Zn(II) and Cu(I) that have completely filled valence bands. While X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) are useful for studying metalloprotein structure, they suffer the limitation that the detected signal is an average of all the various metal centers in the sample, which limits its usefulness for studying metal centers in situ or in cell lysates. It would be desirable to be able to separate the various proteins in a mixture prior to performing X-ray absorption studies, so that the derived signal is from one species only. Here we describe a method for performing X-ray absorption spectroscopy on protein bands following electrophoretic separation and western blotting.
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Affiliation(s)
- Jesse Ward
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL, 60439, USA
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Hummer AA, Heffeter P, Berger W, Filipits M, Batchelor D, Büchel GE, Jakupec MA, Keppler BK, Rompel A. X-ray absorption near edge structure spectroscopy to resolve the in vivo chemistry of the redox-active indazolium trans-[Tetrachlorobis(1H-indazole)ruthenate(III)] (KP1019). J Med Chem 2013; 56:1182-96. [PMID: 23282017 PMCID: PMC3579476 DOI: 10.1021/jm301648f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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Indazolium trans-[tetrachlorobis(1H-indazole)ruthenate(III)] (1, KP1019) and
its analogue
sodium trans-[tetrachlorobis(1H-indazole)ruthenate(III)]
(2, KP1339) are promising redox-active anticancer drug
candidates that were investigated with X-ray absorption near edge
structure spectroscopy. The analysis was based on the concept of the
coordination charge and ruthenium model compounds representing possible
coordinations and oxidation states in vivo. 1 was investigated
in citrate saline buffer (pH 3.5) and in carbonate buffer (pH 7.4)
at 37 °C for different time intervals. Interaction studies on 1 with glutathione in saline buffer and apo-transferrin in
carbonate buffer were undertaken, and the coordination of 1 and 2 in tumor tissues was studied too. The most likely
coordinations and oxidation states of the compound under the above
mentioned conditions were assigned. Microprobe X-ray fluorescence
of tumor thin sections showed the strong penetration of ruthenium
into the tumor tissue, with the highest concentrations near blood
vessels and in the edge regions of the tissue samples.
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Affiliation(s)
- Alfred A Hummer
- Institut für Biophysikalische Chemie, Universität Wien, Althanstrasse 14, 1090 Wien, Austria
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Hummer AA, Rompel A. X-Ray Absorption Spectroscopy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 93:257-305. [DOI: 10.1016/b978-0-12-416596-0.00008-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Higgins KA, Hu HQ, Chivers PT, Maroney MJ. Effects of select histidine to cysteine mutations on transcriptional regulation by Escherichia coli RcnR. Biochemistry 2012; 52:84-97. [PMID: 23215580 DOI: 10.1021/bi300886q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The RcnR metalloregulator represses the transcription of the Co(II) and Ni(II) exporter, RcnAB. Previous studies have shown that Co(II) and Ni(II) bind to RcnR in six-coordinate sites, resulting in derepression. Here, the roles of His60, His64, and His67 in specific metal recognition are examined. His60 and His64 correspond to ligands that are important for Cu(I) binding in the homologous Cu(I)-responsive metalloregulator, CsoR. These residues are known to be functionally important in RcnR transcriptional regulation. X-ray absorption spectroscopy (XAS) was used to examine the structure of bound cognate and noncognate metal ions, and lacZ reporter assays were used to assess the transcription of rcnA in response to metal binding in the three His → Cys mutations, H60C, H64C, and H67C. These studies confirm that both Ni(II) and Co(II) use His64 as a ligand. H64C-RcnR is also the only known mutant that retains a Co(II) response while eliminating the response to Ni(II) binding. XAS data indicate that His60 and His67 are potential Co(II) ligands. The effects of the mutations of His60, His64, and His67 on the structures of the noncognate metal ions [Zn(II) and Cu(I)] reveal that these residues have distinctive roles in binding noncognate metals. None of the His → Cys mutants in RcnR confer any response to Cu(I) binding, including H64C-RcnR, where the ligands involved in Cu(I) binding in CsoR are present. These data indicate that while the secondary, tertiary, and quaternary structures of CsoR and RcnR are quite similar, small changes in primary sequence reveal that the specific mechanisms involved in metal recognition are quite different.
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Affiliation(s)
- Khadine A Higgins
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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Cotelesage JJ, Pushie MJ, Grochulski P, Pickering IJ, George GN. Metalloprotein active site structure determination: Synergy between X-ray absorption spectroscopy and X-ray crystallography. J Inorg Biochem 2012; 115:127-37. [DOI: 10.1016/j.jinorgbio.2012.06.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/21/2012] [Accepted: 06/22/2012] [Indexed: 11/30/2022]
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Hummer AA, Bartel C, Arion VB, Jakupec MA, Meyer-Klaucke W, Geraki T, Quinn PD, Mijovilovich A, Keppler BK, Rompel A. X-ray Absorption Spectroscopy of an Investigational Anticancer Gallium(III) Drug: Interaction with Serum Proteins, Elemental Distribution Pattern, and Coordination of the Compound in Tissue. J Med Chem 2012; 55:5601-13. [DOI: 10.1021/jm3005459] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alfred A. Hummer
- Institut für
Biophysikalische
Chemie, Universität Wien, Althanstraße
14, 1090 Wien, Austria
| | - Caroline Bartel
- Institut für Anorganische
Chemie, Universität Wien, Währinger
Straße 42, 1090 Wien, Austria
| | - Vladimir B. Arion
- Institut für Anorganische
Chemie, Universität Wien, Währinger
Straße 42, 1090 Wien, Austria
| | - Michael A. Jakupec
- Institut für Anorganische
Chemie, Universität Wien, Währinger
Straße 42, 1090 Wien, Austria
| | - Wolfram Meyer-Klaucke
- European Molecular Biology Laboratory Hamburg, Notkestraße 85, 22603
Hamburg, Germany
| | - Tina Geraki
- Diamond Light Source, Harwell Campus, Didcot OX11 0DE,
United Kingdom
| | - Paul D. Quinn
- Diamond Light Source, Harwell Campus, Didcot OX11 0DE,
United Kingdom
| | - Ana Mijovilovich
- Inorganic
Chemistry and Catalysis
Group, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The
Netherlands
| | - Bernhard K. Keppler
- Institut für Anorganische
Chemie, Universität Wien, Währinger
Straße 42, 1090 Wien, Austria
| | - Annette Rompel
- Institut für
Biophysikalische
Chemie, Universität Wien, Althanstraße
14, 1090 Wien, Austria
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Higgins KA, Chivers PT, Maroney MJ. Role of the N-terminus in determining metal-specific responses in the E. coli Ni- and Co-responsive metalloregulator, RcnR. J Am Chem Soc 2012; 134:7081-93. [PMID: 22471551 PMCID: PMC3375346 DOI: 10.1021/ja300834b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
RcnR (resistance to cobalt and nickel regulator) is a 40-kDa homotetrameric protein and metalloregulator that controls the transcription of the Co(II) and Ni(II) exporter, RcnAB, by binding to DNA as an apoprotein and releasing DNA in response to specifically binding Co(II) and Ni(II) ions. Using X-ray absorption spectroscopy (XAS) to examine the structure of metals bound and lacZ reporter assays of the transcription of RcnA in response to metal binding, in WT and mutant proteins, the roles of coordination number, ligand selection, and residues in the N-terminus of the protein were examined as determinants in metal ion recognition. The studies show that the cognate metal ions, Co(II) and Ni(II), which bind in (N/O)(5)S six-coordinate sites, are distinguished from non-cognate metal ions (Cu(I) and Zn(II)), which bind only three protein ligands and one anion from the buffer, by coordination number and ligand selection. Using mutations of residues near the N-terminus, the N-terminal amine is shown to be a ligand of the cognate metal ions that is missing in the complexes with non-cognate metal ions. The side chain of His3 is also shown to play an important role in distinguishing metal ions. The imidazole group is shown to be a ligand in the Co(II) RcnR complex, but not in the Zn(II) complex. Further, His3 does not appear to bind to Ni(II), providing a structural basis for the differential regulation of RcnAB by the two cognate ions. The Zn(II) complexes change coordination number in response to the residue in position three. In H3C-RcnR, the Zn(II) complex is five-coordinate, and in H3E-RcnR the Zn(II) ion is bound to six protein ligands. The metric parameters of this unusual Zn(II) structure resemble those of the WT-Ni(II) complex, and the mutant protein is able to regulate expression of RcnAB in response to binding the non-cognate ion. The results are discussed within a protein allosteric model for gene regulation by metalloregulators.
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Affiliation(s)
- Khadine A. Higgins
- Department of Chemistry , University of Massachusetts, Amherst, Massachusetts 01003
| | - Peter T. Chivers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis MO 63110
| | - Michael J. Maroney
- Department of Chemistry , University of Massachusetts, Amherst, Massachusetts 01003
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Hu J, Chen Q, Yang X, Hu F, Hu H, Yin Z. Extraction of zinc from ammoniacal solution with β-diketone: A comparative study of solvents used. Sep Purif Technol 2012. [DOI: 10.1016/j.seppur.2011.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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A tetrahedral coordination of Zinc during transmembrane transport by P-type Zn(2+)-ATPases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1374-7. [PMID: 22387457 DOI: 10.1016/j.bbamem.2012.02.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 02/15/2012] [Accepted: 02/17/2012] [Indexed: 01/09/2023]
Abstract
Zn(2+) is an essential transition metal required in trace amounts by all living organisms. However, metal excess is cytotoxic and leads to cell damage. Cells rely on transmembrane transporters, with the assistance of other proteins, to establish and maintain Zn(2+) homeostasis. Metal coordination during transport is key to specific transport and unidirectional translocation without the backward release of free metal. The coordination details of Zn(2+) at the transmembrane metal binding site responsible for transport have now been established. Escherichia coli ZntA is a well-characterized Zn(2+)-ATPase responsible for intracellular Zn(2+) efflux. A truncated form of the protein lacking regulatory metal sites and retaining the transport site was constructed. Metrical parameters of the metal-ligand coordination geometry for the zinc bound isolated form were characterized using x-ray absorption spectroscopy (XAS). Our data support a nearest neighbor ligand environment of (O/N)(2)S(2) that is compatible with the proposed invariant metal coordinating residues present in the transmembrane region. This ligand identification and the calculated bond lengths support a tetrahedral coordination geometry for Zn(2+) bound to the TM-MBS of P-type ATPase transporters.
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35
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Isaac M, Latour JM, Sénèque O. Nucleophilic reactivity of Zinc-bound thiolates: subtle interplay between coordination set and conformational flexibility. Chem Sci 2012. [DOI: 10.1039/c2sc21029k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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36
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Martin-Diaconescu V, Bellucci M, Musiani F, Ciurli S, Maroney MJ. Unraveling the Helicobacter pylori UreG zinc binding site using X-ray absorption spectroscopy (XAS) and structural modeling. J Biol Inorg Chem 2011; 17:353-61. [PMID: 22068961 DOI: 10.1007/s00775-011-0857-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 10/24/2011] [Indexed: 01/22/2023]
Abstract
The pathogenicity of Helicobacter pylori depends on the activity of urease for pH modification. Urease activity requires assembly of a dinickel active site that is facilitated in part by GTP hydrolysis by UreG. The proper functioning of Helicobacter pylori UreG (HpUreG) is dependent on Zn(II) binding and dimerization. X-ray absorption spectroscopy and structural modeling were used to elucidate the structure of the Zn(II) site in HpUreG. These studies independently indicated a site at the dimer interface that has trigonal bipyramidal geometry and is composed of two axial cysteines at 2.29(2) Å, two equatorial histidines at 1.99(1) Å, and a solvent-accessible coordination site. The final model for the Zn(II) site structure was determined by refining multiple-scattering extended X-ray absorption fine structure fits using the geometry predicted by homology modeling and ab initio calculations.
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Chamayou AC, Lüdeke S, Brecht V, Freedman TB, Nafie LA, Janiak C. Chirality and diastereoselection of Δ/Λ-configured tetrahedral zinc complexes through enantiopure Schiff base complexes: combined vibrational circular dichroism, density functional theory, 1H NMR, and X-ray structural studies. Inorg Chem 2011; 50:11363-74. [PMID: 22017347 DOI: 10.1021/ic2009557] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The metal-centered Δ/Λ-chirality of four-coordinated, nonplanar Zn(A(^)B)(2) complexes is correlated to the chirality of the bidentate enantiopure (R)-A(^)B or (S)-A(^)B Schiff base building blocks [A(^)B = (R)- or (S)-N-(1-(4-X-phenyl)ethyl)salicylaldiminato-κ(2)N,O with X = OCH(3), Cl, Br]. In the solid-state the (R) ligand chirality induces a Λ-M configuration and the (S) ligand chirality quantitatively gives the Δ-M configuration upon crystallization as deduced from X-ray single crystal studies. The diastereoselections of the pseudotetrahedral zinc-Schiff base complexes in CDCl(3) solution were investigated by (1)H NMR and by vibrational circular dichroism (VCD) spectroscopy. The appearance of two signals for the Schiff-base -CH═N- imine proton in (1)H NMR indicates an equilibrium of both Δ- and Λ-diastereomers with a diastereomeric ratio of roughly 20:80% for all three ligands. VCD proved to be very sensitive to the metal-centered Δ/Λ-chirality because of a characteristic band representing coupled vibrations of the two ligand's C═N stretch modes. The absolute configuration was assigned on the basis of agreement in sign with theoretical VCD spectra from Density Functional Theory calculations.
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Affiliation(s)
- Anne-Christine Chamayou
- Institut für Anorganische und Analytische Chemie, Universität Freiburg, Albertstrasse 21, D-79104 Freiburg, Germany
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Kassim R, Ramseyer C, Enescu M. Oxidation of Zinc–Thiolate Complexes of Biological Interest by Hydrogen Peroxide: A Theoretical Study. Inorg Chem 2011; 50:5407-16. [DOI: 10.1021/ic200267x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rima Kassim
- Centre de Recherche Universitaire de Djibouti (CRUD), University of Djibouti, Avenue Georges Clemenceau, Djibouti
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Bostick BC, Hansel CM, La Force MJ, Fendorf S. Biofortification: a new tool to reduce micronutrient malnutrition. Food Nutr Bull 2011; 35:3823-9. [PMID: 11642439 DOI: 10.1021/es010549d] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
BACKGROUND The density of minerals and vitamins in food staples eaten widely by the poor may be increased either through conventional plant breeding or through the use of transgenic techniques, a process known as biofortification. OBJECTIVE HarvestPlus seeks to develop and distribute varieties of food staples (rice, wheat, maize, cassava, pearl millet, beans, and sweet potato) that are high in iron, zinc, and provitamin A through an interdisciplinary, global alliance of scientific institutions and implementing agencies in developing and developed countries. METHODS In broad terms, three things must happen for biofortification to be successful. First, the breeding must be successful--high nutrient density must be combined with high yields and high profitability. Second, efficacy must be demonstrated--the micronutrient status of human subjects must be shown to improve when they are consuming the biofortified varieties as normally eaten. Thus, sufficient nutrients must be retained in processing and cooking and these nutrients must be sufficiently bioavailable. Third, the biofortified crops must be adopted by farmers and consumed by those suffering from micronutrient malnutrition in significant numbers. RESULTS Biofortified crops offer a rural-based intervention that, by design, initially reaches these more remote populations, which comprise a majority of the undernourished in many countries, and then penetrates to urban populations as production surpluses are marketed. In this way, biofortification complements fortification and supplementation programs, which work best in centralized urban areas and then reach into rural areas with good infrastructure. CONCLUSIONS Initial investments in agricultural research at a central location can generate high recurrent benefits at low cost as adapted, biofortified varieties become available in country after country across time at low recurrent costs.
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Affiliation(s)
- B C Bostick
- Department of Geological and Environmental Sciences, Stanford University, California 94305-2155, USA.
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41
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Sénèque O, Latour JM. Coordination Properties of Zinc Finger Peptides Revisited: Ligand Competition Studies Reveal Higher Affinities for Zinc and Cobalt. J Am Chem Soc 2010; 132:17760-74. [DOI: 10.1021/ja104992h] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Olivier Sénèque
- Laboratoire de Chimie et Biologie des Métaux, CEA/iRTSV/LCBM, UMR 5249 CNRS/Université Joseph Fourier/CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble, France
| | - Jean-Marc Latour
- Laboratoire de Chimie et Biologie des Métaux, CEA/iRTSV/LCBM, UMR 5249 CNRS/Université Joseph Fourier/CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble, France
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Herbst RW, Perovic I, Martin-Diaconescu V, O'Brien K, Chivers PT, Pochapsky SS, Pochapsky TC, Maroney MJ. Communication between the zinc and nickel sites in dimeric HypA: metal recognition and pH sensing. J Am Chem Soc 2010; 132:10338-51. [PMID: 20662514 DOI: 10.1021/ja1005724] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Helicobacter pylori , a pathogen that colonizes the human stomach, requires the nickel-containing metalloenzymes urease and NiFe-hydrogenase to survive this low pH environment. The maturation of both enzymes depends on the metallochaperone, HypA. HypA contains two metal sites, an intrinsic zinc site and a low-affinity nickel binding site. X-ray absorption spectroscopy (XAS) shows that the structure of the intrinsic zinc site of HypA is dynamic and able to sense both nickel loading and pH changes. At pH 6.3, an internal pH that occurs during acid shock, the zinc site undergoes unprecedented ligand substitutions to convert from a Zn(Cys)(4) site to a Zn(His)(2)(Cys)(2) site. NMR spectroscopy shows that binding of Ni(II) to HypA results in paramagnetic broadening of resonances near the N-terminus. NOEs between the beta-CH(2) protons of Zn cysteinyl ligands are consistent with a strand-swapped HypA dimer. Addition of nickel causes resonances from the zinc binding motif and other regions to double, indicating more than one conformation can exist in solution. Although the structure of the high-spin, 5-6 coordinate Ni(II) site is relatively unaffected by pH, the nickel binding stoichiometry is decreased from one per monomer to one per dimer at pH = 6.3. Mutation of any cysteine residue in the zinc binding motif results in a zinc site structure similar to that found for holo-WT-HypA at low pH and is unperturbed by the addition of nickel. Mutation of the histidines that flank the CXXC motifs results in a zinc site structure that is similar to holo-WT-HypA at neutral pH (Zn(Cys)(4)) and is no longer responsive to nickel binding or pH changes. Using an in vitro urease activity assay, it is shown that the recombinant protein is sufficient for recovery of urease activity in cell lysate from a HypA deletion mutant, and that mutations in the zinc-binding motif result in a decrease in recovered urease activity. The results are interpreted in terms of a model wherein HypA controls the flow of nickel traffic in the cell in response to nickel availability and pH.
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Affiliation(s)
- Robert W Herbst
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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Li H, Mapolelo DT, Dingra NN, Keller G, Riggs-Gelasco PJ, Winge DR, Johnson MK, Outten CE. Histidine 103 in Fra2 is an iron-sulfur cluster ligand in the [2Fe-2S] Fra2-Grx3 complex and is required for in vivo iron signaling in yeast. J Biol Chem 2010; 286:867-76. [PMID: 20978135 DOI: 10.1074/jbc.m110.184176] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The BolA homologue Fra2 and the cytosolic monothiol glutaredoxins Grx3 and Grx4 together play a key role in regulating iron homeostasis in Saccharomyces cerevisiae. Genetic studies indicate that Grx3/4 and Fra2 regulate activity of the iron-responsive transcription factors Aft1 and Aft2 in response to mitochondrial Fe-S cluster biosynthesis. We have previously shown that Fra2 and Grx3/4 form a [2Fe-2S](2+)-bridged heterodimeric complex with iron ligands provided by the active site cysteine of Grx3/4, glutathione, and a histidine residue. To further characterize this unusual Fe-S-binding complex, site-directed mutagenesis was used to identify specific residues in Fra2 that influence Fe-S cluster binding and regulation of Aft1 activity in vivo. Here, we present spectroscopic evidence that His-103 in Fra2 is an Fe-S cluster ligand in the Fra2-Grx3 complex. Replacement of this residue does not abolish Fe-S cluster binding, but it does lead to a change in cluster coordination and destabilization of the [2Fe-2S] cluster. In vivo genetic studies further confirm that Fra2 His-103 is critical for control of Aft1 activity in response to the cellular iron status. Using CD spectroscopy, we find that ∼1 mol eq of apo-Fra2 binds tightly to the [2Fe-2S] Grx3 homodimer to form the [2Fe-2S] Fra2-Grx3 heterodimer, suggesting a mechanism for formation of the [2Fe-2S] Fra2-Grx3 heterodimer in vivo. Taken together, these results demonstrate that the histidine coordination and stability of the [2Fe-2S] cluster in the Fra2-Grx3 complex are essential for iron regulation in yeast.
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Affiliation(s)
- Haoran Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
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44
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George GN, Singh SP, Myers GJ, Watson GE, Pickering IJ. The chemical forms of mercury in human hair: a study using X-ray absorption spectroscopy. J Biol Inorg Chem 2010; 15:709-15. [PMID: 20225071 PMCID: PMC3887512 DOI: 10.1007/s00775-010-0638-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 02/12/2010] [Indexed: 10/19/2022]
Abstract
Human hair is frequently used as a bioindicator of mercury exposure. We have used X-ray absorption spectroscopy to examine the chemical forms of mercury in human hair samples taken from individuals with high fish consumption and concomitant exposure to methylmercury. The mercury is found to be predominantly methylmercury-cysteine or closely related species, comprising approximately 80% of the total mercury, with the remainder an inorganic thiolate-coordinated mercuric species. No appreciable role was found for selenium in coordinating mercury in hair.
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Affiliation(s)
- Graham N George
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, SK, Canada.
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Veronesi G, Whitehead SJ, Francia F, Giachini L, Boscherini F, Venturoli G, Cotton NP, Jackson JB. X-ray absorption studies of Zn2+-binding sites in Escherichia coli transhydrogenase and its βH91K mutant. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:494-500. [DOI: 10.1016/j.bbabio.2010.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 01/08/2010] [Accepted: 01/11/2010] [Indexed: 12/01/2022]
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46
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Koutmou KS, Casiano-Negroni A, Getz MM, Pazicni S, Andrews AJ, Penner-Hahn JE, Al-Hashimi HM, Fierke CA. NMR and XAS reveal an inner-sphere metal binding site in the P4 helix of the metallo-ribozyme ribonuclease P. Proc Natl Acad Sci U S A 2010; 107:2479-84. [PMID: 20133747 PMCID: PMC2823894 DOI: 10.1073/pnas.0906319107] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Functionally critical metals interact with RNA through complex coordination schemes that are currently difficult to visualize at the atomic level under solution conditions. Here, we report a new approach that combines NMR and XAS to resolve and characterize metal binding in the most highly conserved P4 helix of ribonuclease P (RNase P), the ribonucleoprotein that catalyzes the divalent metal ion-dependent maturation of the 5' end of precursor tRNA. Extended X-ray absorption fine structure (EXAFS) spectroscopy reveals that the Zn(2+) bound to a P4 helix mimic is six-coordinate, with an average Zn-O/N bond distance of 2.08 A. The EXAFS data also show intense outer-shell scattering indicating that the zinc ion has inner-shell interactions with one or more RNA ligands. NMR Mn(2+) paramagnetic line broadening experiments reveal strong metal localization at residues corresponding to G378 and G379 in B. subtilis RNase P. A new "metal cocktail" chemical shift perturbation strategy involving titrations with , Zn(2+), and confirm an inner-sphere metal interaction with residues G378 and G379. These studies present a unique picture of how metals coordinate to the putative RNase P active site in solution, and shed light on the environment of an essential metal ion in RNase P. Our experimental approach presents a general method for identifying and characterizing inner-sphere metal ion binding sites in RNA in solution.
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Wellenreuther G, Parthasarathy V, Meyer-Klaucke W. Towards a black-box for biological EXAFS data analysis. II. Automatic BioXAS Refinement and Analysis (ABRA). JOURNAL OF SYNCHROTRON RADIATION 2010; 17:25-35. [PMID: 20029108 DOI: 10.1107/s0909049509040576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 10/05/2009] [Indexed: 05/28/2023]
Abstract
In biological systems, X-ray absorption spectroscopy (XAS) can determine structural details of metal binding sites with high resolution. Here a method enabling an automated analysis of the corresponding EXAFS data is presented, utilizing in addition to least-squares refinement the prior knowledge about structural details and important fit parameters. A metal binding motif is characterized by the type of donor atoms and their bond lengths. These fit results are compared by bond valance sum analysis and target distances with established structures of metal binding sites. Other parameters such as the Debye-Waller factor and shift of the Fermi energy provide further insights into the quality of a fit. The introduction of mathematical criteria, their combination and calibration allows an automated analysis of XAS data as demonstrated for a number of examples. This presents a starting point for future applications to all kinds of systems studied by XAS and allows the algorithm to be transferred to data analysis in other fields.
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48
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Giachini L, Veronesi G, Francia F, Venturoli G, Boscherini F. Synergic approach to XAFS analysis for the identification of most probable binding motifs for mononuclear zinc sites in metalloproteins. JOURNAL OF SYNCHROTRON RADIATION 2010; 17:41-52. [PMID: 20029110 DOI: 10.1107/s090904950904919x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 11/18/2009] [Indexed: 05/28/2023]
Abstract
In the present work a data analysis approach, based on XAFS data, is proposed for the identification of most probable binding motifs of unknown mononuclear zinc sites in metalloproteins. This approach combines multiple-scattering EXAFS analysis performed within the rigid-body refinement scheme, non-muffin-tin ab initio XANES simulations, average structural information on amino acids and metal binding clusters provided by the Protein Data Bank, and Debye-Waller factor calculations based on density functional theory. The efficiency of the method is tested by using three reference zinc proteins for which the local structure around the metal is already known from protein crystallography. To show the applicability of the present analysis to structures not deposited in the Protein Data Bank, the XAFS spectra of six mononuclear zinc binding sites present in diverse membrane proteins, for which we have previously proposed the coordinating amino acids by applying a similar approach, is also reported. By comparing the Zn K-edge XAFS features exhibited by these proteins with those pertaining to the reference structures, key spectral characteristics, related to specific binding motifs, are observed. These case studies exemplify the combined data analysis proposed and further support its validity.
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Affiliation(s)
- Lisa Giachini
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia.
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Li H, Mapolelo DT, Dingra NN, Naik SG, Lees NS, Hoffman BM, Riggs-Gelasco PJ, Huynh BH, Johnson MK, Outten CE. The yeast iron regulatory proteins Grx3/4 and Fra2 form heterodimeric complexes containing a [2Fe-2S] cluster with cysteinyl and histidyl ligation. Biochemistry 2009; 48:9569-81. [PMID: 19715344 DOI: 10.1021/bi901182w] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The transcription of iron uptake and storage genes in Saccharomyces cerevisiae is primarily regulated by the transcription factor Aft1. Nucleocytoplasmic shuttling of Aft1 is dependent upon mitochondrial Fe-S cluster biosynthesis via a signaling pathway that includes the cytosolic monothiol glutaredoxins (Grx3 and Grx4) and the BolA homologue Fra2. However, the interactions between these proteins and the iron-dependent mechanism by which they control Aft1 localization are unclear. To reconstitute and characterize components of this signaling pathway in vitro, we have overexpressed yeast Fra2 and Grx3/4 in Escherichia coli. We have shown that coexpression of recombinant Fra2 with Grx3 or Grx4 allows purification of a stable [2Fe-2S](2+) cluster-containing Fra2-Grx3 or Fra2-Grx4 heterodimeric complex. Reconstitution of a [2Fe-2S] cluster on Grx3 or Grx4 without Fra2 produces a [2Fe-2S]-bridged homodimer. UV-visible absorption and CD, resonance Raman, EPR, ENDOR, Mossbauer, and EXAFS studies of [2Fe-2S] Grx3/4 homodimers and the [2Fe-2S] Fra2-Grx3/4 heterodimers indicate that inclusion of Fra2 in the Grx3/4 Fe-S complex causes a change in the cluster stability and coordination environment. Taken together, our analytical, spectroscopic, and mutagenesis data indicate that Grx3/4 and Fra2 form a Fe-S-bridged heterodimeric complex with Fe ligands provided by the active site cysteine of Grx3/4, glutathione, and a histidine residue. Overall, these results suggest that the ability of the Fra2-Grx3/4 complex to assemble a [2Fe-2S] cluster may act as a signal to control the iron regulon in response to cellular iron status in yeast.
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Affiliation(s)
- Haoran Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA
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50
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Provost K, Bouvet-Muller D, Crauste-Manciet S, Olivi L, Vlaic G, Michalowicz A. Degradation of platinum based anticancer drugs by methionine: An EXAFS study. ACTA ACUST UNITED AC 2009. [DOI: 10.1088/1742-6596/190/1/012206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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