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Fakhoury JN, Zhang Y, Edmonds KA, Bringas M, Luebke JL, Gonzalez-Gutierrez G, Capdevila DA, Giedroc DP. Functional asymmetry and chemical reactivity of CsoR family persulfide sensors. Nucleic Acids Res 2021; 49:12556-12576. [PMID: 34755876 PMCID: PMC8643695 DOI: 10.1093/nar/gkab1040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 01/14/2023] Open
Abstract
CstR is a persulfide-sensing member of the functionally diverse copper-sensitive operon repressor (CsoR) superfamily. While CstR regulates the bacterial response to hydrogen sulfide (H2S) and more oxidized reactive sulfur species (RSS) in Gram-positive pathogens, other dithiol-containing CsoR proteins respond to host derived Cu(I) toxicity, sometimes in the same bacterial cytoplasm, but without regulatory crosstalk in cells. It is not clear what prevents this crosstalk, nor the extent to which RSS sensors exhibit specificity over other oxidants. Here, we report a sequence similarity network (SSN) analysis of the entire CsoR superfamily, which together with the first crystallographic structure of a CstR and comprehensive mass spectrometry-based kinetic profiling experiments, reveal new insights into the molecular basis of RSS specificity in CstRs. We find that the more N-terminal cysteine is the attacking Cys in CstR and is far more nucleophilic than in a CsoR. Moreover, our CstR crystal structure is markedly asymmetric and chemical reactivity experiments reveal the functional impact of this asymmetry. Substitution of the Asn wedge between the resolving and the attacking thiol with Ala significantly decreases asymmetry in the crystal structure and markedly impacts the distribution of species, despite adopting the same global structure as the parent repressor. Companion NMR, SAXS and molecular dynamics simulations reveal that the structural and functional asymmetry can be traced to fast internal dynamics of the tetramer. Furthermore, this asymmetry is preserved in all CstRs and with all oxidants tested, giving rise to markedly distinct distributions of crosslinked products. Our exploration of the sequence, structural, and kinetic features that determine oxidant-specificity suggest that the product distribution upon RSS exposure is determined by internal flexibility.
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Affiliation(s)
- Joseph N Fakhoury
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA
| | - Yifan Zhang
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405 USA
| | - Katherine A Edmonds
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA
| | - Mauro Bringas
- Fundación Instituto Leloir, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - Justin L Luebke
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA
| | - Giovanni Gonzalez-Gutierrez
- Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405 USA
| | - Daiana A Capdevila
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA.,Fundación Instituto Leloir, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - David P Giedroc
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405 USA
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Kocyła A, Pomorski A, Krężel A. Molar absorption coefficients and stability constants of metal complexes of 4-(2-pyridylazo)resorcinol (PAR): Revisiting common chelating probe for the study of metalloproteins. J Inorg Biochem 2015; 152:82-92. [PMID: 26364130 DOI: 10.1016/j.jinorgbio.2015.08.024] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/25/2015] [Accepted: 08/26/2015] [Indexed: 01/14/2023]
Abstract
4-(2-Pyridylazo)resorcinol (PAR) is one of the most popular chromogenic chelator used in the determination of the concentrations of various metal ions from the d, p and f blocks and their affinities for metal ion-binding biomolecules. The most important characteristics of such a sensor are the molar absorption coefficient and the metal-ligand complex dissociation constant. However, it must be remembered that these values are dependent on the specific experimental conditions (e.g. pH, solvent components, and reactant ratios). If one uses these values to process data obtained in different conditions, the final result can be under- or overestimated. We aimed to establish the spectral properties and the stability of PAR and its complexes accurately with Zn(2+), Cd(2+), Hg(2+), Co(2+), Ni(2+), Cu(2+), Mn(2+) and Pb(2+) at a multiple pH values. The obtained results account for the presence of different species of metal-PAR complexes in the physiological pH range of 5 to 8 and have been frequently neglected in previous studies. The effective molar absorption coefficient at 492 nm for the ZnHx(PAR)2 complex at pH7.4 in buffered water solution is 71,500 M(-1) cm(-1), and the dissociation constant of the complex in these conditions is 7.08×10(-13) M(2). To confirm these values and estimate the range of the dissociation constants of zinc-binding biomolecules that can be measured using PAR, we performed several titrations of zinc finger peptides and zinc chelators. Taken together, our results provide the updated parameters that are applicable to any experiment conducted using inexpensive and commercially available PAR.
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Affiliation(s)
- Anna Kocyła
- Laboratory of Chemical Biology, University of Wrocław, ul. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Adam Pomorski
- Laboratory of Chemical Biology, University of Wrocław, ul. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Artur Krężel
- Laboratory of Chemical Biology, University of Wrocław, ul. Joliot-Curie 14a, 50-383 Wrocław, Poland.
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Abstract
A key property of metallo-proteins and -enzymes is the affinity of metal ion M for protein ligand P as defined by the dissociation constant KD = [M][P]/[MP]. Its accurate determination is essential for a quantitative understanding of metal selection and speciation. However, the surfaces of proteins are defined by the sidechains of amino acids and so abound in good metal ligands (e.g., imidazole of histidine,thiol of cysteine, carboxylate of aspartic and glutamic acids, etc.). Consequently, adventitious binding of metal ions to protein surfaces is common with KD values > or = 10(-6) M. On the other hand, transport proteins responsible for 'chaperoning' essential metals to their cellular destinations appear to bind the metal ions selectively (KD < 10(-7) M, both for speciation and to minimise the toxic effects of 'free' metal ions. These ions are normally bound with still higher affinities at their ultimate destinations (the active sites of metallo-proteins and -enzymes). This review surveys possible approaches to estimation of these dissociation constants and pinpoints the various problems associated with each approach.
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Affiliation(s)
- Zhiguang Xiao
- University of Melbourne, Parkville, Victoria, Australia.
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Djoko KY, Chong LX, Wedd AG, Xiao Z. Reaction Mechanisms of the Multicopper Oxidase CueO from Escherichia coli Support Its Functional Role as a Cuprous Oxidase. J Am Chem Soc 2010; 132:2005-15. [DOI: 10.1021/ja9091903] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Karrera Y. Djoko
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lee Xin Chong
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Anthony G. Wedd
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Zhiguang Xiao
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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Zimmermann M, Clarke O, Gulbis JM, Keizer DW, Jarvis RS, Cobbett CS, Hinds MG, Xiao Z, Wedd AG. Metal Binding Affinities of Arabidopsis Zinc and Copper Transporters: Selectivities Match the Relative, but Not the Absolute, Affinities of their Amino-Terminal Domains,. Biochemistry 2009; 48:11640-54. [DOI: 10.1021/bi901573b] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Oliver Clarke
- Department of Medical Biology
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Jacqui M. Gulbis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | | | | | | | - Mark G. Hinds
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Zhiguang Xiao
- School of Chemistry
- Bio21 Molecular Science and Biotechnology Institute
| | - Anthony G. Wedd
- School of Chemistry
- Bio21 Molecular Science and Biotechnology Institute
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