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Lepeshkevich SV, Sazanovich IV, Parkhats MV, Gilevich SN, Dzhagarov BM. Towards understanding non-equivalence of α and β subunits within human hemoglobin in conformational relaxation and molecular oxygen rebinding. Chem Sci 2021; 12:7033-7047. [PMID: 34123331 PMCID: PMC8153241 DOI: 10.1039/d1sc00712b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Picosecond to millisecond laser time-resolved transient absorption spectroscopy was used to study molecular oxygen (O2) rebinding and conformational relaxation following O2 photodissociation in the α and β subunits within human hemoglobin in the quaternary R-like structure. Oxy-cyanomet valency hybrids, α2(Fe2+-O2)β2(Fe3+-CN) and α2(Fe3+-CN)β2(Fe2+-O2), were used as models for oxygenated R-state hemoglobin. An extended kinetic model for geminate O2 rebinding in the ferrous hemoglobin subunits, ligand migration between the primary and secondary docking site(s), and nonexponential tertiary relaxation within the R quaternary structure, was introduced and discussed. Significant functional non-equivalence of the α and β subunits in both the geminate O2 rebinding and concomitant structural relaxation was revealed. For the β subunits, the rate constant for the geminate O2 rebinding to the unrelaxed tertiary structure and the tertiary transition rate were found to be greater than the corresponding values for the α subunits. The conformational relaxation following the O2 photodissociation in the α and β subunits was found to decrease the rate constant for the geminate O2 rebinding, this effect being more than one order of magnitude greater for the β subunits than for the α subunits. Evidence was provided for the modulation of the O2 rebinding to the individual α and β subunits within human hemoglobin in the R-state structure by the intrinsic heme reactivity through a change in proximal constraints upon the relaxation of the tertiary structure on a picosecond to microsecond time scale. Our results demonstrate that, for native R-state oxyhemoglobin, O2 rebinding properties and spectral changes following the O2 photodissociation can be adequately described as the sum of those for the α and β subunits within the valency hybrids. The isolated β chains (hemoglobin H) show similar behavior to the β subunits within the valency hybrids and can be used as a model for the β subunits within the R-state oxyhemoglobin. At the same time, the isolated α chains behave differently to the α subunits within the valency hybrids.
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Affiliation(s)
- Sergei V Lepeshkevich
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus 68 Nezavisimosti Ave Minsk 220072 Belarus
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory Harwell Campus OX11 0QX UK
| | - Marina V Parkhats
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus 68 Nezavisimosti Ave Minsk 220072 Belarus
| | - Syargey N Gilevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus 5 Academician V. F. Kuprevich Street Minsk 220141 Belarus
| | - Boris M Dzhagarov
- B. I. Stepanov Institute of Physics, National Academy of Sciences of Belarus 68 Nezavisimosti Ave Minsk 220072 Belarus
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2
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Gianquinto E, Moscetti I, De Bei O, Campanini B, Marchetti M, Luque FJ, Cannistraro S, Ronda L, Bizzarri AR, Spyrakis F, Bettati S. Interaction of human hemoglobin and semi-hemoglobins with the Staphylococcus aureus hemophore IsdB: a kinetic and mechanistic insight. Sci Rep 2019; 9:18629. [PMID: 31819099 PMCID: PMC6901573 DOI: 10.1038/s41598-019-54970-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/21/2019] [Indexed: 12/21/2022] Open
Abstract
Among multidrug-resistant bacteria, methicillin-resistant Staphylococcus aureus is emerging as one of the most threatening pathogens. S. aureus exploits different mechanisms for its iron supply, but the preferred one is acquisition of organic iron through the expression of hemoglobin (Hb) receptors. One of these, IsdB, belonging to the Isd (Iron-Regulated Surface Determinant) system, was shown to be essential for bacterial growth and virulence. Therefore, interaction of IsdB with Hb represents a promising target for the rational design of a new class of antibacterial molecules. However, despite recent investigations, many structural and mechanistic details of complex formation and heme extraction process are still elusive. By combining site-directed mutagenesis, absorption spectroscopy, surface plasmon resonance and molecular dynamics simulations, we tackled most of the so far unanswered questions: (i) the exact complex stoichiometry, (ii) the microscopic kinetic rates of complex formation, (iii) the IsdB selectivity for binding to, and extracting heme from, α and β subunits of Hb, iv) the role of specific amino acid residues and structural regions in driving complex formation and heme transfer, and (v) the structural/dynamic effect played by the hemophore on Hb.
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Affiliation(s)
- Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy
| | - Ilaria Moscetti
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Omar De Bei
- Department of Food and Drug, University of Parma, Parma, 43124, Italy
| | - Barbara Campanini
- Department of Food and Drug, University of Parma, Parma, 43124, Italy.,Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy
| | - Marialaura Marchetti
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy.,Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Santa Coloma de Gramenet, 08921, Spain
| | - Salvatore Cannistraro
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy
| | - Luca Ronda
- Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy.,Department of Medicine and Surgery, University of Parma, Parma, 43126, Italy.,Institute of Biophysics, National Research Council, Pisa, 56124, Italy
| | - Anna Rita Bizzarri
- Department of Environmental and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Turin, 10125, Italy.
| | - Stefano Bettati
- Interdepartment Center Biopharmanet-TEC, University of Parma, Parma, 43124, Italy. .,Department of Medicine and Surgery, University of Parma, Parma, 43126, Italy. .,Institute of Biophysics, National Research Council, Pisa, 56124, Italy.
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Lepeshkevich SV, Gilevich SN, Parkhats MV, Dzhagarov BM. Molecular oxygen migration through the xenon docking sites of human hemoglobin in the R-state. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1110-1121. [DOI: 10.1016/j.bbapap.2016.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 11/25/2022]
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4
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Minute F, Hellmann N, Spinozzi F, Ortore MG, Di Muro P, Bubacco L, Beltramini M. Entrapment and characterization of functional allosteric conformers of hemocyanin in sol–gel matrices. RSC Adv 2016. [DOI: 10.1039/c5ra26377h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Entrapment of hemocyanin in sol–gel stabilizes conformations scarcely populated in solution, allowing for their structural and functional analysis.
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Affiliation(s)
- Fabrizio Minute
- Department of Biology
- University of Padova
- I-35131 Padova
- Italy
| | - Nadja Hellmann
- Institute for Molecular Biophysics
- University of Mainz
- Mainz
- Germany
| | - Francesco Spinozzi
- Department DISVA
- Marche Polytechnic University and CNISM
- I-60131 Ancona
- Italy
| | | | - Paolo Di Muro
- Department of Biology
- University of Padova
- I-35131 Padova
- Italy
| | - Luigi Bubacco
- Department of Biology
- University of Padova
- I-35131 Padova
- Italy
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Shadrina MS, Peslherbe GH, English AM. Quaternary-Linked Changes in Structure and Dynamics That Modulate O2 Migration within Hemoglobin’s Gas Diffusion Tunnels. Biochemistry 2015; 54:5268-78. [DOI: 10.1021/acs.biochem.5b00368] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria S. Shadrina
- Department of Chemistry and
Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Gilles H. Peslherbe
- Department of Chemistry and
Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - Ann M. English
- Department of Chemistry and
Biochemistry, Centre for Research in Molecular Modeling and PROTEO, Concordia University, Montreal, Quebec H4B 1R6, Canada
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Lepeshkevich SV, Parkhats MV, Stasheuski AS, Britikov VV, Jarnikova ES, Usanov SA, Dzhagarov BM. Photosensitized Singlet Oxygen Luminescence from the Protein Matrix of Zn-Substituted Myoglobin. J Phys Chem A 2014; 118:1864-78. [DOI: 10.1021/jp501615h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sergei V. Lepeshkevich
- B.I.
Stepanov Institute of Physics, National Academy of Sciences of Belarus, 68 Nezavisimosti Ave, Minsk 220072, Belarus
| | - Marina V. Parkhats
- B.I.
Stepanov Institute of Physics, National Academy of Sciences of Belarus, 68 Nezavisimosti Ave, Minsk 220072, Belarus
| | - Alexander S. Stasheuski
- B.I.
Stepanov Institute of Physics, National Academy of Sciences of Belarus, 68 Nezavisimosti Ave, Minsk 220072, Belarus
| | - Vladimir V. Britikov
- Institute
of Bioorganic Chemistry, National Academy of Sciences of Belarus, 5 Academician V.F. Kuprevich Street, Minsk 220141, Belarus
| | - Ekaterina S. Jarnikova
- B.I.
Stepanov Institute of Physics, National Academy of Sciences of Belarus, 68 Nezavisimosti Ave, Minsk 220072, Belarus
| | - Sergey A. Usanov
- Institute
of Bioorganic Chemistry, National Academy of Sciences of Belarus, 5 Academician V.F. Kuprevich Street, Minsk 220141, Belarus
| | - Boris M. Dzhagarov
- B.I.
Stepanov Institute of Physics, National Academy of Sciences of Belarus, 68 Nezavisimosti Ave, Minsk 220072, Belarus
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Schotte F, Cho HS, Soman J, Wulff M, Olson JS, Anfinrud PA. Real-time tracking of CO migration and binding in the α and β subunits of human hemoglobin via 150-ps time-resolved Laue crystallography. Chem Phys 2013; 422:98-106. [PMID: 24839343 DOI: 10.1016/j.chemphys.2012.12.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed the method of picosecond Laue crystallography and used this capability to probe ligand dynamics in tetrameric R-state hemoglobin (Hb). Time-resolved, 2 Å-resolution electron density maps of photolyzed HbCO reveal the time-dependent population of CO in the binding (A) and primary docking (B) sites of both α and β subunits from 100 ps to 10 μs. The proximity of the B site in the β subunit is about 0.25 Å closer to its A binding site, and its kBA rebinding rate (~300 μs-1) is six times faster, suggesting distal control of the rebinding dynamics. Geminate rebinding in the β subunit exhibits both prompt and delayed geminate phases. We developed a microscopic model to quantitatively explain the observed kinetics, with three states for the α subunit and four states for the β subunit. This model provides a consistent framework for interpreting rebinding kinetics reported in prior studies of both HbCO and HbO2.
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Affiliation(s)
- Friedrich Schotte
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Hyun Sun Cho
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Jayashree Soman
- Department of Biochemistry and Cell Biology, and W.M. Keck Center for Computational Biology, Rice University, Houston, TX 77251-1892, USA
| | - Michael Wulff
- European Synchrotron Radiation Facility, BP 220, 38043 Grenoble Cedex, France
| | - John S Olson
- Department of Biochemistry and Cell Biology, and W.M. Keck Center for Computational Biology, Rice University, Houston, TX 77251-1892, USA
| | - Philip A Anfinrud
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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Ronda L, Bettati S, Henry ER, Kashav T, Sanders JM, Royer WE, Mozzarelli A. Tertiary and quaternary allostery in tetrameric hemoglobin from Scapharca inaequivalvis. Biochemistry 2013; 52:2108-17. [PMID: 23458680 DOI: 10.1021/bi301620x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The clam Scapharca inaequivalvis possesses two cooperative oxygen binding hemoglobins in its red cells: a homodimeric HbI and a heterotetrameric A2B2 HbII. Each AB dimeric half of HbII is assembled in a manner very similar to that of the well-studied HbI. This study presents crystal structures of HbII along with oxygen binding data both in the crystalline state and in wet nanoporous silica gels. Despite very similar ligand-linked structural transitions observed in HbI and HbII crystals, HbII in the crystal or encapsulated in silica gels apparently exhibits minimal cooperativity in oxygen binding, in contrast with the full cooperativity exhibited by HbI crystals. However, oxygen binding curves in the crystal indicate the presence of a significant functional inequivalence of A and B chains. When this inequivalence is taken into account, both crystal and R state gel functional data are consistent with the conservation of a tertiary contribution to cooperative oxygen binding, quantitatively similar to that measured for HbI, and are in keeping with the structural information. Furthermore, our results indicate that to fully express cooperative ligand binding, HbII requires quaternary transitions hampered by crystal lattice and gel encapsulation, revealing greater complexity in cooperative function than the direct communication across a dimeric interface observed in HbI.
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Affiliation(s)
- Luca Ronda
- Department of Pharmacy, University of Parma , Parco Area delle Scienze, 23/A, 43124 Parma, Italy
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Lepeshkevich SV, Stasheuski AS, Parkhats MV, Galievsky VA, Dzhagarov BM. Does photodissociation of molecular oxygen from myoglobin and hemoglobin yield singlet oxygen? JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 120:130-41. [DOI: 10.1016/j.jphotobiol.2012.12.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 12/20/2012] [Accepted: 12/30/2012] [Indexed: 12/28/2022]
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10
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Vankayala SL, Hargis JC, Woodcock HL. Unlocking the binding and reaction mechanism of hydroxyurea substrates as biological nitric oxide donors. J Chem Inf Model 2012; 52:1288-97. [PMID: 22519847 DOI: 10.1021/ci300035c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydroxyurea is the only FDA approved treatment of sickle cell disease. It is believed that the primary mechanism of action is associated with the pharmacological elevation of nitric oxide in the blood; however, the exact details of this are still unclear. In the current work, we investigate the atomic level details of this process using a combination of flexible-ligand/flexible-receptor virtual screening coupled with energetic analysis that decomposes interaction energies. Utilizing these methods, we were able to elucidate the previously unknown substrate binding modes of a series of hydroxyurea analogs to hemoglobin and the concomitant structural changes of the enzyme. We identify a backbone carbonyl that forms a hydrogen bond with bound substrates. Our results are consistent with kinetic and electron paramagnetic resonance (EPR) measurements of hydroxyurea-hemoglobin reactions, and a full mechanism is proposed that offers new insights into possibly improving substrate binding and/or reactivity.
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Affiliation(s)
- Sai Lakshmana Vankayala
- Department of Chemistry and Center for Molecular Diversity in Drug Design, Discovery, and Delivery, University of South Floridar, Tampa, Florida 33620, USA
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11
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Lepeshkevich SV, Biziuk SA, Lemeza AM, Dzhagarov BM. The kinetics of molecular oxygen migration in the isolated α chains of human hemoglobin as revealed by molecular dynamics simulations and laser kinetic spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1279-88. [DOI: 10.1016/j.bbapap.2011.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 06/16/2011] [Accepted: 06/24/2011] [Indexed: 10/18/2022]
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12
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Orzeł Ł, Jańczyk A, Brindell M, Stopa G, Stochel G. New trends in the application of laser flash photolysis – case studies. J COORD CHEM 2010. [DOI: 10.1080/00958972.2010.507271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ł. Orzeł
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
| | - A. Jańczyk
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
| | - M. Brindell
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
| | - G. Stopa
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
| | - G. Stochel
- a Faculty of Chemistry , Jagiellonian University , Ingardena 3, 30-060 Kraków
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