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Dali A, Sebastiani F, Gabler T, Frattini G, Moreno DM, Estrin DA, Becucci M, Hofbauer S, Smulevich G. Proximal ligand tunes active site structure and reactivity in bacterial L. monocytogenes coproheme ferrochelatase. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124120. [PMID: 38479228 DOI: 10.1016/j.saa.2024.124120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/21/2024] [Accepted: 03/03/2024] [Indexed: 04/02/2024]
Abstract
Ferrochelatases catalyze the insertion of ferrous iron into the porphyrin during the heme b biosynthesis pathway, which is fundamental for both prokaryotes and eukaryotes. Interestingly, in the active site of ferrochelatases, the proximal ligand coordinating the porphyrin iron of the product is not conserved, and its catalytic role is still unclear. Here we compare the L. monocytogenes bacterial coproporphyrin ferrochelatase native enzyme together with selected variants, where the proximal Tyr residue was replaced by a His (i.e. the most common ligand in heme proteins), a Met or a Phe (as in human and actinobacterial ferrochelatases, respectively), in their Fe(III), Fe(II) and Fe(II)-CO adduct forms. The study of the active site structure and the activity of the proteins in solution has been performed by UV-vis electronic absorption and resonance Raman spectroscopies, biochemical characterization, and classical MD simulations. All the mutations alter the H-bond interactions between the iron porphyrin propionate groups and the protein, and induce effects on the activity, depending on the polarity of the proximal ligand. The overall results confirm that the weak or non-existing coordination of the porphyrin iron by the proximal residue is essential for the binding of the substrate and the release of the final product.
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Affiliation(s)
- Andrea Dali
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Federico Sebastiani
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy
| | - Thomas Gabler
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria
| | - Gianfranco Frattini
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Diego M Moreno
- Instituto de Química Rosario (IQUIR, CONICET-UNR) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Darío A Estrin
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Universidad de Buenos Aires, Intendente Güiraldes, 2160 Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Química-Física de los Materiales, Medio Ambiente y Energía (INQUIMAE), Ciudad Universitaria, Pabellón 2, Buenos Aires, Argentina
| | - Maurizio Becucci
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy.
| | - Stefan Hofbauer
- University of Natural Resources and Life Sciences, Department of Chemistry, Institute of Biochemistry, Muthgasse 18, A-1190 Vienna, Austria.
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" (DICUS), Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino (FI), Italy; INSTM Research Unit of Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy.
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2
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Steuer NB, Schlanstein PC, Hannig A, Sibirtsev S, Jupke A, Schmitz-Rode T, Kopp R, Steinseifer U, Wagner G, Arens J. Extracorporeal Hyperoxygenation Therapy (EHT) for Carbon Monoxide Poisoning: In-Vitro Proof of Principle. MEMBRANES 2021; 12:membranes12010056. [PMID: 35054581 PMCID: PMC8779470 DOI: 10.3390/membranes12010056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/28/2021] [Indexed: 11/23/2022]
Abstract
Carbon monoxide (CO) poisoning is the leading cause of poisoning-related deaths globally. The currently available therapy options are normobaric oxygen (NBO) and hyperbaric oxygen (HBO). While NBO lacks in efficacy, HBO is not available in all areas and countries. We present a novel method, extracorporeal hyperoxygenation therapy (EHT), for the treatment of CO poisoning that eliminates the CO by treating blood extracorporeally at elevated oxygen partial pressure. In this study, we proof the principle of the method in vitro using procine blood: Firstly, we investigated the difference in the CO elimination of a hollow fibre membrane oxygenator and a specifically designed batch oxygenator based on the bubble oxygenator principle at elevated pressures (1, 3 bar). Secondly, the batch oxygenator was redesigned and tested for a broader range of pressures (1, 3, 5, 7 bar) and temperatures (23, 30, 37 °C). So far, the shortest measured carboxyhemoglobin half-life in the blood was 21.32 min. In conclusion, EHT has the potential to provide an easily available and effective method for the treatment of CO poisoning.
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Affiliation(s)
- Niklas B. Steuer
- Department of Cardiovascular Engineering, Institute of Applied Medical Engineering, Helmholtz Institute, Medical Faculty, RWTH Aachen University, Pauwelsstraße 20, 52074 Aachen, Germany; (P.C.S.); (A.H.); (U.S.); (G.W.); (J.A.)
- Correspondence: ; Tel.:+49-241-80-88764
| | - Peter C. Schlanstein
- Department of Cardiovascular Engineering, Institute of Applied Medical Engineering, Helmholtz Institute, Medical Faculty, RWTH Aachen University, Pauwelsstraße 20, 52074 Aachen, Germany; (P.C.S.); (A.H.); (U.S.); (G.W.); (J.A.)
| | - Anke Hannig
- Department of Cardiovascular Engineering, Institute of Applied Medical Engineering, Helmholtz Institute, Medical Faculty, RWTH Aachen University, Pauwelsstraße 20, 52074 Aachen, Germany; (P.C.S.); (A.H.); (U.S.); (G.W.); (J.A.)
| | - Stephan Sibirtsev
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany; (S.S.); (A.J.)
| | - Andreas Jupke
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany; (S.S.); (A.J.)
| | - Thomas Schmitz-Rode
- Institute of Applied Medical Engineering, Helmholtz Institute, Medical Faculty, RWTH Aachen University, Pauwelsstraße 20, 52074 Aachen, Germany;
| | - Rüdger Kopp
- Department of Intensive Care Medicine, Medical Faculty, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany;
| | - Ulrich Steinseifer
- Department of Cardiovascular Engineering, Institute of Applied Medical Engineering, Helmholtz Institute, Medical Faculty, RWTH Aachen University, Pauwelsstraße 20, 52074 Aachen, Germany; (P.C.S.); (A.H.); (U.S.); (G.W.); (J.A.)
| | - Georg Wagner
- Department of Cardiovascular Engineering, Institute of Applied Medical Engineering, Helmholtz Institute, Medical Faculty, RWTH Aachen University, Pauwelsstraße 20, 52074 Aachen, Germany; (P.C.S.); (A.H.); (U.S.); (G.W.); (J.A.)
| | - Jutta Arens
- Department of Cardiovascular Engineering, Institute of Applied Medical Engineering, Helmholtz Institute, Medical Faculty, RWTH Aachen University, Pauwelsstraße 20, 52074 Aachen, Germany; (P.C.S.); (A.H.); (U.S.); (G.W.); (J.A.)
- Department of Biomechanical Engineering, Faculty of Engineering Technology, University of Twente, De Horst 2, 7522LW Enschede, The Netherlands
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3
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Gout J, Meuris F, Desbois A, Dorlet P. In vitro coordination of Fe-protoheme with amyloid β is non-specific and exhibits multiple equilibria. J Inorg Biochem 2021; 227:111664. [PMID: 34955310 DOI: 10.1016/j.jinorgbio.2021.111664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
In addition to copper and zinc, heme is thought to play a role in Alzheimer's disease and its metabolism is strongly affected during the course of this disease. Amyloid β, the peptide associated with Alzheimer's disease, was shown to bind heme in vitro with potential catalytic activity linked to oxidative stress. To date, there is no direct determination of the structure of this complex. In this work, we studied the binding mode of heme to amyloid β in different conditions of pH and redox state by using isotopically labelled peptide in combination with advanced magnetic and vibrational spectroscopic methods. Our results show that the interaction between heme and amyloid β leads to a variety of species in equilibrium. The formation of these species seems to depend on many factors suggesting that the binding site is neither very strong nor highly specific. In addition, our data do not support the currently accepted model where a water molecule is bound to the ferric heme as sixth ligand. They also exclude structural models mimicking a peroxidatic site in the amyloid β-Fe-protoheme complexes.
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Affiliation(s)
- Jérôme Gout
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Laboratoire Stress Oxydant et Détoxication, Gif-sur-Yvette, France
| | - Floriane Meuris
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Laboratoire Stress Oxydant et Détoxication, Gif-sur-Yvette, France
| | - Alain Desbois
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Laboratoire Stress Oxydant et Détoxication, Gif-sur-Yvette, France.
| | - Pierre Dorlet
- CNRS, Aix-Marseille Université, BIP, IMM, Marseille, France; Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Laboratoire Stress Oxydant et Détoxication, Gif-sur-Yvette, France.
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4
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Shelby ML, Wildman A, Hayes D, Mara MW, Lestrange PJ, Cammarata M, Balducci L, Artamonov M, Lemke HT, Zhu D, Seideman T, Hoffman BM, Li X, Chen LX. Interplays of electron and nuclear motions along CO dissociation trajectory in myoglobin revealed by ultrafast X-rays and quantum dynamics calculations. Proc Natl Acad Sci U S A 2021; 118:e2018966118. [PMID: 33782122 PMCID: PMC8040624 DOI: 10.1073/pnas.2018966118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ultrafast structural dynamics with different spatial and temporal scales were investigated during photodissociation of carbon monoxide (CO) from iron(II)-heme in bovine myoglobin during the first 3 ps following laser excitation. We used simultaneous X-ray transient absorption (XTA) spectroscopy and X-ray transient solution scattering (XSS) at an X-ray free electron laser source with a time resolution of 80 fs. Kinetic traces at different characteristic X-ray energies were collected to give a global picture of the multistep pathway in the photodissociation of CO from heme. In order to extract the reaction coordinates along different directions of the CO departure, XTA data were collected with parallel and perpendicular relative polarizations of the laser pump and X-ray probe pulse to isolate the contributions of electronic spin state transition, bond breaking, and heme macrocycle nuclear relaxation. The time evolution of the iron K-edge X-ray absorption near edge structure (XANES) features along the two major photochemical reaction coordinates, i.e., the iron(II)-CO bond elongation and the heme macrocycle doming relaxation were modeled by time-dependent density functional theory calculations. Combined results from the experiments and computations reveal insight into interplays between the nuclear and electronic structural dynamics along the CO photodissociation trajectory. Time-resolved small-angle X-ray scattering data during the same process are also simultaneously collected, which show that the local CO dissociation causes a protein quake propagating on different spatial and temporal scales. These studies are important for understanding gas transport and protein deligation processes and shed light on the interplay of active site conformational changes and large-scale protein reorganization.
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Affiliation(s)
- Megan L Shelby
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Andrew Wildman
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Dugan Hayes
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60437
| | - Michael W Mara
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | | | - Marco Cammarata
- Institut de Physique de Rennes, Université de Rennes, 35042 Rennes CEDEX, France
| | - Lodovico Balducci
- Institut de Physique de Rennes, Université de Rennes, 35042 Rennes CEDEX, France
| | - Maxim Artamonov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Henrik T Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Diling Zhu
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Tamar Seideman
- Department of Chemistry, Northwestern University, Evanston, IL 60208
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208;
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, WA 98195;
| | - Lin X Chen
- Department of Chemistry, Northwestern University, Evanston, IL 60208;
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60437
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5
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Milazzo L, Hofbauer S, Howes BD, Gabler T, Furtmüller PG, Obinger C, Smulevich G. Insights into the Active Site of Coproheme Decarboxylase from Listeria monocytogenes. Biochemistry 2018. [PMID: 29536725 PMCID: PMC5940323 DOI: 10.1021/acs.biochem.8b00186] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Coproheme decarboxylases (ChdC) catalyze the hydrogen peroxide-mediated conversion of coproheme to heme b. This work compares the structure and function of wild-type (WT) coproheme decarboxylase from Listeria monocytogenes and its M149A, Q187A, and M149A/Q187A mutants. The UV-vis, resonance Raman, and electron paramagnetic resonance spectroscopies clearly show that the ferric form of the WT protein is a pentacoordinate quantum mechanically mixed-spin state, which is very unusual in biological systems. Exchange of the Met149 residue to Ala dramatically alters the heme coordination, which becomes a 6-coordinate low spin species with the amide nitrogen atom of the Q187 residue bound to the heme iron. The interaction between M149 and propionyl 2 is found to play an important role in keeping the Q187 residue correctly positioned for closure of the distal cavity. This is confirmed by the observation that in the M149A variant two CO conformers are present corresponding to open (A0) and closed (A1) conformations. The CO of the latter species, the only conformer observed in the WT protein, is H-bonded to Q187. In the absence of the Q187 residue or in the adducts of all the heme b forms of ChdC investigated herein (containing vinyls in positions 2 and 4), only the A0 conformer has been found. Moreover, M149 is shown to be involved in the formation of a covalent bond with a vinyl substituent of heme b at excess of hydrogen peroxide.
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Affiliation(s)
- Lisa Milazzo
- Dipartimento di Chimica "Ugo Schiff" , Università di Firenze , Via della Lastruccia 3-13 , 50019 Sesto Fiorentino (Fi) , Italy
| | - Stefan Hofbauer
- Department of Chemistry, Division of Biochemistry , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18 , A-1190 Vienna , Austria
| | - Barry D Howes
- Dipartimento di Chimica "Ugo Schiff" , Università di Firenze , Via della Lastruccia 3-13 , 50019 Sesto Fiorentino (Fi) , Italy
| | - Thomas Gabler
- Department of Chemistry, Division of Biochemistry , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18 , A-1190 Vienna , Austria
| | - Paul G Furtmüller
- Department of Chemistry, Division of Biochemistry , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18 , A-1190 Vienna , Austria
| | - Christian Obinger
- Department of Chemistry, Division of Biochemistry , BOKU - University of Natural Resources and Life Sciences , Muthgasse 18 , A-1190 Vienna , Austria
| | - Giulietta Smulevich
- Dipartimento di Chimica "Ugo Schiff" , Università di Firenze , Via della Lastruccia 3-13 , 50019 Sesto Fiorentino (Fi) , Italy
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6
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Kapetanaki SM, Burton MJ, Basran J, Uragami C, Moody PCE, Mitcheson JS, Schmid R, Davies NW, Dorlet P, Vos MH, Storey NM, Raven E. A mechanism for CO regulation of ion channels. Nat Commun 2018; 9:907. [PMID: 29500353 PMCID: PMC5834611 DOI: 10.1038/s41467-018-03291-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/31/2018] [Indexed: 01/08/2023] Open
Abstract
Despite being highly toxic, carbon monoxide (CO) is also an essential intracellular signalling molecule. The mechanisms of CO-dependent cell signalling are poorly defined, but are likely to involve interactions with heme proteins. One such role for CO is in ion channel regulation. Here, we examine the interaction of CO with KATP channels. We find that CO activates KATP channels and that heme binding to a CXXHX16H motif on the SUR2A receptor is required for the CO-dependent increase in channel activity. Spectroscopic and kinetic data were used to quantify the interaction of CO with the ferrous heme-SUR2A complex. The results are significant because they directly connect CO-dependent regulation to a heme-binding event on the channel. We use this information to present molecular-level insight into the dynamic processes that control the interactions of CO with a heme-regulated channel protein, and we present a structural framework for understanding the complex interplay between heme and CO in ion channel regulation.
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Affiliation(s)
- Sofia M Kapetanaki
- Department of Chemistry and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, England
| | - Mark J Burton
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 9HN, England
| | - Jaswir Basran
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 9HN, England
| | - Chiasa Uragami
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Peter C E Moody
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 9HN, England
| | - John S Mitcheson
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 9HN, England
| | - Ralf Schmid
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 9HN, England
| | - Noel W Davies
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 9HN, England
| | - Pierre Dorlet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marten H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, 91128, Palaiseau Cedex, France
| | - Nina M Storey
- Department of Molecular and Cell Biology and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 9HN, England.
| | - Emma Raven
- Department of Chemistry and Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, England.
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7
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Ciaccio C, Tognaccini L, Battista T, Cervelli M, Howes BD, Santucci R, Coletta M, Mariottini P, Smulevich G, Fiorucci L. The Met80Ala and Tyr67His/Met80Ala mutants of human cytochrome c shed light on the reciprocal role of Met80 and Tyr67 in regulating ligand access into the heme pocket. J Inorg Biochem 2017; 169:86-96. [DOI: 10.1016/j.jinorgbio.2017.01.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/13/2017] [Accepted: 01/20/2017] [Indexed: 10/20/2022]
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8
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Lee T, Kim J, Park J, Pak Y, Kim H, Lim M. Rebinding dynamics of NO to microperoxidase-8 probed by time-resolved vibrational spectroscopy. Phys Chem Chem Phys 2016; 18:5192-202. [PMID: 26813691 DOI: 10.1039/c5cp06336a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Femtosecond vibrational spectroscopy was used to probe the rebinding kinetics of NO to microperoxidase-8 (Mp), an ideal model system for the active site of ligand-binding heme proteins, including myoglobin and hemoglobin, after the photodeligation of MpNO in glycerol/water (G/W) solutions at 294 K. The geminate rebinding (GR) of NO to Mp in viscous solutions was highly efficient and ultrafast and negligibly dependent on the solution viscosity, which was adjusted by changing the glycerol content from 65% to 90% by volume in G/W mixtures. The kinetics of the GR of NO to Mp in viscous solutions was well represented by an exponential function with a time constant of ca. 11 ps. Although the kinetic traces of the GR of NO to Mp in solutions with three different viscosities (18, 81, and 252 cP) almost overlap, they show a slight difference early in the decay process. The kinetic traces were also described by the diffusion-controlled reaction theory with a Coulomb potential. Since the ligand is deligated in a neutral form, an ionic pair of NO(-) and Mp(+) may be produced before forming the Mp-NO bond by an electron transfer from Mp to NO as the deligated NO is sufficiently near to the Fe atom of Mp. The strong reactivity between NO and ferrous heme may arise from the Coulomb interaction between the reacting pair, which is consistent with the harpooning mechanism for NO binding to heme.
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Affiliation(s)
- Taegon Lee
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 46241 Korea.
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9
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Shelby ML, Mara MW, Chen LX. New insight into metalloporphyrin excited state structures and axial ligand binding from X-ray transient absorption spectroscopic studies. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.05.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Ozaki SI, Sato T, Sekine Y, Migita CT, Uchida T, Ishimori K. Spectroscopic studies on HasA from Yersinia pseudotuberculosis. J Inorg Biochem 2014; 138:31-38. [DOI: 10.1016/j.jinorgbio.2014.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 04/21/2014] [Accepted: 04/21/2014] [Indexed: 10/25/2022]
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11
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Mara MW, Shelby M, Stickrath A, Harpham M, Huang J, Zhang X, Hoffman BM, Chen LX. Electronic and Nuclear Structural Snapshots in Ligand Dissociation and Recombination Processes of Iron Porphyrin in Solution: A Combined Optical/X-ray Approach. J Phys Chem B 2013; 117:14089-98. [DOI: 10.1021/jp407094u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael W. Mara
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, U.S.A
| | - Megan Shelby
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, U.S.A
| | | | | | | | | | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, U.S.A
| | - Lin X. Chen
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, U.S.A
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12
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Sun Y, Zeng W, Benabbas A, Ye X, Denisov I, Sligar SG, Du J, Dawson JH, Champion PM. Investigations of heme ligation and ligand switching in cytochromes p450 and p420. Biochemistry 2013; 52:5941-51. [PMID: 23905516 DOI: 10.1021/bi400541v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
It is generally accepted that the inactive P420 form of cytochrome P450 (CYP) involves the protonation of the native cysteine thiolate to form a neutral thiol heme ligand. On the other hand, it has also been suggested that recruitment of a histidine to replace the native cysteine thiolate ligand might underlie the P450 → P420 transition. Here, we discuss resonance Raman investigations of the H93G myoglobin (Mb) mutant in the presence of tetrahydrothiophene (THT) or cyclopentathiol (CPSH), and on pressure-induced cytochrome P420cam (CYP101), that show a histidine becomes the heme ligand upon CO binding. The Raman mode near 220 cm⁻¹, normally associated with the Fe-histidine vibration in heme proteins, is not observed in either reduced P420cam or the reduced H93G Mb samples, indicating that histidine is not the ligand in the reduced state. The absence of a mode near 220 cm⁻¹ is also inconsistent with a generalization of the suggestion that the 221 cm⁻¹ Raman mode, observed in the P420-CO photoproduct of inducible nitric oxide synthase (iNOS), arises from a thiol-bound ferrous heme. This leads us to assign the 218 cm⁻¹ mode observed in the 10 ns P420cam-CO photoproduct Raman spectrum to a Fe-histidine vibration, in analogy to many other histidine-bound heme systems. Additionally, the inverse correlation plots of the νFe-His and νCO frequencies for the CO adducts of P420cam and the H93G analogs provide supporting evidence that histidine is the heme ligand in the P420-CO-bound state. We conclude that, when CO binds to the ferrous P420 state, a histidine ligand is recruited as the heme ligand. The common existence of an HXC-Fe motif in many CYP systems allows the C → H ligand switch to occur with only minor conformational changes. One suggested conformation of P420-CO involves the addition of another turn in the proximal L helix so that, when the protonated Cys ligand is dissociated from the heme, it can become part of the helix, and the heme is ligated by the His residue from the adjoining loop region. In other systems, such as iNOS and CYP3A4 (where the HXC-Fe motif is not found), a somewhat larger conformational change would be necessary to recuit a nearby histidine.
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Affiliation(s)
- Yuhan Sun
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, United States
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13
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Rebinding kinetics of dissociated amino acid ligand and carbon monoxide to ferrous microperoxidase-11 in aqueous solution. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4788-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Jasaitis A, Ouellet H, Lambry JC, Martin JL, Friedman JM, Guertin M, Vos MH. Ultrafast heme–ligand recombination in truncated hemoglobin HbO from Mycobacterium tuberculosis: A ligand cage. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Yoo BK, Lamarre I, Martin JL, Negrerie M. Quaternary structure controls ligand dynamics in soluble guanylate cyclase. J Biol Chem 2012; 287:6851-9. [PMID: 22223482 PMCID: PMC3307277 DOI: 10.1074/jbc.m111.299297] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 01/03/2012] [Indexed: 11/06/2022] Open
Abstract
Soluble guanylate cyclase (sGC) is the mammalian endogenous nitric oxide (NO) receptor. The mechanisms of activation and deactivation of this heterodimeric enzyme are unknown. For deciphering them, functional domains can be overexpressed. We have probed the dynamics of the diatomic ligands NO and CO within the isolated heme domain β(1)(190) of human sGC by piconanosecond absorption spectroscopy. After photo-excitation of nitrosylated sGC, only NO geminate rebinding occurs in 7.5 ps. In β(1)(190), both photo-dissociation of 5c-NO and photo-oxidation occur, contrary to sGC, followed by NO rebinding (7 ps) and back-reduction (230 ps and 2 ns). In full-length sGC, CO geminate rebinding to the heme does not occur. In contrast, CO geminately rebinds to β(1)(190) with fast multiphasic process (35, 171, and 18 ns). We measured the bimolecular association rates k(on) = 0.075 ± 0.01 × 10(6) M(-1) · S(-1) for sGC and 0.83 ± 0.1 × 10(6) M(-1) · S(-1) for β(1)(190). These different dynamics reflect conformational changes and less proximal constraints in the isolated heme domain with respect to the dimeric native sGC. We concluded that the α-subunit and the β(1)(191-619) domain exert structural strains on the heme domain. These strains are likely involved in the transmission of the energy and relaxation toward the activated state after Fe(2+)-His bond breaking. This also reveals the heme domain plasticity modulated by the associated domains and subunit.
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Affiliation(s)
- Byung-Kuk Yoo
- From the Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645 Ecole Polytechnique, 91128 Palaiseau, France
| | - Isabelle Lamarre
- From the Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645 Ecole Polytechnique, 91128 Palaiseau, France
| | - Jean-Louis Martin
- From the Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645 Ecole Polytechnique, 91128 Palaiseau, France
| | - Michel Negrerie
- From the Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645 Ecole Polytechnique, 91128 Palaiseau, France
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16
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Evidence for pH-dependent multiple conformers in iron(II) heme–human serum albumin: spectroscopic and kinetic investigation of carbon monoxide binding. J Biol Inorg Chem 2011; 17:133-47. [DOI: 10.1007/s00775-011-0837-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 08/07/2011] [Indexed: 12/22/2022]
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17
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van Thor JJ. Photoconversion of the Green Fluorescent Protein and Related Proteins. SPRINGER SERIES ON FLUORESCENCE 2011. [DOI: 10.1007/4243_2011_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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18
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Kim JY, Park JH, Chowdhury SA, Lim MH. Picosecond Dynamics of CN--Ligated Ferric Cytochrome c after Photoexcitation Using Time-resolved Vibrational Spectroscopy. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.12.3771] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Park J, Lee T, Lim M. Viscosity-Dependent Dynamics of CO Rebinding to Microperoxidase-8 in Glycerol/Water Solution. J Phys Chem B 2010; 114:10897-904. [DOI: 10.1021/jp1050436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Jaeheung Park
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735 Korea
| | - Taegon Lee
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735 Korea
| | - Manho Lim
- Department of Chemistry and Chemistry Institute of Functional Materials, Pusan National University, Busan, 609-735 Korea
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20
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Karunakaran V, Benabbas A, Sun Y, Zhang Z, Singh S, Banerjee R, Champion PM. Investigations of low-frequency vibrational dynamics and ligand binding kinetics of cystathionine beta-synthase. J Phys Chem B 2010; 114:3294-306. [PMID: 20155941 DOI: 10.1021/jp909700r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Vibrational coherence spectroscopy is used to study the low frequency dynamics of the truncated dimer of human cystathionine beta-synthase (CBS). CBS is a pyridoxal-5'-phosphate-dependent heme enzyme with cysteine and histidine axial ligands that catalyzes the condensation of serine and homocysteine to form cystathionine. A strong correlation between the "detuned" coherence spectrum (which probes higher frequencies) and the Raman spectrum is demonstrated, and a rich pattern of modes below 200 cm(-1) is revealed. Normal coordinate structural decomposition (NSD) of the ferric CBS crystal structure predicts the enhancement of normal modes with significant heme "doming", "ruffling", and "saddling" content, and they are observed in the coherence spectra near approximately 40, approximately 60, and approximately 90 cm(-1). When pH is varied, the relative intensities and frequencies of the low frequency heme modes indicate the presence of a unique protein-induced heme structural perturbation near pH 7 that differs from what is observed at higher or lower pH. For ferric CBS, we observe a new mode near approximately 25 cm(-1), possibly involving the response of the protein, which exhibits a phase jump of approximately pi for excitation on the blue and red side of the Soret band maximum. The low frequency vibrational coherence spectrum of ferrous CBS is also presented, along with our efforts to probe its NO-bound complex. The CO geminate rebinding kinetics of CBS are similar to the CO-bound form of the gene activator protein CooA, but with the appearance of a significant additional kinetic inhomogeneity. Analysis of this inhomogeneity suggests that it arises from the two subunits of CBS and leads to a factor of approximately 20 for the ratio of the average CO geminate rebinding rates of the two subunits.
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Affiliation(s)
- Venugopal Karunakaran
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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21
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Benabbas A, Ye X, Kubo M, Zhang Z, Maes EM, Montfort WR, Champion PM. Ultrafast dynamics of diatomic ligand binding to nitrophorin 4. J Am Chem Soc 2010; 132:2811-20. [PMID: 20121274 DOI: 10.1021/ja910005b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nitrophorin 4 (NP4) is a heme protein that stores and delivers nitric oxide (NO) through pH-sensitive conformational change. This protein uses the ferric state of a highly ruffled heme to bind NO tightly at low pH and release it at high pH. In this work, the rebinding kinetics of NO and CO to NP4 are investigated as a function of iron oxidation state and the acidity of the environment. The geminate recombination process of NO to ferrous NP4 at both pH 5 and pH 7 is dominated by a single approximately 7 ps kinetic phase that we attribute to the rebinding of NO directly from the distal pocket. The lack of pH dependence explains in part why NP4 cannot use the ferrous state to fulfill its function. The kinetic response of ferric NP4NO shows two distinct phases. The relative geminate amplitude of the slower phase increases dramatically as the pH is raised from 5 to 8. We assign the fast phase of NO rebinding to a conformation of the ferric protein with a closed hydrophobic pocket. The slow phase is assigned to the protein in an open conformation with a more hydrophilic heme pocket environment. Analysis of the ultrafast kinetics finds the equilibrium off-rate of NO to be proportional to the open state population as well as the pH-dependent amplitude of escape from the open pocket. When both factors are considered, the off-rate increases by more than an order of magnitude as the pH changes from 5 to 8. The recombination of CO to ferrous NP4 is observed to have a large nonexponential geminate amplitude with rebinding time scales of approximately 10(-11)-10(-9) s at pH 5 and approximately 10(-10)-10(-8) s at pH 7. The nonexponential CO rebinding kinetics at both pH 5 and pH 7 are accounted for using a simple model that has proven effective for understanding CO binding in a variety of other heme systems (Ye, X.; et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 14682).
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Affiliation(s)
- Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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22
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Zhang Z, Benabbas A, Ye X, Yu A, Champion PM. Measurements of heme relaxation and ligand recombination in strong magnetic fields. J Phys Chem B 2009; 113:10923-33. [PMID: 19588986 DOI: 10.1021/jp9031805] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Heme cooling signals and diatomic ligand recombination kinetics are measured in strong magnetic fields (up to 10 T). We examined diatomic ligand recombination to heme model compounds (NO and CO), myoglobin (NO and O(2)), and horseradish peroxidase (NO). No magnetic field induced rate changes in any of the samples were observed within the experimental detection limit. However, in the case of CO binding to heme in glycerol and O(2) binding to myoglobin, we observe a small magnetic field dependent change in the early time amplitude of the optical response that is assigned to heme cooling. One possibility, consistent with this observation, is that there is a weak magnetic field dependence of the nonradiative branching ratio into the vibrationally hot electronic ground state during CO photolysis. Ancillary studies of the "spin-forbidden" CO binding reaction in a variety of heme compounds in the absence of magnetic field demonstrate a surprisingly wide range for the Arrhenius prefactor. We conclude that CO binding to heme is not always retarded by unfavorable spin selection rules involving a double spin-flip superexchange mechanism. In fact, it appears that the small prefactor ( approximately 10(9) s(-1)) found for CO rebinding to Mb may be anomalous, rather than the general rule for heme-CO rebinding. These results point to unresolved fundamental issues that underlie the theory of heme-ligand photolysis and rebinding.
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Affiliation(s)
- Zhenyu Zhang
- Department of Physics and Center for interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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23
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Guo L, Park J, Lee T, Chowdhury P, Lim M, Gai F. Probing the role of hydration in the unfolding transitions of carbonmonoxy myoglobin and apomyoglobin. J Phys Chem B 2009; 113:6158-63. [PMID: 19348439 DOI: 10.1021/jp900009x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We show that the equilibrium unfolding transition of horse carbonmonoxy myoglobin monitored by the stretching vibration of the CO ligand, a local environmental probe, is very sharp and, thus, quite different from those measured by global conformational reporters. In addition, the denatured protein exhibits an A(0)-like CO band. We hypothesize that this sharp transition reports penetration of water into the heme pocket of the protein. Parallel experiments on horse apomyoglobin, wherein an environment-sensitive fluorescent probe, nile red, was used, also reveals a similar putative hydration event. Given the importance of dehydration in protein folding and also the recent debate over the interpretation of probe-dependent unfolding transitions, these results have strong implications on the mechanism of protein folding.
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Affiliation(s)
- Lin Guo
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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24
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25
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26
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Nicoletti FP, Howes BD, Fittipaldi M, Fanali G, Fasano M, Ascenzi P, Smulevich G. Ibuprofen Induces an Allosteric Conformational Transition in the Heme Complex of Human Serum Albumin with Significant Effects on Heme Ligation. J Am Chem Soc 2008; 130:11677-88. [DOI: 10.1021/ja800966t] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Francesco P. Nicoletti
- Dipartimento di Chimica and INSTM, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, Dipartimento di Biologia Strutturale e Funzionale, and Centro di Neuroscienze, Università dell’Insubria, Via Alberto da Giussano 12, I-21052 Busto Arsizio (VA), Italy, Centro Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Via della Vasca Navale 79, I-00146 Roma, Italy, and Istituto Nazionale per le Malattie Infettive I.R.C.C.S. ‘Lazzaro Spallanzani’, Via Portuense
| | - Barry D. Howes
- Dipartimento di Chimica and INSTM, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, Dipartimento di Biologia Strutturale e Funzionale, and Centro di Neuroscienze, Università dell’Insubria, Via Alberto da Giussano 12, I-21052 Busto Arsizio (VA), Italy, Centro Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Via della Vasca Navale 79, I-00146 Roma, Italy, and Istituto Nazionale per le Malattie Infettive I.R.C.C.S. ‘Lazzaro Spallanzani’, Via Portuense
| | - Maria Fittipaldi
- Dipartimento di Chimica and INSTM, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, Dipartimento di Biologia Strutturale e Funzionale, and Centro di Neuroscienze, Università dell’Insubria, Via Alberto da Giussano 12, I-21052 Busto Arsizio (VA), Italy, Centro Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Via della Vasca Navale 79, I-00146 Roma, Italy, and Istituto Nazionale per le Malattie Infettive I.R.C.C.S. ‘Lazzaro Spallanzani’, Via Portuense
| | - Gabriella Fanali
- Dipartimento di Chimica and INSTM, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, Dipartimento di Biologia Strutturale e Funzionale, and Centro di Neuroscienze, Università dell’Insubria, Via Alberto da Giussano 12, I-21052 Busto Arsizio (VA), Italy, Centro Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Via della Vasca Navale 79, I-00146 Roma, Italy, and Istituto Nazionale per le Malattie Infettive I.R.C.C.S. ‘Lazzaro Spallanzani’, Via Portuense
| | - Mauro Fasano
- Dipartimento di Chimica and INSTM, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, Dipartimento di Biologia Strutturale e Funzionale, and Centro di Neuroscienze, Università dell’Insubria, Via Alberto da Giussano 12, I-21052 Busto Arsizio (VA), Italy, Centro Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Via della Vasca Navale 79, I-00146 Roma, Italy, and Istituto Nazionale per le Malattie Infettive I.R.C.C.S. ‘Lazzaro Spallanzani’, Via Portuense
| | - Paolo Ascenzi
- Dipartimento di Chimica and INSTM, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, Dipartimento di Biologia Strutturale e Funzionale, and Centro di Neuroscienze, Università dell’Insubria, Via Alberto da Giussano 12, I-21052 Busto Arsizio (VA), Italy, Centro Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Via della Vasca Navale 79, I-00146 Roma, Italy, and Istituto Nazionale per le Malattie Infettive I.R.C.C.S. ‘Lazzaro Spallanzani’, Via Portuense
| | - Giulietta Smulevich
- Dipartimento di Chimica and INSTM, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy, Dipartimento di Biologia Strutturale e Funzionale, and Centro di Neuroscienze, Università dell’Insubria, Via Alberto da Giussano 12, I-21052 Busto Arsizio (VA), Italy, Centro Interdipartimentale di Microscopia Elettronica, Università Roma Tre, Via della Vasca Navale 79, I-00146 Roma, Italy, and Istituto Nazionale per le Malattie Infettive I.R.C.C.S. ‘Lazzaro Spallanzani’, Via Portuense
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27
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Yamashita T, Bouzhir-Sima L, Lambry JC, Liebl U, Vos MH. Ligand Dynamics and Early Signaling Events in the Heme Domain of the Sensor Protein Dos from Escherichia coli. J Biol Chem 2008; 283:2344-52. [DOI: 10.1074/jbc.m708123200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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28
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Investigations of vibrational coherence in the low-frequency region of ferric heme proteins. Biophys J 2007; 94:2252-68. [PMID: 18065461 DOI: 10.1529/biophysj.107.122119] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Femtosecond coherence spectroscopy is applied to a series of ferric heme protein samples. The low-frequency vibrational spectra that are revealed show dominant oscillations near 40 cm(-1). MbCN is taken as a typical example of a histidine-ligated, six-coordinate, ferric heme and a comprehensive spectroscopic analysis is carried out. The results of this analysis reveal a new heme photoproduct species, absorbing near 418 nm, which is consistent with the photolysis of the His(93) axial ligand. The photoproduct undergoes subsequent rebinding/recovery with a time constant of approximately 4 ps. The photoproduct lineshapes are consistent with a photolysis quantum yield of 75-100%, although the observation of a relatively strong six-coordinate heme coherence near 252 cm(-1) (assigned to nu(9) in the MbCN Raman spectrum) suggests that the 75% lower limit is much more likely. The phase and amplitude excitation profiles of the low-frequency mode at 40 cm(-1) suggest that this mode is strongly coupled to the MbCN photoproduct species and it is assigned to the doming mode of the transient penta-coordinated material. The absolute phase of the 40 cm(-1) mode is found to be pi/2 on the red side of 418 nm and it jumps to 3pi/2 as excitation is tuned to the blue side of 418 nm. The absolute phase of the 40 cm(-1) signal is not explained by the standard theory for resonant impulsive stimulated Raman scattering. New mechanisms that give a dominant momentum impulse to the resonant wavepacket, rather than a coordinate displacement, are discussed. The possibilities of heme iron atom recoil after photolysis, as well as ultrafast nonradiative decay, are explored as potential ways to generate the strong momentum impulse needed to understand the phase properties of the 40 cm(-1) mode.
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29
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Ye X, Ionascu D, Gruia F, Yu A, Benabbas A, Champion PM. Temperature-dependent heme kinetics with nonexponential binding and barrier relaxation in the absence of protein conformational substates. Proc Natl Acad Sci U S A 2007; 104:14682-7. [PMID: 17804802 PMCID: PMC1976205 DOI: 10.1073/pnas.0702622104] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present temperature-dependent kinetic measurements of ultrafast diatomic ligand binding to the "bare" protoheme (L(1)-FePPIX-L(2), where L(1) = H(2)O or 2-methyl imidazole and L(2) = CO or NO). We found that the binding of CO is temperature-dependent and nonexponential over many decades in time, whereas the binding of NO is exponential and temperature-independent. The nonexponential nature of CO binding to protoheme, as well as its relaxation above the solvent glass transition, mimics the kinetics of CO binding to myoglobin (Mb) but on faster time scales. This demonstrates that the nonexponential kinetic response observed for Mb is not necessarily due to the presence of protein conformational substates but rather is an inherent property of the solvated heme. The nonexponential kinetic data were analyzed by using a linear coupling model with a distribution of enthalpic barriers that fluctuate on slower time scales than the heme-CO recombination time. Below the solvent glass transition (T(g) approximately 180 K), the average enthalpic rebinding barrier for H(2)O-PPIX-CO was found to be approximately 1 kJ/mol. Above T(g), the barrier relaxes and is approximately 6 kJ/mol at 290 K. Values for the first two moments of the heme doming coordinate distribution extracted from the kinetic data suggest significant anharmonicity above T(g). In contrast to Mb, the protoheme shows no indication of the presence of "distal" enthalpic barriers. Moreover, the wide range of Arrhenius prefactors (10(9) to 10(11) s(-1)) observed for CO binding to heme under differing conditions suggests that entropic barriers may be an important source of control in this class of biochemical reactions.
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Affiliation(s)
- Xiong Ye
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - Dan Ionascu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - Florin Gruia
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - Anchi Yu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - Abdelkrim Benabbas
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 360 Huntington Avenue, Boston, MA 02115
| | - Paul M. Champion
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 360 Huntington Avenue, Boston, MA 02115
- To whom correspondence should be addressed. E-mail:
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30
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Denisov IG, Grinkova YV, McLean MA, Sligar SG. The One-electron Autoxidation of Human Cytochrome P450 3A4. J Biol Chem 2007; 282:26865-26873. [PMID: 17650504 DOI: 10.1074/jbc.m704747200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Monomeric cytochrome P450 3A4 (CYP3A4), the most prevalent cytochrome P450 in human liver, can simultaneously bind one, two, or three molecules of substrates and effectors. The difference in the functional properties of such binding intermediates gives rise to homotropic and heterotropic cooperative kinetics of this enzyme. To understand the overall kinetic processes operating in CYP3A4, we documented the kinetics of autoxidation of the oxy-ferrous intermediate of CYP3A4 as a function of testosterone concentration. The rate of autoxidation in the presence of testosterone was significantly lower than that observed with no substrate present. Stability of the oxy-ferrous complex in CYP3A4 and the amplitude of the geminate CO rebinding increased significantly as a result of binding of just one testosterone molecule. In contrast, the slow phase in the kinetics of cyanide binding to the ferric CYP3A4 correlated with a shift of the heme iron spin state, which is only caused by the association of a second molecule of testosterone. Our results show that the first substrate binding event prevents the escape of diatomic ligands from the distal heme binding pocket, stabilizes the oxy-ferrous complex, and thus serves as an important modulator of the uncoupling channel in the cytochromes P450.
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Affiliation(s)
- Ilia G Denisov
- Departments of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Yelena V Grinkova
- Departments of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Mark A McLean
- Departments of Biochemistry, University of Illinois, Urbana, Illinois 61801
| | - Stephen G Sligar
- Departments of Biochemistry, University of Illinois, Urbana, Illinois 61801; Departments of Chemistry, University of Illinois, Urbana, Illinois 61801; Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois 61801; College of Medicine, University of Illinois, Urbana, Illinois 61801.
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31
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Gruia F, Ye X, Ionascu D, Kubo M, Champion PM. Low frequency spectral density of ferrous heme: perturbations induced by axial ligation and protein insertion. Biophys J 2007; 93:4404-13. [PMID: 17766351 PMCID: PMC2098722 DOI: 10.1529/biophysj.107.114736] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Femtosecond coherence spectroscopy is used to probe low frequency (20-400 cm(-1)) modes of the ferrous heme group in solution, with and without 2-methyl imidazole (2MeIm) as an axial ligand. The results are compared to heme proteins (CPO, P450(cam), HRP, Mb) where insertion of the heme into the protein results in redistribution of the low frequency spectral density and in (approximately 60%) longer damping times for the coherent signals. The major effect of imidazole ligation to the ferrous heme is the "softening" of the low frequency force constants by a factor of approximately 0.6 +/- 0.1. The functional consequences of imidazole ligation are assessed and it is found that the enthalpic CO rebinding barrier is increased significantly when imidazole is bound. The force constant softening analysis, combined with the kinetics results, indicates that the iron is displaced by only approximately 0.2 A from the heme plane in the absence of the imidazole ligand, whereas it is displaced by approximately 0.4 A when imidazole (histidine) is present. This suggests that binding of imidazole (histidine) as an axial ligand, and the concomitant softening of the force constants, leads to an anharmonic distortion of the heme group that has significant functional consequences.
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Affiliation(s)
- Flaviu Gruia
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts, USA
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32
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Ye X, Yu A, Champion PM. Dynamics of nitric oxide rebinding and escape in horseradish peroxidase. J Am Chem Soc 2006; 128:1444-5. [PMID: 16448103 PMCID: PMC2768277 DOI: 10.1021/ja057172m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultrafast kinetic measurements of NO rebinding to horseradish peroxidase (HRP) are reported for the first time. The geminate kinetics are found to be exponential for all HRP samples studied. The ferric forms of HRP have NO geminate recombination time constants in the range of 15-30 ps, while the ferrous form has a time constant of approximately 7 ps. The simple exponential NO geminate kinetics found for HRP demonstrate that heme relaxation is not the underlying source of the nonexponential NO rebinding in myoglobin (Mb). The NO ligand escape rates from HRP are also determined, and they are found to depend dramatically on the presence or absence of the competitive inhibitor benzohydroxamic acid (BHA). The kinetic results indicate that, in contrast to Mb, there is direct solvent access to the distal heme pocket of HRP.
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33
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Khoroshun DV, Musaev DG, Morokuma K. Electronic reorganization: Origin of sigma trans promotion effect. J Comput Chem 2006; 28:423-41. [PMID: 17143866 DOI: 10.1002/jcc.20551] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Binding of two ligands trans to each other by some transition metal complexes may be cooperative [Khoroshun et al., Mol Phys 2002, 100, 523]. Several interesting consequent effects include (i) inverse relationship between bond strength and binding affinity; (ii) smaller coordination barriers to formation of weaker bonds; (iii) enhancement of Lewis acidity with increased number of ligands. We describe a simple model, sigma trans promotion effect (TPE), which considers electronic reorganization between two Lewis structures, and predicts the above-mentioned effects. The applied result of present study is the unified perspective on several facts of heme chemistry. Particularly, we reiterate an important but often overlooked notion, developed previously within the spin pairing model [Drago and Corden, Acc Chem Res 1980, 13, 353], that, in hemoproteins, the proximal histidine and the distal ligand such as O2 or CO cooperate in promoting electronic reorganization. As a result, depopulation of dz2 orbital upon ligand binding contributes to the phenomenon of hemoglobin cooperativity. The presented density functional (B3LYP) calculations on realistic models, the processes of carbon monoxide binding by Fe(II) porphyrins and dinitrogen binding by triamido/triamidoamine Mo(III) complexes, particularly the evaluation of the coordination barriers due to spin-state change by location of the minima on seams of crossing, support the TPE model predictions. From a broader theoretical perspective, the present study would hopefully stimulate the development of much needed frameworks and tools for facile comparisons of wave functions and their properties between different geometries, species, and electronic states. Advancement of practical wave function comparisons may yield fresh qualitative perspectives on chemical reactivity, and promote better understanding of related concepts such as electronic reorganization.
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Affiliation(s)
- Dmitry V Khoroshun
- Cherry L. Emerson Center for Scientific Computation, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA
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Ionascu D, Gruia F, Ye X, Yu A, Rosca F, Beck C, Demidov A, Olson JS, Champion PM. Temperature-dependent studies of NO recombination to heme and heme proteins. J Am Chem Soc 2005; 127:16921-34. [PMID: 16316238 PMCID: PMC2553725 DOI: 10.1021/ja054249y] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rebinding kinetics of NO to the heme iron of myoglobin (Mb) is investigated as a function of temperature. Below 200 K, the transition-state enthalpy barrier associated with the fastest (approximately 10 ps) recombination phase is found to be zero and a slower geminate phase (approximately 200 ps) reveals a small enthalpic barrier (approximately 3 +/- 1 kJ/mol). Both of the kinetic rates slow slightly in the myoglobin (Mb) samples above 200 K, suggesting that a small amount of protein relaxation takes place above the solvent glass transition. When the temperature dependence of the NO recombination in Mb is studied under conditions where the distal pocket is mutated (e.g., V68W), the rebinding kinetics lack the slow phase. This is consistent with a mechanism where the slower (approximately 200 ps) kinetic phase involves transitions of the NO ligand into the distal heme pocket from a more distant site (e.g., in or near the Xe4 cavity). Comparison of the temperature-dependent NO rebinding kinetics of native Mb with that of the bare heme (PPIX) in glycerol reveals that the fast (enthalpically barrierless) NO rebinding process observed below 200 K is independent of the presence or absence of the proximal histidine ligand. In contrast, the slowing of the kinetic rates above 200 K in MbNO disappears in the absence of the protein. Generally, the data indicate that, in contrast to CO, the NO ligand binds to the heme iron through a "harpoon" mechanism where the heme iron out-of-plane conformation presents a negligible enthalpic barrier to NO rebinding. These observations strongly support a previous analysis (Srajer et al. J. Am. Chem. Soc. 1988, 110, 6656-6670) that primarily attributes the low-temperature stretched exponential rebinding of MbCO to a quenched distribution of heme geometries. A simple model, consistent with this prior analysis, is presented that explains a variety of MbNO rebinding experiments, including the dependence of the kinetic amplitudes on the pump photon energy.
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Affiliation(s)
- Dan Ionascu
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | - Flaviu Gruia
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | - Xiong Ye
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | - Anchi Yu
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | - Florin Rosca
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | - Chris Beck
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | - Andrey Demidov
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
| | | | - Paul M. Champion
- Dept. of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston 02115
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