1
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Fry HC, Liu Y, Taylor SK. Design and Function of α-Helix-Rich, Heme-Binding Peptide Materials. Biomacromolecules 2024; 25:3398-3408. [PMID: 38752597 DOI: 10.1021/acs.biomac.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Peptide materials often employ short peptides that self-assemble into unique nanoscale architectures and have been employed across many fields relevant to medicine and energy. A majority of peptide materials are high in β-sheet, secondary structure content, including heme-binding peptide materials. To broaden the structural diversity of heme-binding peptide materials, a small series of peptides were synthesized to explore the design criteria required for (1) folding into an α-helix structure, (2) assembling into a nanoscale material, (3) binding heme, and (4) demonstrating functions similar to that of heme proteins. One peptide was identified to meet all four criteria, including the heme protein function of CO binding and its microsecond-to-millisecond recombination rates, as measured by transient absorption spectroscopy. Implications of new design criteria and peptide material function through heme incorporation are discussed.
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Affiliation(s)
- H Christopher Fry
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, Illinois 60439, United States
| | - Yuzi Liu
- Center for Nanoscale Materials, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, Illinois 60439, United States
| | - Sunny K Taylor
- Pritzker School for Molecular Engineering, University of Chicago, 5640 S. Ellis Ave., Chicago, Illinois 60637, United States
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2
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Andrew CR, Petrova ON, Lamarre I, Lambry JC, Rappaport F, Negrerie M. The Dynamics Behind the Affinity: Controlling Heme-Gas Affinity via Geminate Recombination and Heme Propionate Conformation in the NO Carrier Cytochrome c'. ACS Chem Biol 2016; 11:3191-3201. [PMID: 27709886 DOI: 10.1021/acschembio.6b00599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nitric oxide (NO) sensors are heme proteins which may also bind CO and O2. Control of heme-gas affinity and their discrimination are achieved by the structural properties and reactivity of the heme and its distal and proximal environments, leading to several energy barriers. In the bacterial NO sensor cytochrome c' from Alcaligenes xylosoxidans (AXCP), the single Leu16Ala distal mutation boosts the affinity for gas ligands by a remarkable 106-108-fold, transforming AXCP from one of the lowest affinity gas binding proteins to one of the highest. Here, we report the dynamics of diatomics after photodissociation from wild type and L16A-AXCP over 12 orders of magnitude in time. For the L16A variant, the picosecond geminate rebinding of both CO and NO appears with an unprecedented 100% yield, and no exit of these ligands from protein to solvent could be observed. Molecular dynamic simulations saliently demonstrate that dissociated CO stays within 4 Å from Fe2+, in contrast to wild-type AXCP. The L16A mutation confers a heme propionate conformation and docking site which traps the diatomics, maximizing the probability of recombination and directly explaining the ultrahigh affinities for CO, NO, and O2. Overall, our results point to a novel mechanism for modulating heme-gas affinities in proteins.
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Affiliation(s)
- Colin R. Andrew
- Department
of Chemistry and Biochemistry, Eastern Oregon University, La Grande, Oregon 97850, United States
| | - Olga N. Petrova
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Isabelle Lamarre
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Jean-Christophe Lambry
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
| | - Fabrice Rappaport
- Laboratoire
de Physiologie Membranaire et Moléculaire du Chloroplaste, CNRS, Université Pierre et Marie Curie, 75005 Paris, France
| | - Michel Negrerie
- Laboratoire
d’Optique et Biosciences, INSERM, Ecole Polytechnique, 91128 Palaiseau, France
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3
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Zhao Z, Wang D, Wang M, Sun X, Wang L, Huang X, Ma L, Li Z. Proximal environment controlling the reactivity between inorganic sulfide and heme-peptide model. RSC Adv 2016. [DOI: 10.1039/c6ra14100e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synthesized deuterohemin-peptide, which is lack of the distal protein structure, is used as a heme model to investigate the effects of the proximal environment on the reactivity of inorganic sulfide to heme center.
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Affiliation(s)
- Zijian Zhao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- College of Life Science
- Jilin University
- Changchun 130012
- PR China
| | - Dandan Wang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- College of Life Science
- Jilin University
- Changchun 130012
- PR China
| | - Mingyang Wang
- National Engineering Laboratory for AIDS Vaccine
- Jilin University
- Changchun 130012
- PR China
| | - Xiaoli Sun
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- PR China
| | - Liping Wang
- National Engineering Laboratory for AIDS Vaccine
- Jilin University
- Changchun 130012
- PR China
| | - Xuri Huang
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- PR China
| | - Li Ma
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- College of Life Science
- Jilin University
- Changchun 130012
- PR China
| | - Zhengqiang Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education
- College of Life Science
- Jilin University
- Changchun 130012
- PR China
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4
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Ramos-Alvarez C, Yoo BK, Pietri R, Lamarre I, Martin JL, Lopez-Garriga J, Negrerie M. Reactivity and dynamics of H2S, NO, and O2 interacting with hemoglobins from Lucina pectinata. Biochemistry 2013; 52:7007-21. [PMID: 24040745 DOI: 10.1021/bi400745a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hemoglobin HbI from the clam Lucina pectinata is involved in H2S transport, whereas homologous heme protein HbII/III is involved in O2 metabolism. Despite similar tertiary structures, HbI and HbII/III exhibit very different reactivity toward heme ligands H2S, O2, and NO. To investigate this reactivity at the heme level, we measured the dynamics of ligand interaction by time-resolved absorption spectroscopy in the picosecond to nanosecond time range. We demonstrated that H2S can be photodissociated from both ferric and ferrous HbI. H2S geminately rebinds to ferric and ferrous out-of-plane iron with time constants (τgem) of 12 and 165 ps, respectively, with very different proportions of photodissociated H2S exiting the protein (24% in ferric and 80% in ferrous HbI). The Gln(E7)His mutation considerably changes H2S dynamics in ferric HbI, indicating the role of Gln(E7) in controling H2S reactivity. In ferric HbI, the rate of diffusion of H2S from the solvent into the heme pocket (kentry) is 0.30 μM(-1) s(-1). For the HbII/III-O2 complex, we observed mainly a six-coordinate vibrationally excited heme-O2 complex with O2 still bound to the iron. This explains the low yield of O2 photodissociation and low koff from HbII/III, compared with those of HbI and Mb. Both isoforms behave very differently with regard to NO and O2 dynamics. Whereas the amplitude of geminate rebinding of O2 to HbI (38.5%) is similar to that of myoglobin (34.5%) in spite of different distal heme sites, it appears to be much larger for HbII/III (77%). The distal Tyr(B10) side chain present in HbII/III increases the energy barrier for ligand escape and participates in the stabilization of bound O2 and NO.
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Affiliation(s)
- Cacimar Ramos-Alvarez
- Department of Chemistry, University of Puerto Rico , Mayagüez Campus, Mayagüez 00680, Puerto Rico
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5
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How does hemoglobin generate such diverse functionality of physiological relevance? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1873-84. [PMID: 23643742 DOI: 10.1016/j.bbapap.2013.04.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 04/22/2013] [Accepted: 04/23/2013] [Indexed: 11/24/2022]
Abstract
The absolute values of the O2-affinities (P50, Klow, and Khigh) of hemoglobin (Hb) are regulated neither by changes in the static T-/R-quaternary and associated tertiary structures nor the ligation states. They are pre-determined and regulated by the extrinsic environmental factors such as pH, buffers, and heterotropic effectors. The effect and role of O2 on Hb are reversibly to drive the structural allosteric equilibrium between the T(deoxy)- and R(oxy)-Hb toward R(oxy)-Hb (the structural allostery). R(oxy)-Hb has a higher O2-affinity (Khigh) relative to that (Klow) of the T(deoxy)-Hb (Khigh>Klow) under any fixed environmental conditions. The apparent O2-affinity of Hb is high, as the globin matrix interferes with the dissociation process of O2, forcing the dissociated O2 geminately to re-bind to the heme Fe. This artificially increases [oxy-Hb] and concomitantly decreases [deoxy-Hb], leading to the apparent increases of the O2-affinity of Hb. The effector-linked high-frequency thermal fluctuations of the globin matrix act as a gating mechanism to modulate such physical, energetic, and kinetic barriers to enhance the dissociation process of O2, resulted in increases in [deoxy-Hb] and concomitant decrease in [oxy-Hb], leading to apparent reductions of the O2-affinity of Hb (the entropic allostery). The heme in Hb is simply a low-affinity O2-trap, the coordination structure of which is not altered by static T-/R-quaternary and associated tertiary structural changes of Hb. Thus, heterotrophic effectors are the signal molecule, which acts as a functional link between these two allosteries and generates the diverse functionality of Hb of physiological relevance. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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6
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Astudillo L, Bernad S, Derrien V, Sebban P, Miksovska J. Conformational dynamics in human neuroglobin: effect of His64, Val68, and Cys120 on ligand migration. Biochemistry 2012; 51:9984-94. [PMID: 23176629 DOI: 10.1021/bi301016u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Neuroglobin belongs to the family of hexacoordinate hemoglobins and has been implicated in the protection of neuronal tissue under hypoxic and ischemic conditions. Here we present transient absorption and photoacoustic calorimetry studies of CO photodissociation and bimolecular rebinding to neuroglobin focusing on the ligand migration process and the role of distal pocket residues (His64 and Val68) and two Cys residues (Cys55 and Cys120). Our results indicate that His64 has a minor impact on the migration of CO between the distal heme pocket and protein exterior, whereas the Val68 side chain regulates the transition of the photodissociated ligand between the distal pocket and internal hydrophobic cavities, which is evident from the increased geminate quantum yield in this mutated protein (Φ(gem) = 0.32 for WT and His64Gln, and Φ(gem) = 0.85 for Val68Phe). The interface between helix G and the A-B loop provides an escape pathway for the photodissociated ligand, which is evident from a decrease in the reaction enthalpy for the transition between the CO-bound hNgb and five-coordinate hNgb in the Cys120Ser mutant (ΔH = -3 ± 4 kcal mol(-1)) compared to that of the WT protein (ΔH = 20 ± 4 kcal mol(-1)). The extensive electrostatic/hydrogen binding network that includes heme propionate groups, Lys67, His64, and Tyr44 not only restricts the heme binding but also modulates the energetics of binding of CO to the five-coordinate hNgb as substitution of His64 with Gln leads to an endothermic association of CO with the five-coordinate hNgb (ΔH = 6 ± 3 kcal mol(-1)).
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Affiliation(s)
- Luisana Astudillo
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
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7
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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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8
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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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9
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D’Abramo M, Di Nola A, Amadei A. Kinetics of Carbon Monoxide Migration and Binding in Solvated Myoglobin as Revealed by Molecular Dynamics Simulations and Quantum Mechanical Calculations. J Phys Chem B 2009; 113:16346-53. [DOI: 10.1021/jp903165p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco D’Abramo
- Institut de Recerca Biomèdica, Parc Cientific de Barcelona Josep Samitier 1-5, Barcelona 08028 and Barcelona Supercomputing Center Jordi Girona 29, Barcelona 08034, Spain, Departament de Bioquimica, Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647 Barcelona 08028, Spain, Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5 00185 Rome, Italy, and Departimento di Scienze e Tecnologie Chimiche, Università di Roma “Tor Vergata”, via della Ricerca Scientifica 00133 Rome,
| | - Alfredo Di Nola
- Institut de Recerca Biomèdica, Parc Cientific de Barcelona Josep Samitier 1-5, Barcelona 08028 and Barcelona Supercomputing Center Jordi Girona 29, Barcelona 08034, Spain, Departament de Bioquimica, Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647 Barcelona 08028, Spain, Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5 00185 Rome, Italy, and Departimento di Scienze e Tecnologie Chimiche, Università di Roma “Tor Vergata”, via della Ricerca Scientifica 00133 Rome,
| | - Andrea Amadei
- Institut de Recerca Biomèdica, Parc Cientific de Barcelona Josep Samitier 1-5, Barcelona 08028 and Barcelona Supercomputing Center Jordi Girona 29, Barcelona 08034, Spain, Departament de Bioquimica, Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647 Barcelona 08028, Spain, Dipartimento di Chimica, Università di Roma “La Sapienza”, P.le A. Moro 5 00185 Rome, Italy, and Departimento di Scienze e Tecnologie Chimiche, Università di Roma “Tor Vergata”, via della Ricerca Scientifica 00133 Rome,
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10
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Silkstone G, Jasaitis A, Wilson MT, Vos MH. Ligand Dynamics in an Electron Transfer Protein. J Biol Chem 2007; 282:1638-49. [PMID: 17114183 DOI: 10.1074/jbc.m605760200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Substitution of the heme coordination residue Met-80 of the electron transport protein yeast iso-1-cytochrome c allows external ligands like CO to bind and thus increase the effective redox potential. This mutation, in principle, turns the protein into a quasi-native photoactivable electron donor. We have studied the kinetic and spectral characteristics of geminate recombination of heme and CO in a series of single M80X (X = Ala, Ser, Asp, Arg) mutants, using femtosecond transient absorption spectroscopy. In these proteins, all geminate recombination occurs on the picosecond and early nanosecond time scale, in a multiphasic manner, in which heme relaxation takes place on the same time scale. The extent of geminate recombination varies from >99% (Ala, Ser) to approximately 70% (Arg), the latter value being in principle low enough for electron injection studies. The rates and extent of the CO geminate recombination phases are much higher than in functional ligand-binding proteins like myoglobin, presumably reflecting the rigid and hydrophobic properties of the heme environment, which are optimized for electron transfer. Thus, the dynamics of CO recombination in cytochrome c are a tool for studying the heme pocket, in a similar way as NO in myoglobin. We discuss the differences in the CO kinetics between the mutants in terms of the properties of the heme environment and strategies to enhance the CO escape yield. Experiments on double mutants in which Phe-82 is replaced by Asp or Gly as well as the M80D substitution indicate that such steric changes substantially increase the motional freedom-dissociated CO.
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Affiliation(s)
- Gary Silkstone
- Department of Biological Sciences, Wivenhoe Park, University of Essex, Colchester CO4 3SQ, United Kingdom
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11
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Negrerie M, Kruglik SG, Lambry JC, Vos MH, Martin JL, Franzen S. Role of Heme Iron Coordination and Protein Structure in the Dynamics and Geminate Rebinding of Nitric Oxide to the H93G Myoglobin Mutant. J Biol Chem 2006; 281:10389-98. [PMID: 16476730 DOI: 10.1074/jbc.m513375200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The influence of the heme iron coordination on nitric oxide binding dynamics was investigated for the myoglobin mutant H93G (H93G-Mb) by picosecond absorption and resonance Raman time-resolved spectroscopies. In the H93G-Mb, the glycine replacing the proximal histidine does not interact with the heme iron so that exogenous substituents like imidazole may coordinate to the iron at the proximal position. Nitrosylation of H93G-Mb leads to either 6- or 5-coordinate species depending on the imidazole concentration. At high concentrations, (imidazole)-(NO)-6-coordinate heme is formed, and the photoinduced rebinding kinetics reveal two exponential picosecond phases ( approximately 10 and approximately 100 ps) similar to those of wild type myoglobin. At low concentrations, imidazole is displaced by the trans effect leading to a (NO)-5-coordinate heme, becoming 4-coordinate immediately after photolysis as revealed from the transient Raman spectrum. In this case, NO rebinding kinetics remain bi-exponential with no change in time constant of the fast component whose amplitude increases with respect to the 6-coordinate species. Bi-exponential NO geminate rebinding in 5-coordinate H93G-Mb is in contrast with the single-exponential process reported for nitrosylated soluble guanylate cyclase (Negrerie, M., Bouzhir, L., Martin, J. L., and Liebl, U. (2001) J. Biol. Chem. 276, 46815-46821). Thus, our data show that the iron coordination state or the heme iron out-of-plane motion are not at the origin of the bi-exponential kinetics, which depends upon the protein structure, and that the 4-coordinate state favors the fast phase of NO geminate rebinding. Consequently, the heme coordination state together with the energy barriers provided by the protein structure control the dynamics and affinity for NO-binding enzymes.
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Affiliation(s)
- Michel Negrerie
- INSERM U696, Laboratoire d'Optique et Biosciences, Ecole Polytechnique, Palaiseau F91120, 91128 Palaiseau Cedex, France.
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12
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Dantsker D, Roche C, Samuni U, Blouin G, Olson JS, Friedman JM. The Position 68(E11) Side Chain in Myoglobin Regulates Ligand Capture, Bond Formation with Heme Iron, and Internal Movement into the Xenon Cavities. J Biol Chem 2005; 280:38740-55. [PMID: 16155005 DOI: 10.1074/jbc.m506333200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
After photodissociation, ligand rebinding to myoglobin exhibits complex kinetic patterns associated with multiple first-order geminate recombination processes occurring within the protein and a simpler bimolecular phase representing second-order ligand rebinding from the solvent. A smooth transition from cryogenic-like to solution phase properties can be obtained by using a combination of sol-gel encapsulation, addition of glycerol as a bathing medium, and temperature tuning (-15 --> 65 degrees C). This approach was applied to a series of double mutants, myoglobin CO (H64L/V68X, where X = Ala, Val, Leu, Asn, and Phe), which were designed to examine the contributions of the position 68(E11) side chain to the appearance and disappearance of internal rebinding phases in the absence of steric and polar interactions with the distal histidine. Based on the effects of viscosity, temperature, and the stereochemistry of the E11 side chain, the three major phases, B --> A, C --> A, and D --> A, can be assigned, respectively, to ligand rebinding from the following: (i) the distal heme pocket, (ii) the xenon cavities prior to large amplitude side chain conformational relaxation, and (iii) the xenon cavities after significant conformational relaxation of the position 68(E11) side chain. The relative amplitudes of the B --> A and C --> A phases depend markedly on the size and shape of the E11 side chain, which regulates sterically both ligand return to the heme iron atom and ligand migration to the xenon cavities. The internal xenon cavities provide a transient docking site that allows side chain relaxations and the entry of water into the vacated distal pocket, which in turn slows ligand recombination markedly.
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Affiliation(s)
- David Dantsker
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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13
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Ye X, Yu A, Georgiev GY, Gruia F, Ionascu D, Cao W, Sage JT, Champion PM. CO rebinding to protoheme: investigations of the proximal and distal contributions to the geminate rebinding barrier. J Am Chem Soc 2005; 127:5854-61. [PMID: 15839683 PMCID: PMC2768272 DOI: 10.1021/ja042365f] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The rebinding kinetics of CO to protoheme (FePPIX) in the presence and absence of a proximal imidazole ligand reveals the magnitude of the rebinding barrier associated with proximal histidine ligation. The ligation states of the heme under different solvent conditions are also investigated using both equilibrium and transient spectroscopy. In the absence of imidazole, a weak ligand (probably water) is bound on the proximal side of the FePPIX-CO adduct. When the heme is encapsulated in micelles of cetyltrimethylammonium bromide (CTAB), photolysis of FePPIX-CO induces a complicated set of proximal ligation changes. In contrast, the use of glycerol-water solutions leads to a simple two-state geminate kinetic response with rapid (10-100 ps) CO recombination and a geminate amplitude that can be controlled by adjusting the solvent viscosity. By comparing the rate of CO rebinding to protoheme in glycerol solution with and without a bound proximal imidazole ligand, we find the enthalpic contribution to the proximal rebinding barrier, H(p), to be 11 +/- 2 kJ/mol. Further comparison of the CO rebinding rate of the imidazole bound protoheme with the analogous rate in myoglobin (Mb) leads to a determination of the difference in their distal free energy barriers: DeltaG(D) approximately 12 +/- 1 kJ/mol. Estimates of the entropic contributions, due to the ligand accessible volumes in the distal pocket and the xenon-4 cavity of myoglobin ( approximately 3 kJ/mol), then lead to a distal pocket enthalpic barrier of H(D) approximately 9 +/- 2 kJ/mol. These results agree well with the predictions of a simple model and with previous independent room-temperature measurements of the enthalpic MbCO rebinding barrier (18 +/- 2 kJ/mol).
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14
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Dantsker D, Samuni U, Ouellet Y, Wittenberg BA, Wittenberg JB, Milani M, Bolognesi M, Guertin M, Friedman JM. Viscosity-dependent Relaxation Significantly Modulates the Kinetics of CO Recombination in the Truncated Hemoglobin TrHbN from Mycobacterium tuberculosis. J Biol Chem 2004; 279:38844-53. [PMID: 15234986 DOI: 10.1074/jbc.m401513200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Kinetic traces were generated for the nanosecond and slower rebinding of photodissociated CO to trHbN in solution and in porous sol-gel matrices as a function of viscosity, conformation, and mutation. TrHbN is one of the two truncated hemoglobins from Mycobacterium tuberculosis. The kinetic traces were analyzed in terms of three distinct phases. These three phases are ascribed to rebinding: (i) from the distal heme pocket, (ii) from the adjacent apolar tunnel prior to conformational relaxation, and (iii) from the apolar tunnel subsequent to conformational relaxation. The fractional content of each of these phases was shown to be a function of the viscosity and, in the case of the sol-gel-encapsulated samples, sample preparation history. The observed kinetic patterns support a model consisting of the following elements: (i) the viscosity and conformation-sensitive dynamics of the Tyr(B10) side chain facilitate diffusion of the dissociated ligand from the distal heme pocket into the adjacent tunnel; (ii) the distal heme pocket architecture determines ligand access from the tunnel back to the heme iron; (iii) the distal heme pocket architecture is governed by a ligand-dependent hydrogen bonding network that limits the range of accessible side chain positions; and (iv) the apolar tunnel linking the heme site to the solvent biases the competition between water and ligand for occupancy of the vacated polar distal heme pocket greatly toward the nonpolar ligand. Implications of these finding with respect to biological function are discussed.
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Affiliation(s)
- David Dantsker
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Cao W, Ye X, Sjodin T, Christian JF, Demidov AA, Berezhna S, Wang W, Barrick D, Sage JT, Champion PM. Investigations of Photolysis and Rebinding Kinetics in Myoglobin Using Proximal Ligand Replacements. Biochemistry 2004; 43:11109-17. [PMID: 15323570 DOI: 10.1021/bi049077g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We use laser flash photolysis and time-resolved Raman spectroscopy of CO-bound H93G myoglobin (Mb) mutants to study the influence of the proximal ligand on the CO rebinding kinetics. In H93G mutants, where the proximal linkage with the protein is eliminated and the heme can bind exogenous ligands (e.g., imidazole, 4-bromoimidazole, pyridine, or dibromopyridine), we observe significant effects on the CO rebinding kinetics in the 10 ns to 10 ms time window. Resonance Raman spectra of the various H93G Mb complexes are also presented to aid in the interpretation of the kinetic results. For CO-bound H93G(dibromopyridine), we observe a rapid large-amplitude geminate phase with a fundamental CO rebinding rate that is approximately 45 times faster than for wild-type MbCO at 293 K. The absence of an iron proximal ligand vibrational mode in the 10 ns photoproduct Raman spectrum of CO-bound H93G(dibromopyridine) supports the hypothesis that proximal ligation has a significant influence on the kinetics of diatomic ligand binding to the heme.
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Affiliation(s)
- Wenxiang Cao
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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Cao W, Ye X, Georgiev GY, Berezhna S, Sjodin T, Demidov AA, Wang W, Sage JT, Champion PM. Proximal and Distal Influences on Ligand Binding Kinetics in Microperoxidase and Heme Model Compounds†. Biochemistry 2004; 43:7017-27. [PMID: 15170339 DOI: 10.1021/bi0497291] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We use laser flash photolysis and time-resolved Raman spectroscopy of CO-bound heme complexes to study proximal and distal influences on ligand rebinding kinetics. We report kinetics of CO rebinding to microperoxidase (MP) and 2-methylimidazole ligated Fe protoporphyrin IX in the 10 ns to 10 ms time window. We also report CO rebinding kinetics of MP in the 150 fs to 140 ps time window. For dilute, micelle-encapsulated (monodisperse) samples of MP, we do not observe the large amplitude geminate decay at approximately 100 ps previously reported in time-resolved IR measurements on highly concentrated samples [Lim, M., Jackson, T. A., and Anfinrud, P. A. (1997) J. Biol. Inorg. Chem. 2, 531-536]. However, for high concentration aggregated samples, we do observe the large amplitude picosecond CO geminate rebinding and find that it is correlated with the absence of the iron-histidine vibrational mode in the time-resolved Raman spectrum. On the basis of these results, the energetic significance of a putative distal pocket CO docking site proposed by Lim et al. may need to be reconsidered. Finally, when high concentration samples of native myoglobin (Mb) were studied as a control, an analogous increase in the geminate rebinding kinetics was not observed. This verifies that studies of Mb under dilute conditions are applicable to the more concentrated regime found in the cellular milieu.
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Affiliation(s)
- Wenxiang Cao
- Department of Physics and Center for Interdisciplinary Research on Complex System, Northeastern University, Boston, Massachusetts 02115, USA
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17
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Nienhaus K, Deng P, Olson JS, Warren JJ, Nienhaus GU. Structural dynamics of myoglobin: ligand migration and binding in valine 68 mutants. J Biol Chem 2003; 278:42532-44. [PMID: 12907676 DOI: 10.1074/jbc.m306888200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have combined Fourier transform infrared/temperature derivative (FTIR-TDS) spectroscopy at cryogenic temperatures and flash photolysis at ambient temperature to examine the effects of polar and bulky amino acid replacements of the highly conserved distal valine 68 in sperm whale myoglobin. In FTIR-TDS experiments, the CO ligand can serve as an internal voltmeter that monitors the local electrostatic field not only at the active site but also at intermediate ligand docking sites. Mutations of residue 68 alter size, shape, and electric field of the distal pocket, especially in the vicinity of the primary docking site (state B). As a consequence, the infrared bands associated with the ligand at site B are shifted. The effect is most pronounced in mutants with large aromatic side chains. Polar side chains (threonine or serine) have only little effect on the peak frequencies. Ligands that migrate toward more remote sites C and D give rise to IR bands with altered frequencies. TDS experiments separate the photoproducts according to their recombination temperatures. The rates and extent of ligand migration among internal cavities at cryogenic temperatures can be used to interpret geminate and bimolecular O2 and CO recombination at room temperature. The kinetics of geminate recombination can be explained by steric arguments alone, whereas both the polarity and size of the position 68 side chain play major roles in regulating bimolecular ligand binding from the solvent.
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Affiliation(s)
- Karin Nienhaus
- Department of Biophysics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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Angeloni L, Feis A. Protein relaxation in the photodissociation of myoglobin-CO complexes. Photochem Photobiol Sci 2003; 2:730-40. [PMID: 12911220 DOI: 10.1039/b301756g] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Laser-induced optoacoustic spectroscopy has been applied to the study of the photodissociation of myoglobin-CO complexes. Time-resolved optoacoustic signals have been measured from aqueous solutions of horse myoglobin-CO complex (hMbCO) at pH 3.5 and 8, and of sperm whale myoglobin-CO complex (swMbCO) at pH 8, in the temperature range 273-300 K. The signal of hMbCO at pH 8 exhibits three components. The first, which is faster than 20 ns and is associated with a reaction enthalpy of 61 kJ mol(-1), corresponds to Fe-CO bond breakage. The second component has a decay time of 80 ns at 293 K and is associated with an exothermic protein relaxation (-13 kJ mol(-1)) and a volume change of -3 ml mol(-1). The relaxation, which involves a state where the photo-dissociated CO is still in a protein docking site, is thermally activated, with an activation enthalpy of 51 kJ mol(-1). The third component has a decay time of 800 ns at 293 K and an activation enthalpy of 39 kJ mol(-1), and is associated with an endothermic process (26 kJ mol(-1)) and an expansion of 19 ml mol(-1). This process is ascribed to the migration of the photodissociated CO to the bulk solvent. At acidic pH, the latter process becomes faster (230 ns) and the volume change decreases. These features are correlated with the presence of an open form of the protein. swMbCO exhibits two components only, due to the overlap of the two fastest processes. The first involves a reaction enthalpy of 49 kJ mol(-1) and a volume contraction of -4.9 ml mol(-1). The second component (900 ns at 293 K, activation enthalpy 45 kJ mol(-1)) is associated with a reaction enthalpy of 38 kJ mol(-1) and a volume expansion of 15.3 ml mol(-1). These experimental findings have been interpreted by means of a new model, which also takes into account both laser flash photolysis results and structural information. The model is based on a two-dimensional scheme which describes both protein relaxation and the CO pathway following photodissociation.
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Affiliation(s)
- Leonardo Angeloni
- Department of Chemistry, University of Florence, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Firenze, Italy.
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Silkstone G, Stanway G, Brzezinski P, Wilson MT. Production and characterisation of Met80X mutants of yeast iso-1-cytochrome c: spectral, photochemical and binding studies on the ferrous derivatives. Biophys Chem 2002; 98:65-77. [PMID: 12128190 DOI: 10.1016/s0301-4622(02)00085-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The iron ligand, Met80, of yeast iso-1-cytochrome c has been mutated to residues that are unable to bind to the iron. The resultant proteins, Met80Ala, Ser, Asp, Glu, have been expressed and purified. All mutant proteins exhibit well defined pH dependent spectral transitions that report the binding, at high pH, of an intrinsic ligand (probably the nitrogen of an epsilon-NH(2) of a lysine) that drives the heme low-spin. The pK values are mutant dependent. All the mutant proteins bind extrinsic ligands, such as CO, in their ferrous states and we report the apparent quantum yield (phi) for CO photo-dissociation. The values of phi range from 0.004 for Met80Ala to 0.04 for Met80Asp. We also report values for the rate constant for binding the intrinsic lysine residue. The values for this constant, for phi and for the pK values are discussed in terms of the rigidity of the cytochrome structure. We also show that the mutant proteins bind with high affinity to cytochrome c oxidase, both in the ferric and ferrous states. The potential of these proteins to act as light activated electron donors for the study of electron transfer is discussed.
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Affiliation(s)
- Gary Silkstone
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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Enhanced geminate ligand rebinding upon photo-dissociation of silica gel-embedded myoglobin–CO. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)01027-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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