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Teixeira LR, Cordas CM, Fonseca MP, Duke NEC, Pokkuluri PR, Salgueiro CA. Modulation of the Redox Potential and Electron/Proton Transfer Mechanisms in the Outer Membrane Cytochrome OmcF From Geobacter sulfurreducens. Front Microbiol 2020; 10:2941. [PMID: 32010071 PMCID: PMC6971198 DOI: 10.3389/fmicb.2019.02941] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/06/2019] [Indexed: 11/13/2022] Open
Abstract
The monoheme outer membrane cytochrome F (OmcF) from Geobacter sulfurreducens plays an important role in Fe(III) reduction and electric current production. The electrochemical characterization of this cytochrome has shown that its redox potential is modulated by the solution pH (redox-Bohr effect) endowing the protein with the necessary properties to couple electron and proton transfer in the physiological range. The analysis of the OmcF structures in the reduced and oxidized states showed that with the exception of the side chain of histidine 47 (His47), all other residues with protonatable side chains are distant from the heme iron and, therefore, are unlikely to affect the redox potential of the protein. The protonatable site at the imidazole ring of His47 is in the close proximity to the heme and, therefore, this residue was suggested as the redox-Bohr center. In the present work, we tested this hypothesis by replacing the His47 with non-protonatable residues (isoleucine – OmcFH47I and phenylalanine – OmcFH47F). The structure of the mutant OmcFH47I was determined by X-ray crystallography to 1.13 Å resolution and showed only minimal changes at the site of the mutation. Both mutants were 15N-labeled and their overall folding was confirmed to be the same as the wild-type by NMR spectroscopy. The pH dependence of the redox potential of the mutants was measured by cyclic voltammetry. Compared to the wild-type protein, the magnitude of the redox-Bohr effect in the mutants was smaller, but not fully abolished, confirming the role of His47 on the pH modulation of OmcF’s redox potential. However, the pH effect on the heme substituents’ NMR chemical shifts suggested that the heme propionate P13 also contributes to the overall redox-Bohr effect in OmcF. In physiological terms, the contribution of two independent acid–base centers to the observed redox-Bohr effect confers OmcF a higher versatility to environmental changes by coupling electron/proton transfer within a wider pH range.
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Affiliation(s)
- Liliana R Teixeira
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Cristina M Cordas
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Marta P Fonseca
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Norma E C Duke
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Phani Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Carlos A Salgueiro
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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2
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Wang H, Wei X, Li J. Synthesis and characterization of six-coordinate iron(II/III) 5,10,15,20-tetrakis(pentafluorophenyl) porphyrinato complexes with non-hindered imidazole ligands. J PORPHYR PHTHALOCYA 2018. [DOI: 10.1142/s1088424618500530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Four bis-imidazole iron(II/III) 5,10,15,20-tetrakis(pentafluorophenyl)porphyrinato (TFPP) complexes, [Fe(TFPP)(1-MeIm)[Formula: see text]], [Fe(TFPP)(1-VinylIm)[Formula: see text]], [Fe(TFPP)(4-MeHIm)[Formula: see text]]Cl and [Fe(TFPP)(1-EtIm)[Formula: see text]]BF[Formula: see text] (1-MeIm [Formula: see text] 1-methylimidazole, 1-VinylIm [Formula: see text] 1-vinylimidazole, 4-MeHIm [Formula: see text] 4-methylimidazole and 1-EtIm [Formula: see text] 1-ethylimidazole) were synthesized and characterized by single-crystal X-ray and UV-vis spectroscopy. A negative correlation is found between the absolute imidazole orientation ([Formula: see text] and the Fe–N[Formula: see text] distance for the [Fe(II)(Porph)(Im)[Formula: see text]] (Im [Formula: see text] 1-MeIm or 4-MeHIm) complexes where the smaller [Formula: see text] angle corresponds to a longer axial distance. Hydrogen bonding, which might affect the orientations of the axial imidazoles is found for Fe(TFPP)(4-MeHIm)[Formula: see text]]Cl (A and B). The autoreduction of [Fe(III)(TFPP)]Cl to [Fe(II)(TFPP)(1-MeIm)[Formula: see text]] with 1-methylimidazole has been monitored by UV-vis spectroscopic titration.
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Affiliation(s)
- Haimang Wang
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, P. R. China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing, 101408, P. R. China
| | - Xuehong Wei
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, P. R. China
- Scientific Instrument Center, Shanxi University, Taiyuan, 030006, P. R. China
| | - Jianfeng Li
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Yanqi Lake, Huairou District, Beijing, 101408, P. R. China
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3
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Adomeit S, Rabeah J, Surkus AE, Bentrup U, Brückner A. Effects of Imidazole-Type Ligands in CuI/TEMPO-Mediated Aerobic Alcohol Oxidation. Inorg Chem 2016; 56:684-691. [DOI: 10.1021/acs.inorgchem.6b02925] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Sven Adomeit
- Leibniz-Institut für
Katalyse, Universität Rostock, Albert-Einstein Straße 29A, 18059 Rostock, Germany
| | - Jabor Rabeah
- Leibniz-Institut für
Katalyse, Universität Rostock, Albert-Einstein Straße 29A, 18059 Rostock, Germany
| | - Annette E. Surkus
- Leibniz-Institut für
Katalyse, Universität Rostock, Albert-Einstein Straße 29A, 18059 Rostock, Germany
| | - Ursula Bentrup
- Leibniz-Institut für
Katalyse, Universität Rostock, Albert-Einstein Straße 29A, 18059 Rostock, Germany
| | - Angelika Brückner
- Leibniz-Institut für
Katalyse, Universität Rostock, Albert-Einstein Straße 29A, 18059 Rostock, Germany
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4
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Molecular mechanisms of heme based sensors from sediment organisms capable of extracellular electron transfer. J Inorg Biochem 2014; 133:104-9. [DOI: 10.1016/j.jinorgbio.2013.10.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/15/2013] [Accepted: 10/23/2013] [Indexed: 11/18/2022]
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5
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Quintas PO, Cepeda AP, Borges N, Catarino T, Turner DL. Relative importance of driving force and electrostatic interactions in the reduction of multihaem cytochromes by small molecules. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:745-50. [DOI: 10.1016/j.bbabio.2013.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 02/08/2013] [Accepted: 02/12/2013] [Indexed: 11/26/2022]
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6
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Patra R, Sahoo D, Dey S, Sil D, Rath SP. Switching Orientation of Two Axial Imidazole Ligands between Parallel and Perpendicular in Low-Spin Fe(III) and Fe(II) Nonplanar Porphyrinates. Inorg Chem 2012; 51:11294-305. [DOI: 10.1021/ic300229u] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ranjan Patra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India
| | - Dipankar Sahoo
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India
| | - Soumyajit Dey
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India
| | - Debangsu Sil
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, India
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7
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Homotropic and heterotropic interactions in cytochromes c
3
from sulphate reducing bacteria. FEBS Lett 2011; 586:494-503. [DOI: 10.1016/j.febslet.2011.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 07/04/2011] [Indexed: 11/23/2022]
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8
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Quintas PO, Catarino T, Todorovic S, Turner DL. Highly selective ligand binding by Methylophilus methylotrophus cytochrome c''. Biochemistry 2011; 50:5624-32. [PMID: 21599015 DOI: 10.1021/bi200480a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c'' (cyt c'') from Methylophilus methylotrophus is unusual insofar as the heme has two axial histidine ligands in the oxidized form but one is detached when the protein is reduced. Despite cyt c'' having an axial site available for binding small ligands, we show here that only NO binds readily to the ferrous cyt c''. Binding of CO, as well as CN(-), on the other hand requires considerable structural reorganization, or reduction of the disulfide bridge close to the heme. Standard free energies for the binding of NO and CO reveal high selectivity of the ferrous cyt c'' for NO, indicating its putative physiological role. In this work, we characterize in detail the kinetics of NO binding and the structural features of the Fe(2+)-NO adduct by stopped-flow and resonance Raman spectroscopy, respectively.
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Affiliation(s)
- Pedro O Quintas
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
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9
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Patra R, Chaudhary A, Ghosh SK, Rath SP. Axial Ligand Orientations in a Distorted Porphyrin Macrocycle: Synthesis, Structure, and Properties of Low-Spin Bis(imidazole)iron(III) and Iron(II) Porphyrinates†Dedicated to Prof. Animesh Chakravorty on the occasion of his 75th birthday. Inorg Chem 2010; 49:2057-67. [DOI: 10.1021/ic9016504] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ranjan Patra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Arvind Chaudhary
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Sudip Kumar Ghosh
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Sankar Prasad Rath
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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10
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Noronha M, Santos R, Paci E, Santos H, Maçanita AL. Fluorescence lifetimes of tyrosine residues in cytochrome c'' as local probes to study protein unfolding. J Phys Chem B 2009; 113:4466-74. [PMID: 19249841 DOI: 10.1021/jp805781r] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Time-resolved fluorescence spectroscopy was used to show that multiple tyrosine residues of a protein can serve as localized probes of structural changes during thermal unfolding. Cytochrome c'' from Methylophilus methylotrophus, which has four tyrosine residues, was chosen as a model protein. The procedure involved, first, the assignment of the experimental decay times to the tyrosine residues, followed by the interpretation of the changes in the decay times and pre-exponential coefficients with temperature. We found that the fluorescence decays of cytochrome c'' are double-exponential from 23 to 80 degrees C, with decay times much shorter than those of the parent compound N-acetyl-tyrosinamide; this quenching was ascribed to dipole-dipole energy transfer from the tyrosine residues to the heme. The tyrosine-heme distances (R) and theoretical decay times, tau(comp), were estimated for each tyrosine residue. The analysis of the simulated decay generated with tau(comp), showed that a double-exponential fit is sufficient to describe the four decay times with two pre-exponential coefficients close to values observed from the experimental decay. Therefore, the decay times at 23 degrees C could be assigned to the individual tyrosine residues as tau(1) to Tyr-10 and Tyr-23 (at 20.3 A) and tau(2) to Tyr-12 and Tyr-115 (at 12-14 A). On the basis of this assignment and MD simulations, the temperature dependence of the decay times and pre-exponential coefficients suggest that upon unfolding, Tyr-12 is displaced from the heme, with loss of the structure of alpha-helix I. Moreover, Tyr-115 remains close to the heme and the structure in this region of the protein is not altered significantly. Altogether the data support the view that the protein core, comprising the heme and the four alpha-helices II to V, is clearly more stable than the remaining region that includes alpha-helix I and the loop between residues 19-27.
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Affiliation(s)
- Melinda Noronha
- Departamento de Quimica, Instituto Superior Tecnico, Universidade Tecnica de Lisboa, Portugal
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11
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Li J, Nair SM, Noll BC, Schulz CE, Scheidt WR. Relative axial ligand orientation in bis(imidazole)iron(II) porphyrinates: are "picket fence" derivatives different? Inorg Chem 2008; 47:3841-50. [PMID: 18351735 DOI: 10.1021/ic702498c] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of three new bis(imidazole)-ligated iron(II) picket fence porphyrin derivatives, [Fe(TpivPP)(1-RIm) 2] 1-RIm = 1-methyl-, 1-ethyl-, or 1-vinylimidazole) are reported. X-ray structure determinations reveal that the steric requirements of the four alpha,alpha,alpha,alpha-o-pivalamidophenyl groups lead to very restricted rotation of the imidazole ligand on the picket side of the porphyrin plane; the crowding leads to an imidazole plane orientation eclipsing an iron-porphyrin nitrogen bond. An unusual feature for these diamagnetic iron(II) species is that all three derivatives have the two axial ligands with a relative perpendicular orientation; the dihedral angles between the two imidazole planes are 77.2 degrees , 62.4 degrees , and 78.5 degrees . All three derivatives have nearly planar porphyrin cores. Mössbauer spectroscopic characterization shows that all three derivatives have quadrupole splitting constants around 1.00 mm/s at 100K.
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Affiliation(s)
- Jianfeng Li
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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12
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Enguita FJ, Pohl E, Turner DL, Santos H, Carrondo MA. Structural evidence for a proton transfer pathway coupled with haem reduction of cytochrome c″ from Methylophilus methylotrophus. J Biol Inorg Chem 2005; 11:189-96. [PMID: 16341897 DOI: 10.1007/s00775-005-0065-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Accepted: 11/11/2005] [Indexed: 11/29/2022]
Abstract
The crystal structures of the oxidized and reduced forms of cytochrome c" from Methylophilus methylotrophus were solved from X-ray synchrotron data to atomic resolution. The overall fold of the molecule in the two redox states is very similar and is comparable to that of the oxygen-binding protein from the purple phototrophic bacterium Rhodobacter sphaeroides. However, significant modifications occur near the haem group, in particular the detachment from axial binding of His95 observed upon reduction as well as the adoption of different conformations of some protonatable residues that form a possible proton path from the haem pocket to the protein surface. These changes are associated with the previously well characterized redox-Bohr behaviour of this protein. Furthermore they provide a model for one of the presently proposed mechanisms of proton translocation in the much more complex protein cytochrome c oxidase.
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Affiliation(s)
- Francisco J Enguita
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, P.O. Box 127, 2781-901 Oeiras, Portugal
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13
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Hu C, Noll BC, Schulz CE, Scheidt WR. Ligand orientation control in low-spin six-coordinate (porphinato)iron(II) species. Inorg Chem 2005; 44:4346-58. [PMID: 15934765 PMCID: PMC1502394 DOI: 10.1021/ic050320p] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis of a low-spin six-coordinate iron(II) porphyrinate in which the two axial ligands are forced to have a relative perpendicular orientation has been successfully accomplished for the first time. The reaction of four-coordinate (tetramesitylporphinato)iron(II) with 2-methylimidazole leads to the preparation of [Fe(TMP)(2-MeHIm)(2)] which cocrystallizes with five-coordinate [Fe(TMP)(2-MeHIm)]. The six-coordinate complex accommodates the sterically crowded pair of imidazoles with a strongly ruffled core and relative perpendicular orientation. This leads to shortened equatorial bonds of 1.963(6) A and slightly elongated axial Fe-N bond lengths of 2.034(9) A that are about 0.04 A shorter and 0.03 A longer, respectively, in comparison to those of the bis-imidazole-ligated iron(II) species with parallel oriented axial ligands. The Mossbauer spectrum shows a pair of quadrupole doublets that can be assigned to the components of the cocrystallized crystalline solid. High-spin five-coordinate [Fe(TMP)(2-MeHIm)] has DeltaE(Q) = 2.25 mm/s and delta = 0.90 mm/s at 15 K. The quadrupole splitting, DeltaE(Q), for [Fe(TMP)(2-MeHIm)(2)] is 1.71 mm/s, and the isomer shift is 0.43 mm/s at 15 K. The quadrupole splitting value is significantly larger than that found for low-spin iron(II) derivatives with relative parallel orientations for the two axial ligands. Mossbauer spectra thus provide a probe for ligand orientation when structural data are otherwise not available.
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Affiliation(s)
- Chuanjiang Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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14
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Xavier AV. Thermodynamic and choreographic constraints for energy transduction by cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1658:23-30. [PMID: 15282170 DOI: 10.1016/j.bbabio.2004.03.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2004] [Revised: 03/30/2004] [Accepted: 03/30/2004] [Indexed: 10/26/2022]
Abstract
Cooperative effects are fundamental for electroprotonic energy transduction processes, crucial to sustain much of life chemistry. However, the primary cooperative mechanism by which transmembrane proteins couple the downhill transfer of electrons to the uphill activation (acidification) of protic groups is still a matter of great controversy. To understand cooperative processes fully, it is necessary to obtain the microscopic thermodynamic parameters of the functional centres and relate them to the relevant structural features, a task difficult to achieve for large proteins. The approach discussed here explores how this may be done by extrapolation from mechanisms used by simpler proteins operative in similar processes. The detailed study of small, soluble cytochromes performing electroprotonic activation has shown how they use anti-electrostatic effects to control the synchronous movement of charges. These include negative e(-)/H(+) (redox-Bohr effect) cooperativities. This capacity is the basis to discuss an unorthodox mechanism consistent with the available experimental data on the process of electroprotonic energy transduction performed by cytochrome c oxidase (CcO).
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Affiliation(s)
- António V Xavier
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6 Apt. 127, 2780-156 Oeiras, Portugal.
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15
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Walker FA. Models of the Bis-Histidine-Ligated Electron-Transferring Cytochromes. Comparative Geometric and Electronic Structure of Low-Spin Ferro- and Ferrihemes. Chem Rev 2004; 104:589-615. [PMID: 14871136 DOI: 10.1021/cr020634j] [Citation(s) in RCA: 176] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- F Ann Walker
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721-0041, USA.
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16
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Xavier AV. A mechano-chemical model for energy transduction in cytochrome c oxidase: the work of a Maxwell's god. FEBS Lett 2002; 532:261-6. [PMID: 12482576 DOI: 10.1016/s0014-5793(02)03692-x] [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: 11/26/2022]
Abstract
Cytochrome c3 has a central role in the energetics of Desulfovibrio sp., where it performs an electroprotonic energy transduction step. This process uses a network of cooperativities, largely based on anti-Coulomb components, resulting from a mechano-chemical energy coupling mechanism. This mechanism provides a model coherent with the data available for the redox chemistry of haem a of cytochrome c oxidase and its link to the activation of protons. A crucial feature of the model is an anti-Coulomb effect that sets the stage for a molecular ratchet, ensuring vectoriality for the redox-driven localised movement of protons across the membrane, against an electrochemical gradient.
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Affiliation(s)
- António V Xavier
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6 - Apt. 127, 2780-156, Oeiras, Portugal.
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17
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Rivas L, Murgida D, Hildebrandt P. Surface-enhanced resonance Raman study of cytochrome c″ from Methylophilus Methylotrophus. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(00)00850-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Brennan L, Turner DL, Fareleira P, Santos H. Solution structure of Methylophilus methylotrophus cytochrome c": insights into the structural basis of haem-ligand detachment. J Mol Biol 2001; 308:353-65. [PMID: 11327772 DOI: 10.1006/jmbi.2001.4600] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytochrome c" from Methylophilus methylotrophus is a monohaem protein with 124 amino acid residues. The iron has two histidine ligands in the oxidised form, one of which detaches and picks up a proton when the protein is reduced. Thus, both forms are paramagnetic. The structure of the oxidised form in solution, determined from NMR data is presented. The family of structures has an average backbone rmsd value of 0.53 A, and a heavy atom rmsd value of 0.95 A, within a target function range of 32 %. This structure is related to class I cytochromes with an additional helix at the N terminus. The haem-binding site occurs in a domain essentially lacking secondary structure motifs and the axial histidinyl residues were found in an unusual near perpendicular orientation. Moreover, a disulfide bridge is present, an uncommon structural feature among c-type cytochromes. The disulfide bridge, linking cysteine residues 96 and 104, forms a loop that confers rigidity and is essential to the detachment of the axial histidine (His95) as demonstrated by chemical disruption of the S-S bond. A route for protonation of the distal histidine involving haem propionate 17 is proposed and discussed in the light of available models for complex membrane proton pumps.
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Affiliation(s)
- L Brennan
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande, 6 Apt. 127, Oeiras, Portugal
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19
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Shifman JM, Gibney BR, Sharp RE, Dutton PL. Heme redox potential control in de novo designed four-alpha-helix bundle proteins. Biochemistry 2000; 39:14813-21. [PMID: 11101297 DOI: 10.1021/bi000927b] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effects of various mechanisms of metalloporphyrin reduction potential modulation were investigated experimentally using a robust, well-characterized heme protein maquette, synthetic protein scaffold H10A24 [¿CH(3)()CONH-CGGGELWKL.HEELLKK.FEELLKL.AEERLKK. L-CONH(2)()¿(2)](2). Removal of the iron porphyrin macrocycle from the high dielectric aqueous environment and sequestration within the hydrophobic core of the H10A24 maquette raises the equilibrium reduction midpoint potential by 36-138 mV depending on the hydrophobicity of the metalloporphyrin structure. By incorporating various natural and synthetic metalloporphyrins into a single protein scaffold, we demonstrate a 300-mV range in reduction potential modulation due to the electron-donating/withdrawing character of the peripheral macrocycle substituents. Solution pH is used to modulate the metalloporphyrin reduction potential by 160 mV, regardless of the macrocycle architecture, by controlling the protonation state of the glutamate involved in partial charge compensation of the ferric heme. Attempts to control the reduction potential by inserting charged amino acids into the hydrophobic core at close proximity to the metalloporphyrin lead to varied success, with H10A24-L13E lowering the E(m8.5) by 40 mV, H10A24-E11Q raising it by 50 mV, and H10A24-L13R remaining surprisingly unaltered. Modifying the charge of the adjacent metalloporphyrin, +1 for iron(III) protoporphyrin IX or neutral for zinc(II) protoporphyrin IX resulted in a loss of 70 mV [Fe(III)PPIX](+) - [Fe(III)PPIX](+) interaction observed in maquettes. Using these factors in combination, we illustrate a 435-mV variation of the metalloporphyrin reduction midpoint potential in a simple heme maquette relative to the about 800-mV range observed for natural cytochromes. Comparison between the reduction potentials of the heme maquettes and other de novo designed heme proteins reveals global trends in the E(m) values of synthetic cytochromes.
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Affiliation(s)
- J M Shifman
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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20
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Price NJ, Brennan L, Faria TQ, Vijgenboom E, Canters GW, Turner DL, Santos H. High yield of Methylophilus methylotrophus cytochrome c by coexpression with cytochrome c maturation gene cluster from Escherichia coli. Protein Expr Purif 2000; 20:444-50. [PMID: 11087684 DOI: 10.1006/prep.2000.1318] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Heterologous expression of c-type cytochromes in the periplasm of Escherichia coli often results in low soluble product yield, apoprotein formation, or protein degradation. We have expressed cytochrome c from Methylophilus methylotrophus in E. coli by coexpression of the gene encoding the cytochrome (cycA) with the host-specific cytochrome c maturation elements, within the ccmA-H gene cluster. Aerobic cultures produced up to 10 mg holoprotein per liter after induction with IPTG. In the absence of the maturation factors E. coli failed to produce a stable haem protein. Cytochrome c" isolated from the natural host was compared with the recombinant protein. No structural differences were detected using SDS-PAGE, UV-Visible spectroscopy, differential scanning calorimetry, and (1)H-NMR spectroscopy. The success in expressing the mature cytochrome c in E. coli allows the engineering of the cycA gene by site-directed mutagenesis thereby providing an ideal method for producing mutant protein for studying the structure/function relationship.
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Affiliation(s)
- N J Price
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-156 Oeiras, Portugal
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21
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Indiani C, de Sanctis G, Neri F, Santos H, Smulevich G, Coletta M. Effect of pH on axial ligand coordination of cytochrome c" from Methylophilus methylotrophus and horse heart cytochrome c. Biochemistry 2000; 39:8234-42. [PMID: 10889031 DOI: 10.1021/bi000266i] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of protons on the axial ligand coordination and on structural aspects of the protein moiety of cytochrome c' ' from Methylophilus methylotrophus, an obligate methylotroph, has been investigated down to very low pH (i.e., 0.3). The unusual resistance of this cytochrome to very low pH values has been exploited to carry out this study in comparison with horse heart cytochrome c. The experiments were undertaken at a constant phosphate concentration to minimize the variation of ionic strength with pH. The pH-linked effects have been monitored at 23 degrees C in the oxidized forms of both cytochromes by following the variations in the electronic absorption, circular dichroism and resonance Raman spectra. This approach has enabled the conformational changes of the heme surroundings to be monitored and compared with the concomitant overall structural rearrangements of the molecule. The results indicate that horse heart cytochrome c undergoes a first conformational change at around pH 2.0. This event is possibly related to the cleavage of the Fe-Met80 bond and a likely coordination of a H(2)O molecule as a sixth axial ligand. Conversely, in cytochrome c" from M. methylotrophus, a variation of the axial ligand coordination occurs at a pH that is about 1 unit lower. Further, it appears that a concerted cleavage of both His ligands takes place, suggesting indeed that the different axial ligands present in horse heart cytochrome c (Met/His) and in cytochrome c" from M. methylotrophus (His/His) affect the heme conformational changes.
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Affiliation(s)
- C Indiani
- Dipartimento di Chimica, Università di Firenze, Via Gino Capponi 9, I-50121 Firenze, Italy
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22
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Price NJ, Vijgenboom E, Ribeiro G, Costa JV, Canters GW, Santos H. Cloning and sequence analysis of the gene encoding Methylophilus methylotrophus cytochrome c", a unique protein with a perpendicular orientation of the histidinyl ligands. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1413:55-61. [PMID: 10524262 DOI: 10.1016/s0005-2728(99)00085-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Cytochrome c" from Methylophilus methylotrophus is an unusual monohaem protein that undergoes a major redox-linked spin-state transition: one of the two axial histidines bound to the iron in the oxidised form is detached upon reduction and a proton is taken up. A 3.5-kb DNA fragment, containing the gene encoding cytochrome c" (cycA), has been cloned and sequenced. The cytochrome c" gene codes for a pre-protein with a typical prokaryotic 20-residue signal sequence, suggesting that the protein is synthesised as a precursor which is processed during its secretion into the periplasm. The C-terminus of cytochrome c" has homology with the corresponding region of an oxygen-binding haem protein (SHP) from phototrophically grown Rhodobacter sphaeroides. SHP is similar in size and in the location of its haem-binding site. Immediately downstream from cytochrome c" a second open reading frame (ORF) codes for a 23-kDa protein with similarity to the cytochrome b-type subunit of Ni-Fe hydrogenase. The possibility of coordinated expression of cycA and this ORF is discussed.
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Affiliation(s)
- N J Price
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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23
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Klarskov K, Leys D, Backers K, Costa HS, Santos H, Guisez Y, Van Beeumen JJ. Cytochrome c" from the obligate methylotroph Methylophilus methylotrophus, an unexpected homolog of sphaeroides heme protein from the phototroph Rhodobacter sphaeroides. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1412:47-55. [PMID: 10354493 DOI: 10.1016/s0005-2728(99)00050-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The complete primary structure of an unusual soluble cytochrome c isolated from the obligate methylotrophic bacterium Methylophilus methylotrophus has been determined to contain 124 amino acids and to have an average molecular mass of 14293.0 Da. The sequence has two unusual features: firstly, the location of the heme-binding cysteines is far downstream from the N-terminus, namely at positions 49 and 52; secondly, an extra pair of cysteine residues is present near the C-terminus. In both respects, cytochrome c" is similar to the oxygen-binding heme protein SHP from the purple phototrophic bacterium Rhodobacter sphaeroides. In contrast to SHP, cytochrome c" changes from low-spin to high-spin upon reduction, due to dissociation of a sixth heme ligand histidine which is identified as His-95 by analogy to the class I cytochromes c. The distance of His-95 from the heme (41 residues) and the presence of certain consensus residues suggests that cytochrome c" is the second example of a variant class I cytochrome c.
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Affiliation(s)
- K Klarskov
- Department of Biochemistry, Physiology and Microbiology, Laboratory of Protein Biochemistry and Protein Engineering, State University of Gent, Ledeganckstraat 35, B-9000, Gent, Belgium
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24
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Shifman JM, Moser CC, Kalsbeck WA, Bocian DF, Dutton PL. Functionalized de novo designed proteins: mechanism of proton coupling to oxidation/reduction in heme protein maquettes. Biochemistry 1998; 37:16815-27. [PMID: 9843452 DOI: 10.1021/bi9816857] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proton exchange with aqueous media coupled to heme oxidation/reduction is commonly seen but not understood in natural cytochromes. Our synthetic tetrahelix bundle heme protein maquettes successfully reproduce natural proton coupling to heme oxidation/reduction. Potentiometry reveals major pK shifts from 4.2 to 7.0 and from 9.4 to 10.3 in the maquette-associated acid/base group(s) upon heme reduction. Consequently, a 210 mV decrease in the heme redox potential is observed between the two extremes of pH. Potentiometry with resonance Raman and FTIR spectroscopy performed over a wide pH range strongly implicates glutamate side chains as the source of proton coupling below pH 8.0, whereas lysine side chains are suggested above pH 8.0. Remarkably, the pK values of several glutamates in the maquette are elevated from their solution value (4.4) to values as high as 7.0. It is suggested that these glutamates are recruited into the interior of the bundle as part of a structural rearrangement that occurs upon heme binding. Glutamate to glutamine variants of the prototype protein demonstrate that removal of the glutamate closest to the heme diminishes but does not abolish proton exchange. It is necessary to remove additional glutamates before pH-independent heme oxidation/reduction profiles are achieved. The mechanism of redox-linked proton coupling appears to be rooted in distributed partial charge compensation, the magnitude of which is governed by the dielectric distance between the ferric heme and acid/base side chains. A similar mechanism is likely to exist in native redox proteins which undergo charge change upon cofactor oxidation/reduction.
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Affiliation(s)
- J M Shifman
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia 19104, USA
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25
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Safo MK, Nesset MJM, Walker FA, Debrunner PG, Scheidt WR. Models of the Cytochromes. Axial Ligand Orientation and Complex Stability in Iron(II) Porphyrinates: The Case of the Noninteracting dπ Orbitals. J Am Chem Soc 1997. [DOI: 10.1021/ja9715657] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martin K. Safo
- Contribution from the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Department of Physics, University of Illinois, Urbana, Illinois 61801
| | - Marlys J. M. Nesset
- Contribution from the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Department of Physics, University of Illinois, Urbana, Illinois 61801
| | - F. Ann Walker
- Contribution from the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Department of Physics, University of Illinois, Urbana, Illinois 61801
| | - Peter G. Debrunner
- Contribution from the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Department of Physics, University of Illinois, Urbana, Illinois 61801
| | - W. Robert Scheidt
- Contribution from the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, Department of Chemistry, University of Arizona, Tucson, Arizona 85721, and Department of Physics, University of Illinois, Urbana, Illinois 61801
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26
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Coletta M, Costa H, De Sanctis G, Neri F, Smulevich G, Turner DL, Santos H. pH dependence of structural and functional properties of oxidized cytochrome c" from Methylophilus methylotrophus. J Biol Chem 1997; 272:24800-4. [PMID: 9312076 DOI: 10.1074/jbc.272.40.24800] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cytochrome c" from Methylophilus methylotrophus is an unusual monoheme protein that undergoes a major redox-linked change in the heme arrangement: one of the two axial histidines bound to the iron in the oxidized form is detached upon reduction and a proton is taken up. The kinetics of reduction by sodium dithionite and the spectroscopic properties of the oxidized cytochrome c" have been investigated over the pH range between 1.4 and 10.0. The rate of reduction displays proton-linked transitions of pKa congruent with 5.5 and 2.4, and a spectroscopic transition with a pKa congruent with 2.4 is also observed. The protein displays a complete reversibility after exposure to low pH, and both electronic absorption and resonance Raman spectroscopic properties suggest that the transition at lower pH brings about a drastic change in the heme coordination geometry. Circular dichroism spectra indicate that over the same proton-linked transition, the protein undergoes a marked decrease (approximately 60%) of the alpha-helical content toward a random coil arrangement, which is recovered upon increasing the ionic strength. The structural change at low pH is linked to a concerted two-proton transition, suggesting the detachment and protonation of axial histidine(s). Such kinetic and spectroscopic features along with the remarkable capacity of this protein to recover its native structure after exposure to extremely low pH values makes it a promising model for studying folding processes and stability in heme proteins.
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Affiliation(s)
- M Coletta
- Department of Experimental Medicine and Biochemical Sciences, University of Roma Tor Vergata, Via di Tor Vergata 135, I-00133 Roma, Italy
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27
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Grodzicki M, Flint H, Winkler H, Walker FA, Trautwein AX. Electronic Structure, Porphyrin Core Distortion, and Fluxional Behavior of Bis-Ligated Low-Spin Iron(II) Porphyrinates. J Phys Chem A 1997. [DOI: 10.1021/jp963039s] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael Grodzicki
- Institut für Physik, Medizinische Universität zu Lübeck, 160 Ratzeburger Allee, 23538 Lübeck, Germany, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - Holger Flint
- Institut für Physik, Medizinische Universität zu Lübeck, 160 Ratzeburger Allee, 23538 Lübeck, Germany, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - Heiner Winkler
- Institut für Physik, Medizinische Universität zu Lübeck, 160 Ratzeburger Allee, 23538 Lübeck, Germany, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - F. Ann Walker
- Institut für Physik, Medizinische Universität zu Lübeck, 160 Ratzeburger Allee, 23538 Lübeck, Germany, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - Alfred X. Trautwein
- Institut für Physik, Medizinische Universität zu Lübeck, 160 Ratzeburger Allee, 23538 Lübeck, Germany, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
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28
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Nesset MJM, Shokhirev NV, Enemark PD, Jacobson SE, Walker FA. Models of the Cytochromes. Redox Properties and Thermodynamic Stabilities of Complexes of “Hindered” Iron(III) and Iron(II) Tetraphenylporphyrinates with Substituted Pyridines and Imidazoles. Inorg Chem 1996. [DOI: 10.1021/ic960491h] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Paul D. Enemark
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | | | - F. Ann Walker
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721
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29
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Munro OQ, Marques HM. Heme-Peptide Models for Hemoproteins. 1. Solution Chemistry of N-Acetylmicroperoxidase-8. Inorg Chem 1996; 35:3752-3767. [PMID: 11666562 DOI: 10.1021/ic9502842] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An improved method for the preparation of the heme octapeptide acetyl-MP8, obtained by proteolysis of horse heart cytochrome c, is described. AcMP8 obeys Beer's law at pH 7.0 in aqueous solution up to a concentration of 3 x 10(-)(5) M. The self-association constant measured at 25 degrees C (log K(D) = 4.04) is an order of magnitude lower than that for MP8, reflecting the role of the N-acetyl protecting group in abolishing intermolecular coordination. However, AcMP8 does form pi-stacked dimers in aqueous solution with increasing ionic strength. A more weakly packed pi-pi dimer reaches a maximum abundance at approximately 3 M ionic strength, but a more tightly packed dimer is favored at &mgr; > 3 M. An equilibrium model based on charge neutralization by specific binding of Na(+) ions gives a total molecular charge of 3- for AcMP8 at pH 7.0 and a self-association constant log K(D) = 4.20. AcMP8 exhibits six spectroscopically active pH-dependent transitions. The Glu-21 c-terminal carboxylate binds to the heme iron at low pH (pK(a) = 2.1) but is substituted by His-18 (pK(a) = 3.12) as the pH increases. The two heme propanoic acid substituents ionize with pK(a)'s of 4.95 and 6.1. This is followed by ionization of iron-bound water with a pK(a) = 9.59, DeltaH = 48 +/- 1 kJ mol(-)(1), and DeltaS = -22 +/- 3 J K(-)(1) mol(-)(1). The electronic spectra indicate that AcMP8 is predominantly in the S = (5)/(2) state at pH 7.0, while the hydroxo complex at pH 10.5 corresponds to an equilibrium mixture of S = (5)/(2) and S = (1)/(2) states at 25 degrees C. In the final transition, His-18 ionizes to form the S = (1)/(2) histidinate complex with a pK(a) of 12.71. AcMP8 is relatively stable under alkaline conditions, dimerizing slowly at high pH (k = 2.59 +/- 0.14 M(-)(1) s(-)(1)) to form a high-spin &mgr;-oxo-bridged species. The pH-dependent behavior of AcMP8 in the presence of excess 3-cyanopyridine, however, is markedly different. At low pH, AcMP8 simultaneously binds the exogenous ligand and the Glu-21 c-terminal carboxylate with a pK(a) < 2. His-18 replaces the carboxylate ligand at higher pH (pK(a) = 2.60), and both heme propanoic acid groups ionize with a mean pK(a) = 5.10. Unlike AcMP8.OH(-), the axial histidine of the 3-CNPy complex ionizes at near neutral pH (pK(a) = 7.83), prior to being replaced by OH(-) (pK(a) = 10.13). The sixth transition in the AcMP8/3-CNPy system produces the bis(hydroxo) complex (pK(a) > 13).
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Affiliation(s)
- Orde Q. Munro
- Centre for Molecular Design, Department of Chemistry, University of the Witwatersrand, Wits 2050, Johannesburg, South Africa
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30
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Turner DL, Salgueiro CA, Catarino T, LeGall J, Xavier AV. Homotropic and heterotropic cooperativity in the tetrahaem cytochrome c3 from Desulfovibrio vulgaris. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1187:232-5. [PMID: 8075117 DOI: 10.1016/0005-2728(94)90117-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The thermodynamic parameters which govern the homotropic (e-/e-) and heterotropic (e-/H+) cooperativity in the tetrahaem cytochrome c3 isolated from Desulfovibrio vulgaris (Hildenborough) were determined, using the paramagnetic shifts of haem methyl groups in the NMR spectra of intermediate oxidized states at different pH levels. A model is put forward to explain how the network of positive and negative cooperativities between the four haems and acid/base group(s) enables the protein to achieve a proton-assisted 2e- step.
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Affiliation(s)
- D L Turner
- Instituto de Tecnologia Química e Biolígica, Universidade Nova de Lisboa, Oeiras, Portugal
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31
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Costa HS, Santos H, Turner DL. An unusual conformation of the methionine haem ligand in cytochrome cL established by two-dimensional 1H-NMR. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 223:783-9. [PMID: 8055954 DOI: 10.1111/j.1432-1033.1994.tb19053.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A complete relaxation-matrix analysis of NOESY cross-peak intensities was used to determine the conformation of the methionine ligand to the haem group in two ferrocytochromes cL from Methylophilus methylotrophus and Methylobacterium extorquens, including the configuration at the sulphur. The conformation of the axial methionine is of a type reported only for the cytochromes c5 from Pseudomonas mendocina and Azotobacter vinelandii. Although the conformation of the methionine is unusual, the paramagnetic shifts of the haem methyl proton resonances in the oxidized proteins indicate that the electronic structure of the haem groups is similar to that found in the mitochondrial type of cytochrome c.
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Affiliation(s)
- H S Costa
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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32
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Chen L, Pereira MM, Teixeira M, Xavier AV, Le Gall J. Isolation and characterization of a high molecular weight cytochrome from the sulfate reducing bacterium Desulfovibrio gigas. FEBS Lett 1994; 347:295-9. [PMID: 8034021 DOI: 10.1016/0014-5793(94)00563-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A high molecular weight c-type cytochrome (Hmc) was purified and characterized from Desulfovibrio gigas. The molecular weight was estimated to be 67 kDa by SDS-PAGE and its N-terminus is homologous to those of the 16 hemes containing high molecular weight cytochrome c from Desulfovibrio vulgaris strains Hildenborough and Miyazaki. The purified hemoprotein shows c-type cytochrome absorption spectrum with e533 (red) = 368 mM-1.cm-1. A band at 640 nm, characteristic of high-spin hemes, was detected. The EPR spectra show the presence of two high-spin heme species, plus several non-equivalent low-spin hemes. The heme reduction potentials, at pH 7.6, range from -50 mV to -315 mV. In contrast to what has been described for D. vulgaris Hmc, the protein isolated from D. gigas directly accepts electrons from hydrogenase and further reduces other redox proteins.
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Affiliation(s)
- L Chen
- Department of Biochemistry, University of Georgia, Athens 30602
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33
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Abstract
Cytochromes c are small soluble proteins, which have been extensively studied by nuclear magnetic resonance spectroscopy. The specific NMR features of paramagnetic proteins are discussed for the oxidized form (paramagnetic shift and line broadening). Early NMR studies have focused on the electronic structure of the heme and its direct environment. The conformations of cytochromes c are now investigated by two-dimensional 1H NMR spectroscopy combined with restrained molecular dynamics. 15N and 13C NMR, which greatly benefit from isotopic enrichment, may help in obtaining reliable 1H assignments and thus high quality solution structure. Finally, hydrogen exchange rates provide insight in the rigidity (and stability) of cytochromes c in both redox states at the atomic level.
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Affiliation(s)
- D Marion
- Institut de Biologie Structurale Jean-Pierre Ebel, CNRS-CEA, Grenoble, France
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34
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Chen L, Liu MY, Legall J, Fareleira P, Santos H, Xavier AV. Purification and characterization of an NADH-rubredoxin oxidoreductase involved in the utilization of oxygen by Desulfovibrio gigas. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 216:443-8. [PMID: 8375383 DOI: 10.1111/j.1432-1033.1993.tb18162.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
An NADH--rubredoxin oxidoreductase previously isolated from Desulfovibrio gigas [LeGall, J. (1968) Ann. Inst. Pasteur 114, 109-115] has now been fully purified and further characterized. It contains two subunits of 27 kDa and 32 kDa. With two mid-point redox potentials of -295 mV and -325 mV, this FMN- and FAD-containing protein can induce the specific reduction of D. gigas rubredoxin. In contrast, rubredoxins from the other Desulfovibrio species or desulforedoxin from D. gigas show very low reaction rates with the same enzyme. The phylogenetic significance of the narrow specificity of the enzyme toward the rubredoxin from the same organism is discussed. The purified enzyme has NADH oxidase activity with H2O2 as a final product of O2 reduction. The reaction is half-inhibited by 4.2 microM p-chloromercuribenzoate, whereas cyanide and azide are not significant inhibitors in this reaction. The role of this protein as a part of the enzymic equipment that allows the formation of ATP in the presence of oxygen from the degradation of carbon reserves is discussed.
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Affiliation(s)
- L Chen
- Department of Biochemistry, University of Georgia, Athens
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35
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Costa HS, Santos H, Turner DL. Characterization of the haem environment in Methylophilus methylotrophus ferricytochrome c" by 1H-NMR. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 215:817-24. [PMID: 8394812 DOI: 10.1111/j.1432-1033.1993.tb18097.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Two-dimensional NMR techniques have been used to assign proton resonances in the haem cavity of Methylophilus methylotrophus cytochrome c", a monohaem protein with bis-histidinyl ligation which has been shown to couple electron and proton transfer. All the assignments were made directly for the oxidized paramagnetic form of the cytochrome. Nearly all of the haem protons (90%) and the protons of both axial ligands have been assigned; the side-chain protons from four other residues in the haem pocket have also been identified. The data indicate a highly symmetric unpaired-electron distribution in the haem group, which agrees with a perpendicular orientation of the axial imidazole planes. The two haem propionate groups have contrasting degrees of exposure to the solvent, with the propionate group at position 13 being highly exposed. To obtain information on the dynamics of the haem environment, measurements of the 1H/2H-exchange rates of amide protons located in the haem cavity were performed. The two faces of the haem are found to differ markedly with respect to water accessibility. All of this information, together with additional protein sequencing data, indicates that His52 remains attached upon reduction and that the redox-linked protonation occurs via a channel running through the haem cleft on the opposite face.
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Affiliation(s)
- H S Costa
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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36
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Xavier AV, Turner DL, Santos H. Two-dimensional nuclear magnetic resonance of paramagnetic metalloproteins. Methods Enzymol 1993; 227:1-16. [PMID: 8255222 DOI: 10.1016/0076-6879(93)27003-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- A V Xavier
- Instituto de Tecnologia Qúimica e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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