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Construction of a Biosensor Based on a Combination of Cytochrome c, Graphene, and Gold Nanoparticles. SENSORS 2018; 19:s19010040. [PMID: 30583520 PMCID: PMC6339241 DOI: 10.3390/s19010040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 02/04/2023]
Abstract
A biosensor based on a combination of cytochrome c (Cyt c), electrochemical reduced graphene oxides (ERGO), and gold nanoparticles (AuNPs) on a glassy carbon electrode (GCE) was fabricated. The proposed biosensor electrode was denoted as GCE/ERGO-Nafion/AuNPs/Cyt c/Nafion, where ERGO-Nafion was deposited by dropping graphene oxides-Nafion mixed droplet first and following electrochemical reduction, AuNPs were directly deposited on the surface of the ERGO-Nafion modified electrode by electrochemical reduction, and other components were deposited by the dropping-dry method. The effect of the deposition amount of AuNPs on direct electrochemistry of Cyt c in the proposed electrode was investigated. The hydrogen peroxide was taken to evaluate the performance of the proposed biosensor. The results showed that the biosensor has great analytical performance, including a high sensitivity, a wide linear range, a low detection limit, and good stability, reproducibility, and reliability.
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2
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Kimura Y, Kasuga S, Unno M, Furusawa T, Osoegawa S, Sasaki Y, Ohno T, Wang-Otomo ZY. The roles of C-terminal residues on the thermal stability and local heme environment of cytochrome c' from the thermophilic purple sulfur bacterium Thermochromatium tepidum. PHOTOSYNTHESIS RESEARCH 2015; 124:19-29. [PMID: 25519852 DOI: 10.1007/s11120-014-0069-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 12/11/2014] [Indexed: 06/04/2023]
Abstract
A soluble cytochrome (Cyt) c' from thermophilic purple sulfur photosynthetic bacterium Thermochromatium (Tch.) tepidum exhibits marked thermal tolerance compared with that from the closely related mesophilic counterpart Allochromatium vinosum. Here, we focused on the difference in the C-terminal region of the two Cyts c' and examined the effects of D131 and R129 mutations on the thermal stability and local heme environment of Cyt c' by differential scanning calorimetry (DSC) and resonance Raman (RR) spectroscopy. In the oxidized forms, D131K and D131G mutants exhibited denaturing temperatures significantly lower than that of the recombinant control Cyt c'. In contrast, R129K and R129A mutants denatured at nearly identical temperatures with the control Cyt c', indicating that the C-terminal D131 is an important residue maintaining the enhanced thermal stability of Tch. tepidum Cyt c'. The control Cyt c' and all of the mutants increased their thermal stability upon the reduction. Interestingly, D131K exhibited narrow DSC curves and unusual thermodynamic parameters in both redox states. The RR spectra of the control Cyt c' exhibited characteristic bands at 1,635 and 1,625 cm(-1), ascribed to intermediate spin (IS) and high spin (HS) states, respectively. The IS/HS distribution was differently affected by the D131 and R129 mutations and pH changes. Furthermore, R129 mutants suggested the lowering of their redox potentials. These results strongly indicate that the D131 and R129 residues play significant roles in maintaining the thermal stability and modulating the local heme environment of Tch. tepidum Cyt c'.
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Affiliation(s)
- Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Nada, Kobe, 657-8501, Japan,
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3
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Hough MA, Andrew CR. Cytochromes c': Structure, Reactivity and Relevance to Haem-Based Gas Sensing. Adv Microb Physiol 2015; 67:1-84. [PMID: 26616515 DOI: 10.1016/bs.ampbs.2015.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cytochromes c' are a group of class IIa cytochromes with pentacoordinate haem centres and are found in photosynthetic, denitrifying and methanotrophic bacteria. Their function remains unclear, although roles in nitric oxide (NO) trafficking during denitrification or in cellular defence against nitrosoative stress have been proposed. Cytochromes c' are typically dimeric with each c-type haem-containing monomer folding as a four-α-helix bundle. Their hydrophobic and crowded distal sites impose severe restrictions on the binding of distal ligands, including diatomic gases. By contrast, NO binds to the proximal haem face in a similar manner to that of the eukaryotic NO sensor, soluble guanylate cyclase and bacterial analogues. In this review, we focus on how structural features of cytochromes c' influence haem spectroscopy and reactivity with NO, CO and O2. We also discuss the relevance of cytochrome c' to understanding the mechanisms of gas binding to haem-based sensor proteins.
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 540] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Tsai AL, Martin E, Berka V, Olson JS. How do heme-protein sensors exclude oxygen? Lessons learned from cytochrome c', Nostoc puntiforme heme nitric oxide/oxygen-binding domain, and soluble guanylyl cyclase. Antioxid Redox Signal 2012; 17:1246-63. [PMID: 22356101 PMCID: PMC3430480 DOI: 10.1089/ars.2012.4564] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SIGNIFICANCE Ligand selectivity for dioxygen (O(2)), carbon monoxide (CO), and nitric oxide (NO) is critical for signal transduction and is tailored specifically for each heme-protein sensor. Key NO sensors, such as soluble guanylyl cyclase (sGC), specifically recognized low levels of NO and achieve a total O(2) exclusion. Several mechanisms have been proposed to explain the O(2) insensitivity, including lack of a hydrogen bond donor and negative electrostatic fields to selectively destabilize bound O(2), distal steric hindrance of all bound ligands to the heme iron, and restriction of in-plane movements of the iron atom. RECENT ADVANCES Crystallographic structures of the gas sensors, Thermoanaerobacter tengcongensis heme-nitric oxide/oxygen-binding domain (Tt H-NOX(1)) or Nostoc puntiforme (Ns) H-NOX, and measurements of O(2) binding to site-specific mutants of Tt H-NOX and the truncated β subunit of sGC suggest the need for a H-bonding donor to facilitate O(2) binding. CRITICAL ISSUES However, the O(2) insensitivity of full length sGC with a site-specific replacement of isoleucine by a tyrosine on residue 145 and the very slow autooxidation of Ns H-NOX and cytochrome c' suggest that more complex mechanisms have evolved to exclude O(2) but retain high affinity NO binding. A combined graphical analysis of ligand binding data for libraries of heme sensors, globins, and model heme shows that the NO sensors dramatically inhibit the formation of six-coordinated NO, CO, and O(2) complexes by direct distal steric hindrance (cyt c'), proximal constraints of in-plane iron movement (sGC), or combinations of both following a sliding scale rule. High affinity NO binding in H-NOX proteins is achieved by multiple NO binding steps that produce a high affinity five-coordinate NO complex, a mechanism that also prevents NO dioxygenation. FUTURE DIRECTIONS Knowledge advanced by further extensive test of this "sliding scale rule" hypothesis should be valuable in guiding novel designs for heme based sensors.
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Affiliation(s)
- Ah-Lim Tsai
- Division of Hematology, University of Texas Health Science Center at Houston, Houston, Texas 77225, USA.
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6
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Stewart JJP. Application of the PM6 method to modeling proteins. J Mol Model 2008; 15:765-805. [DOI: 10.1007/s00894-008-0420-y] [Citation(s) in RCA: 236] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 10/14/2008] [Indexed: 11/29/2022]
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7
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Benini S, Rypniewski WR, Wilson KS, Ciurli S. High resolution crystal structure of Rubrivivax gelatinosus cytochrome c′. J Inorg Biochem 2008; 102:1322-8. [DOI: 10.1016/j.jinorgbio.2008.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 01/06/2008] [Accepted: 01/09/2008] [Indexed: 11/16/2022]
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8
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Ohgo Y, Hoshino A, Uekusa H, Nakamura M. Peculiar sandwich-like π–π interaction regulating the nonplanarity of the model heme crystals. INORG CHEM COMMUN 2006. [DOI: 10.1016/j.inoche.2006.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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9
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Weiss R, Gold A, Terner J. Cytochromes c‘: Biological Models for the S = 3/2,5/2 Spin-State Admixture? Chem Rev 2006; 106:2550-79. [PMID: 16771459 DOI: 10.1021/cr040416l] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raymond Weiss
- Laboratoire de Chimie Supramoléculaires, Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur de Strasbourg, 8 Allée Gaspard Monge, B.P.70028, F-67083 Strasbourg Cedex, France
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10
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Huston WM, Andrew CR, Servid AE, McKay AL, Leech AP, Butler CS, Moir JWB. Heterologous Overexpression and Purification of Cytochrome c‘ from Rhodobacter capsulatus and a Mutant (K42E) in the Dimerization Region. Mutation Does Not Alter Oligomerization but Impacts the Heme Iron Spin State and Nitric Oxide Binding Properties. Biochemistry 2006; 45:4388-95. [PMID: 16584174 DOI: 10.1021/bi052605j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rhodobacter capsulatus cytochrome c' (RCCP) has been overexpressed in Escherichia coli, and its spectroscopic and ligand-binding properties have been investigated. It is concluded that the heterologously expressed protein is assembled correctly, as judged by UV-vis absorption, EPR, and resonance Raman (RR) spectroscopy of the unligated protein as well as forms in which the heme is ligated by CO or NO. To probe the oligomerization state of RCCP and its potential influence on heme reactivity, we have compared the properties of wild-type RCCP with a mutant (K42E) that lacks a salt bridge at the subunit interface. Analytical ultracentrifugation indicates that wild-type and K42E proteins are both monomeric in solution, contrary to the homodimeric structure of the crystalline state. Surprisingly, the K42E mutation produces a number of changes at the heme center (nearly 20 A distant), including perturbation of the ferric spin-state equilibrium and a change in the ferrous heme-nitrosyl complex from a six-coordinate/five-coordinate mixture to a predominantly five-coordinate heme-NO species. RR spectra indicate that ferrous K42E and wild-type RCCP both have relatively high Fe-His stretching frequencies, suggesting that the more favored five-coordinate heme-nitrosyl formation in K42E is not caused by a weaker Fe2+-His bond. Nevertheless, the altered reactivity of ferrous K42E with NO, together with its modified ferric spin state, shows that structural changes originating at the dimer interface can affect the properties of the heme center, raising the exciting possibility that intermolecular encounters at the protein surface might modulate the reactivity of cytochrome c' in vivo.
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Affiliation(s)
- Wilhelmina M Huston
- Department of Biology (Area 10), University of York, Heslington, York, YO10 5YW, United Kingdom
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11
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Andrew CR, Kemper LJ, Busche TL, Tiwari AM, Kecskes MC, Stafford JM, Croft LC, Lu S, Moënne-Loccoz P, Huston W, Moir JWB, Eady RR. Accessibility of the distal heme face, rather than Fe-His bond strength, determines the heme-nitrosyl coordination number of cytochromes c': evidence from spectroscopic studies. Biochemistry 2005; 44:8664-72. [PMID: 15952773 DOI: 10.1021/bi050428g] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The heme coordination chemistry and spectroscopic properties of Rhodobacter capsulatus cytochrome c' (RCCP) have been compared to data from Alcaligenes xylosoxidans (AXCP), with the aim of understanding the basis for their different reactivities with nitric oxide (NO). Whereas ferrous AXCP reacts with NO to form a predominantly five-coordinate heme-nitrosyl complex via a six-coordinate intermediate, RCCP forms an equilibrium mixture of six-coordinate and five-coordinate heme-nitrosyl species in approximately equal proportions. Ferrous RCCP and AXCP both exhibit high Fe-His stretching frequencies (227 and 231 cm(-)(1), respectively), suggesting that factors other than the Fe-His bond strength account for their differences in heme-nitrosyl coordination number. Resonance Raman spectra of ferrous-nitrosyl RCCP confirm the presence of both five-coordinate and six-coordinate heme-NO complexes. The six-coordinate heme-nitrosyl of RCCP exhibits a fairly typical Fe-NO stretching frequency (569 cm(-)(1)), in contrast to the relatively high value (579 cm(-)(1)) of the AXCP six-coordinate heme-nitrosyl intermediate. It is proposed that NO experiences greater steric hindrance in binding to the distal face of AXCP, as compared to RCCP, leading to a more distorted Fe-N-O geometry and an elevated Fe-NO stretching frequency. Evidence that RCCP has a more accessible distal coordination site than in AXCP stems from the fact that ferric RCCP readily forms a heme complex with exogenous imidazole, whereas AXCP does not. A model is proposed in which distal heme-face accessibility, rather than the proximal Fe-His bond strength, determines the heme-nitrosyl coordination number in cytochromes c'.
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Affiliation(s)
- Colin R Andrew
- Department of Chemistry & Biochemistry, Eastern Oregon University, La Grande, Oregon 97850-2899, USA.
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12
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Choi PS, Grigoryants VM, Abruña HD, Scholes CP, Shapleigh JP. Regulation and function of cytochrome c' in Rhodobacter sphaeroides 2.4.3. J Bacteriol 2005; 187:4077-85. [PMID: 15937170 PMCID: PMC1151734 DOI: 10.1128/jb.187.12.4077-4085.2005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cytochrome c' (Cyt c') is a c-type cytochrome with a pentacoordinate heme iron. The gene encoding this protein in Rhodobacter sphaeroides 2.4.3, designated cycP, was isolated and sequenced. Northern blot analysis and beta-galactosidase assays demonstrated that cycP transcription increased as oxygen levels decreased and was not repressed under denitrifying conditions as observed in another Rhodobacter species. CO difference spectra performed with extracts of cells grown under different conditions revealed that Cyt c' levels were highest during photosynthetic denitrifying growth conditions. The increase in Cyt c' under this condition was higher than would be predicted from transcriptional studies. Electron paramagnetic resonance analysis of whole cells demonstrated that Cyt c' binds NO during denitrification. Mass spectrometric analysis of nitrogen oxides produced by cells and purified protein did not indicate that Cyt c' has NO reductase activity. Taken together, these results suggest a model where Cyt c' in R. sphaeroides 2.4.3 may shuttle NO to the membrane, where it can be reduced.
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Affiliation(s)
- Peter S Choi
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853, USA
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13
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Usov OM, Choi PST, Shapleigh JP, Scholes CP. ENDOR Investigation of the Liganding Environment of Mixed-Spin Ferric Cytochrome c‘. J Am Chem Soc 2005; 127:9485-94. [PMID: 15984875 DOI: 10.1021/ja043994s] [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: 11/29/2022]
Abstract
The electronic structure of the 5-coordinate quantum-mechanically mixed-spin (sextet-quartet) heme center in cytochrome c' was investigated by electron nuclear double resonance (ENDOR), a technique not previously applied to this mixed-spin system. Cytochrome c' was obtained from overexpressing variants of Rhodobacter sphaeroides 2.4.3. ENDOR for this study was done at the g(//) = 2.00 extremum where single-crystal-like, well-resolved spectra prevail. The heme meso protons of cytochrome c' showed a contact interaction that implied spin delocalization arising from the heme (d(z)(2)) orbital enhanced by iron out-of-planarity. An exchangeable proton ENDOR feature appeared from the proximal His123 Ndelta hydrogen. This Ndelta hydrogen, which crystallographically has no hydrogen-bonding partner and thus belongs to a neutral imidazole, showed a larger hyperfine coupling than the corresponding hydrogen-bonded Ndelta proton from metmyoglobin. The unique residue Phe14 occludes binding of a sixth ligand in cytochrome c', and ENDOR from a proton of the functionally important Phe14 ring, approximately 3.3 A away from the heme iron, was detected. ENDOR of the nitrogen ligand hyperfine structure is a direct probe into the sigma-antibonding (d(z)(2)) and (d(x)(2)-d(y)(2)) orbitals whose energies alter the relative stability and admixture of sextet and quartet states and whose electronic details were thus elucidated. ENDOR frequencies showed for cytochrome c' larger hyperfine couplings to the histidine nitrogen and smaller hyperfine couplings to the heme nitrogens than for high-spin ferric hemes. Both of these findings followed from the mixed-spin ground state, which has less (d(x)(2)-d(y)(2)) character than have fully high-spin ferric heme systems.
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Affiliation(s)
- Oleg M Usov
- Department of Chemistry, Center for Biochemistry and Biophysics, University at Albany, SUNY, Albany, New York 12222, USA
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14
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Evers TH, Merkx M. Successful recombinant production of Allochromatium vinosum cytochrome c' requires coexpression of cmm genes in heme-rich Escherichia coli JCB712. Biochem Biophys Res Commun 2005; 327:668-74. [PMID: 15649399 DOI: 10.1016/j.bbrc.2004.12.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Indexed: 11/17/2022]
Abstract
Cytochrome c' from the purple photosynthetic bacterium Allochromatium vinosum (CCP) displays a unique, reversible dimer-to-monomer transition upon binding of NO, CO, and CN(-). This small, four helix bundle protein represents an attractive model for the study of other heme protein biosensors, provided a recombinant expression system is available. Here we report the development of an efficient expression system for CCP that makes use of a maltose binding protein fusion strategy to enhance periplasmic expression and allow easy purification by affinity chromatography. Coexpression of cytochrome c maturase genes and the use of a heme-rich Escherichia coli strain were found to be necessary to obtain reasonable yields of cytochrome c'. Characterization using circular dichroism, UV-vis spectroscopy, and size-exclusion chromatography confirms the native-like properties of the recombinant protein, including its ligand-induced monomerization.
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Affiliation(s)
- Toon H Evers
- Laboratory of Macromolecular and Organic Chemistry, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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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: 186] [Impact Index Per Article: 9.3] [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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Ma D, Musto R, Smith KM, La Mar GN. Solution NMR characterization of the electronic structure and magnetic properties of high-spin ferrous heme in deoxy myoglobin from Aplysia limacina. J Am Chem Soc 2003; 125:8494-504. [PMID: 12848555 DOI: 10.1021/ja035256u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solution (1)H NMR has been used to elucidate the magnetic properties and electronic structure of the prosthetic group in high-spin, ferrous deoxy myoglobin from the sea hare Aplysia limacina. A sufficient number of dipolar shifted residue signals were assigned to allow the robust determination of the orientation and anisotropy of the paramagnetic susceptibility tensor, chi. The resulting quantitative description of dipolar shifts allows a determination of the contact shifts for the heme. Chi was found to be axial, with Deltachi(ax) = -2.07 x 10(-8) m(3)/mol, with the major axis tilted (approximately 76 degrees) almost into the heme plane and in the general direction of the orientation of the axial HisF8 imidazole plane which coincides approximately with the beta-,delta-meso axis. The factored contact shifts for the heme are shown to be consistent with the transfer of positive pi spin density into one of the two components of the highest filled pi molecular orbital, 3e(pi), and the transfer of negative pi-spin density, via spin-spin correlation, into the orthogonal excited-state component of the 3e(pi) molecular orbital. The thermal population of the excited state leads to strong deviation from the Curie law for the heme substituents experiencing primarily the negative pi-spin density. The much larger transfer of negative spin density via the spin-paired dpi orbital into the excited state 3e(pi) in high-spin iron(II) than in low-spin iron(III) hemoproteins is attributed to the much stronger correlation exerted by the four unpaired spin on the iron in the former, as compared to the single unpaired spins on iron in the latter.
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Affiliation(s)
- Dejian Ma
- Department of Chemistry, University of California, Davis, California 95616, USA
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17
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Bergmann DJ, Hooper AB. Cytochrome P460 of Nitrosomonas europaea. Formation of the heme-lysine cross-link in a heterologous host and mutagenic conversion to a non-cross-linked cytochrome c'. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1935-41. [PMID: 12709052 DOI: 10.1046/j.1432-1033.2003.03550.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The heme of cytochrome P460 of Nitrosomonas europaea, which is covalently crosslinked to two cysteines of the polypeptide as with all c-type cytochromes, has an additional novel covalent crosslink to lysine 70 of the polypeptide [Arciero, D.M. & Hooper, A.B. (1997) FEBS Lett.410, 457-460]. The protein can catalyze the oxidation of hydroxylamine. The gene for this protein, cyp, was expressed in Pseudomonas aeruginosa strain PAO lacI, resulting in formation of a holo-cytochrome P460 which closely resembled native cytochrome P460 purified from N. europaea in its UV-visible spectroscopic, ligand binding and catalytic properties. Mutant versions of cytochrome P460 of N. europaea in which Lys70 70 was replaced by Arg, Ala, or Tyr, retained ligand-binding ability but lost catalytic ability and differed in optical spectra which, instead, closely resembled those of cytochromes c'. Tryptic fragments containing the c-heme joined only by two thioether linkages were observed by MALDI-TOF for the mutant cytochromes P460 K70R and K70A but not in wild-type cytochrome P460, consistent with the structural modification of the c-heme only in the wild-type cytochrome. The present observations support the hypothesized evolutionary relationship between cytochromes P460 and cytochromes c' in N. europaea and M. capsulatus[Bergmann, D.J., Zahn, J.A., & DiSpirito, A.A. (2000) Arch. Microbiol. 173, 29-34], confirm the importance of a heme-crosslink to the spectroscopic properties and catalysis and suggest that the crosslink might form auto-catalytically.
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Affiliation(s)
- David J Bergmann
- Department of Biology, Black Hills State University, Spearfish, SD, USA
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18
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Upadhyay AK, Petasis DT, Arciero DM, Hooper AB, Hendrich MP. Spectroscopic characterization and assignment of reduction potentials in the tetraheme cytochrome C554 from Nitrosomonas europaea. J Am Chem Soc 2003; 125:1738-47. [PMID: 12580599 DOI: 10.1021/ja020922x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The tetraheme cytochrome c(554) (cyt c(554)) from Nitrosomonas europaea is an essential electron transfer component in the biological oxidation of ammonia. The protein contains one 5-coordinate heme and three bis-His coordinated hemes in a 3D arrangement common to a newly characterized class of multiheme proteins. The ligand binding, electrochemical properties, and heme-heme interactions are investigated with Mössbauer and X- and Q-band (parallel/perpendicular mode) EPR spectroscopy. The results indicate that the 5-coordinate heme will not bind the common heme ligands, CN(-), F(-), CO, and NO in a wide pH range. Thus, cyt c(554) functions only in electron transfer. Analysis of a series of electrochemically poised and chemically reduced samples allows assignment of reduction potentials for heme 1 through 4 of +47, +47, -147, and -276 mV, respectively. The spectroscopic results indicate that the hemes are weakly exchange-coupled (J approximately -0.5 cm(-)(1)) in two separate pairs and in accordance with the structure: hemes 2/4 (high-spin/low-spin), hemes 1/3 (low-spin/low-spin). There is no evidence of exchange coupling between the pairs. A comparison of the reduction potentials between homologous hemes of cyt c(554) and other members of this new class of multiheme proteins is discussed. Heme 1 has a unique axial N(delta)-His coordination which contributes to a higher potential relative to the homologous hemes of hydroxylamine oxidoreductase (HAO) and the split-Soret cytochrome. Heme 2 is 300 mV more positive than heme 4 of HAO, which is attributed to hydroxide coordination to heme 4 of HAO.
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Affiliation(s)
- Anup K Upadhyay
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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Shokhireva TK, Shokhirev NV, Walker FA. Assignment of heme resonances and determination of the electronic structures of high- and low-spin nitrophorin 2 by 1H and 13C NMR spectroscopy: an explanation of the order of heme methyl resonances in high-spin ferriheme proteins. Biochemistry 2003; 42:679-93. [PMID: 12534280 DOI: 10.1021/bi026765w] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The (1)H NMR resonances of the heme substituents of the low-spin Fe(III) form of nitrophorin 2, as its complexes with N-methylimidazole (NP2-NMeIm) and imidazole (NP2-ImH), have been assigned by a combination of (1)H homonuclear two-dimensional NMR techniques and (1)H-(13)C HMQC. Complete assignment of the proton and partial assignment of the (13)C resonances of the heme of these complexes has been achieved. Due to favorable rates of ligand exchange, it was also possible to assign part of the (1)H resonances of the high-spin heme via saturation transfer between high- and low-spin protein forms in a partially liganded NP2-NMeIm sample; additional resonances (vinyl and propionate) were assigned by NOESY techniques. The order of heme methyl resonances in the high-spin form of the protein over the temperature range of 10-37 degrees C is 8 = 5 > 1 > 3; the NMeIm complex has 5 > 1 > 3 > 8 as the order of heme methyl resonances at <30 degrees C, while above that temperature, the order is 5 > 3 > 1 > 8, due to crossover of the closely spaced 3- and 1-methyl resonances of the low-spin complex at higher temperatures. This crossover defines the nodal plane of the heme orbital used for spin delocalization as being oriented 162 +/- 2 degrees clockwise from the heme N(II)-Fe-N(IV) axis for the heme in the B orientation. For the NP2-ImH complex, the order of heme methyl resonances is 3 > 5 > 1 > 8, which defines the orientation of the nodal plane of the heme orbital used for spin delocalization as being oriented approximately 150-155 degrees clockwise from the heme N(II)-Fe-N(IV) axis. In both low-spin complexes, the results are most consistent with the exogenous planar ligand controlling the orientation of the nodal plane of the heme orbital. In the high-spin form of NP2, the proximal histidine plane is shown to be oriented 135 degrees clockwise from the heme N(II)-Fe-N(IV) axis, again for the B heme orientation. A correlation between the order of heme methyl resonances in the high-spin form of NP2 and several other ferriheme proteins and an apparent 90 degrees shift in the nodal plane of the orbital involved in spin delocalization from that expected on the basis of the orientation of the axial histidine imidazole nodal plane have been explained in terms of bonding interactions between Fe(III), the axial histidine imidazole nitrogen, and the porphyrin pi orbitals of the high-spin protein.
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20
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Ikezaki A, Nakamura M. Models for cytochromes c': spin states of mono(imidazole)-ligated (meso-tetramesitylporphyrinato)iron(III) complexes as studied by UV-Vis, 13C NMR, 1H NMR, and EPR spectroscopy. Inorg Chem 2002; 41:6225-36. [PMID: 12444764 DOI: 10.1021/ic020378t] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A number of mono(imidazole)-ligated complexes of perchloro(meso-tetramesitylporphyrinato)iron(III), [Fe(TMP)L]ClO(4), have been prepared, and their spin states have been examined by (1)H NMR, (13)C NMR, and EPR spectroscopy as well as solution magnetic moments. All the complexes examined have shown a quantum mechanical spin admixed state of high and intermediate-spin (S = 5/2 and 3/2) states though the contribution of the S = 3/2 state varies depending on the nature of axial ligands. While the complex with extremely bulky 2-tert-butylimidazole (2-(t)()BuIm) has exhibited an essentially pure S = 5/2 state, the complex with electron-deficient 4,5-dichloroimidazole (4,5-Cl(2)Im) adopts an S = 3/2 state with 30% of the S = 5/2 spin admixture. On the basis of the (1)H and (13)C NMR results, we have concluded that the S = 3/2 contribution at ambient temperature increases according to the following order: 2-(t)BuIm < 2-(1-EtPr)Im < 2-MeIm <or= 2-EtIm <or= 2-(i)PrIm < 4,5-Cl(2)Im. The effective magnetic moments determined by the Evans method in CH(2)Cl(2) solution are 5.9 and 5.0 mu(B) at 25 degrees C for [Fe(TMP)(2-(t)BuIm)]ClO(4) and [Fe(TMP)(2-MeIm)]ClO(4), respectively, which further verify the order given above. Comparison of the NMR and EPR data has revealed that the S = 3/2 contribution changes sensitively by the temperature; the S = 3/2 contribution decreases as the temperature is lowered for all the mono(imidazole) complexes examined in this study. The solvent polarity also affects the spin state; polar solvents such as methanol and acetonitrile increase the S = 3/2 contribution while nonpolar solvents such as benzene decrease it. These results are explained in terms of the structurally flexible nature of the mono(imidazole) complexes; structural parameters such as the Fe(III)-N(axial) bond length, displacement of the iron from the N4 core, tilting of the Fe(III)-N(axial) bond to the heme normal, orientation of the coordinated imidazole ligand, etc., could be altered by the nature of the axial ligands as well as by the solvent polarity and temperature. Some mysteries on the spin states of cytochromes c' isolated from various bacterial sources are possibly explained in terms of the flexible nature of the mono(imidazole)-ligated structure.
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Affiliation(s)
- Akira Ikezaki
- Department of Chemistry, School of Medicine, Toho University, Tokyo 143-8540, Japan
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21
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Hill EE, Morea V, Chothia C. Sequence conservation in families whose members have little or no sequence similarity: the four-helical cytokines and cytochromes. J Mol Biol 2002; 322:205-33. [PMID: 12215425 DOI: 10.1016/s0022-2836(02)00653-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Proteins for which there are good structural, functional and genetic similarities that imply a common evolutionary origin, can have sequences whose similarities are low or undetectable by conventional sequence comparison procedures. Do these proteins have sequence conservation beyond the simple conservation of hydrophobic and hydrophilic character at specific sites and if they do what is its nature? To answer these questions we have analysed the structures and sequences of two superfamilies: the four-helical cytokines and cytochromes c'-b(562). Members of these superfamilies have sequence similarities that are either very low or not detectable. The cytokine superfamily has within it a long chain family and a short chain family. The sequences of known representative structures of the two families were aligned using structural information. From these alignments we identified the regions that conserve the same main-chain conformation: the common core (CC). For members of the same family, the CC comprises some 50% of the individual structures; for the combination of both families it is 30%. We added homologous sequences to the structural alignment. Analysis of the residues occurring at sites within the CCs showed that 30% have little or no conservation, whereas about 40% conserve the polar/neutral or hydrophobic/neutral character of their residues. The remaining 30% conserve hydrophobic residues with strong or medium limitations on their volume variations. Almost all of these residues are found at sites that form the "buried spine" of each helix (at sites i, i+3, i+7, i+10, etc., or i, i+4, i+7, i+11, etc.) and they pack together at the centre of each structure to give a pattern of residue-residue contacts that is almost absolutely conserved. These CC conserved hydrophobic residues form only 10-15% of all the residues in the individual structures.A similar analysis of the cytochromes c'-b(562), which bind haem and have a very different function to that of the cytokines, gave very similar results. Again some 30% of the CC residues have hydrophobic residues with strong or medium conservation. Most of these form the buried spine of each helix and play the same role as those in the cytokines. The others, and some spine residues bind the haem co-factor.
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Affiliation(s)
- Emma E Hill
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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22
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Molecular structures and mixed spin states of chloroiron(III) complexes of the 2,3-diethyl-(detpp), 2,3,7,8-tetraethyl-(cis-tetpp), 2,3,12,13-tetraethyl-(trans-tetpp) and 2,3,7,8,12,13-hexaethyl-(hetpp) 5,10,15,20-tetraphenylporphyrin complexes. CR CHIM 2002. [DOI: 10.1016/s1631-0748(02)01404-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Arteca GA, Tapia O. Protein Denaturation in Vacuo. Behavior of the Four-α-Helix Bundle of Apocytochrome c‘ under Centrifugal Unfolding Conditions. J Phys Chem B 2002. [DOI: 10.1021/jp012692z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Gustavo A. Arteca
- Département de Chimie et Biochimie, Laurentian University, Ramsey Lake Road, Sudbury, Ontario P3E 2C6, Canada
| | - O. Tapia
- Department of Physical Chemistry, Uppsala University, Box 532, Uppsala S-751 21, Sweden
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24
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Lawson DM, Stevenson CE, Andrew CR, Eady RR. Unprecedented proximal binding of nitric oxide to heme: implications for guanylate cyclase. EMBO J 2000; 19:5661-71. [PMID: 11060017 PMCID: PMC305806 DOI: 10.1093/emboj/19.21.5661] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microbial cytochromes c' contain a 5-coordinate His-ligated heme that forms stable adducts with nitric oxide (NO) and carbon monoxide (CO), but not with dioxygen. We report the 1.95 and 1.35 A resolution crystal structures of the CO- and NO-bound forms of the reduced protein from Alcaligenes xylosoxidans. NO disrupts the His-Fe bond and binds in a novel mode to the proximal face of the heme, giving a 5-coordinate species. In contrast, CO binds 6-coordinate on the distal side. A second CO molecule, not bound to the heme, is located in the proximal pocket. Since the unusual spectroscopic properties of cytochromes c' are shared by soluble guanylate cyclase (sGC), our findings have potential implications for the activation of sGC induced by the binding of NO or CO to the heme domain.
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Affiliation(s)
- D M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK.
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25
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Ge B, Meyer T, Schöning M, Wollenberger U, Lisdat F. Cytochrome c′ from Chromatium vinosum on gold electrodes. Electrochem commun 2000. [DOI: 10.1016/s1388-2481(00)00082-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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26
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Mayburd AL, Tan Y, Kassner RJ. Complex formation between Chromatium vinosum ferric cytochrome c' and bromophenol blue. Arch Biochem Biophys 2000; 378:40-4. [PMID: 10871042 DOI: 10.1006/abbi.2000.1783] [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
An unusual complex has been observed between the common electrophoresis tracer bromophenol blue (BPB) and the cytochrome c' from Chromatium vinosum during polyacrylamide gel electrophoresis. Complex formation results in a shift and increase in the intensity of the visible absorption band of BPB. Differential spectrophotometric titration of BPB with cytochrome c' indicates that one BPB binds to each of the two subunits of cytochrome c' with a binding constant of 4.2(0.5) x 10(5). The absence of a significant effect of ionic strength on the binding constant and the effect of Triton X-100 on the spectrum of BPB suggest that hydrophobic interactions are important to binding. An analysis of the structure of C. vinosum cytochrome c' shows the presence of a surface hydrophobic patch which may participate in the binding interaction. Many of the hydrophobic amino acids in the patch are well conserved by type among all known sequences of cytochrome c' and are found in loop elements of the 3D structure, suggesting a functional basis for conservation. It is proposed that the binding of BPB may mimic a relevant interaction involving the cytochrome c' biological function.
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Affiliation(s)
- A L Mayburd
- Department of Chemistry, University of Illinois at Chicago, 60607, USA
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27
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Tsan P, Hus JC, Caffrey M, Marion D, Blackledge M. Rotational Diffusion Anisotropy and Local Backbone Dynamics of Carbon Monoxide-Bound Rhodobacter capsulatus Cytochrome c‘. J Am Chem Soc 2000. [DOI: 10.1021/ja993654k] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pascale Tsan
- Contribution from the Institut de Biologie Structurale, Jean-Pierre Ebel C.N.R.S.−C.E.A., 41, Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Jean-Christophe Hus
- Contribution from the Institut de Biologie Structurale, Jean-Pierre Ebel C.N.R.S.−C.E.A., 41, Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Michael Caffrey
- Contribution from the Institut de Biologie Structurale, Jean-Pierre Ebel C.N.R.S.−C.E.A., 41, Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Dominique Marion
- Contribution from the Institut de Biologie Structurale, Jean-Pierre Ebel C.N.R.S.−C.E.A., 41, Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Martin Blackledge
- Contribution from the Institut de Biologie Structurale, Jean-Pierre Ebel C.N.R.S.−C.E.A., 41, Rue Jules Horowitz, 38027 Grenoble Cedex, France
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28
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Hus JC, Marion D, Blackledge M. De novo determination of protein structure by NMR using orientational and long-range order restraints. J Mol Biol 2000; 298:927-36. [PMID: 10801359 DOI: 10.1006/jmbi.2000.3714] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from the nuclear Overhauser effect. By exploiting the complementary geometric dependence of paramagnetic pseudocontact shifts and the recently proposed Curie-dipolar cross correlated relaxation effect, in combination with orientational constraints derived from residual dipolar coupling, autorelaxation rate ratios and secondary structure constraints, it is possible to define uniquely the fold and refine the tertiary structure of the protein (0.73 A backbone rmsd for 82/129 amino acid residues) starting from random atomic Cartesian coordinates. The structure calculation protocol, developed using specific models to describe the novel constraint interactions, is robust, requiring no precise a priori estimation of the various interaction strengths, and provides unambiguous convergence based only on the value of the target function. Tensor eigenvalues and their component orientations are allowed to float freely, and are thus simultaneously determined, and found to converge, during the structure calculation.
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Affiliation(s)
- J C Hus
- Jean-Pierre Ebel C.N.R.S. C.E.A., Institut de Biologie Structurale, 41, rue Jules Horowitz, Grenoble Cedex, 38027, France
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29
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Cross R, Aish J, Paston SJ, Poole RK, Moir JW. Cytochrome c' from Rhodobacter capsulatus confers increased resistance to nitric oxide. J Bacteriol 2000; 182:1442-7. [PMID: 10671472 PMCID: PMC94437 DOI: 10.1128/jb.182.5.1442-1447.2000] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the cloning and sequencing of the gene containing cytochrome c' (cycP) from the photosynthetic purple bacterium Rhodobacter capsulatus and the regions flanking that gene. Mutant strains unable to synthesize cytochrome c' had increased sensitivity to nitrosothiols and to nitric oxide (which binds to the heme moiety of cytochrome c').
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Affiliation(s)
- R Cross
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
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30
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Déméné H, Tsan P, Gans P, Marion D. NMR Determination of the Magnetic Susceptibility Anisotropy of Cytochrome c‘ of Rhodobacter Capsulatus by 1JHN Dipolar Coupling Constants Measurement: Characterization of Its Monomeric State in Solution. J Phys Chem B 2000. [DOI: 10.1021/jp994318t] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hélène Déméné
- Laboratoire de Résonance Magnétique Nucléaire, Institut de Biologie Structurale “Jean Pierre Ebel” (CEA-CNRS), 41 Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Pascale Tsan
- Laboratoire de Résonance Magnétique Nucléaire, Institut de Biologie Structurale “Jean Pierre Ebel” (CEA-CNRS), 41 Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Pierre Gans
- Laboratoire de Résonance Magnétique Nucléaire, Institut de Biologie Structurale “Jean Pierre Ebel” (CEA-CNRS), 41 Rue Jules Horowitz, 38027 Grenoble Cedex, France
| | - Dominique Marion
- Laboratoire de Résonance Magnétique Nucléaire, Institut de Biologie Structurale “Jean Pierre Ebel” (CEA-CNRS), 41 Rue Jules Horowitz, 38027 Grenoble Cedex, France
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31
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Boisbouvier J, Gans P, Blackledge M, Brutscher B, Marion D. Long-Range Structural Information in NMR Studies of Paramagnetic Molecules from Electron Spin−Nuclear Spin Cross-Correlated Relaxation. J Am Chem Soc 1999. [DOI: 10.1021/ja991228t] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jérôme Boisbouvier
- Institut de Biologie Structurale-Jean-Pierre Ebel C.N.R.S.-C.E.A., 41, rue Jules Horowitz 38027 Grenoble Cedex, France
| | - Pierre Gans
- Institut de Biologie Structurale-Jean-Pierre Ebel C.N.R.S.-C.E.A., 41, rue Jules Horowitz 38027 Grenoble Cedex, France
| | - Martin Blackledge
- Institut de Biologie Structurale-Jean-Pierre Ebel C.N.R.S.-C.E.A., 41, rue Jules Horowitz 38027 Grenoble Cedex, France
| | - Bernhard Brutscher
- Institut de Biologie Structurale-Jean-Pierre Ebel C.N.R.S.-C.E.A., 41, rue Jules Horowitz 38027 Grenoble Cedex, France
| | - Dominique Marion
- Institut de Biologie Structurale-Jean-Pierre Ebel C.N.R.S.-C.E.A., 41, rue Jules Horowitz 38027 Grenoble Cedex, France
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32
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Watmough NJ, Butland G, Cheesman MR, Moir JW, Richardson DJ, Spiro S. Nitric oxide in bacteria: synthesis and consumption. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1411:456-74. [PMID: 10320675 DOI: 10.1016/s0005-2728(99)00032-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- N J Watmough
- School of Biological Sciences, Centre for Metalloprotein Spectroscopy and Biology, University of East Anglia, Norwich NR4 7TJ, UK.
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33
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Tsan P, Caffrey M, Daku ML, Cusanovich M, Marion D, Gans P. Unusual Contact Shifts and Magnetic Tensor Orientation in Rhodobacter capsulatus Ferrocytochrome c‘: NMR, Magnetic Susceptibility, and EPR Studies. J Am Chem Soc 1999. [DOI: 10.1021/ja9820745] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pascale Tsan
- Contribution from the Institut de Biologie Structurale “Jean-Pierre Ebel” (CEA-CNRS), 41 Avenue des Martyrs, 38027 Grenoble Cedex, France, DRFMC-SCIB-SCPM, 85X, CEN-Grenoble, 38041 Grenoble Cedex, France, and Department of Biochemistry, University of Arizona, Tucson, Arizona 85721
| | - Michael Caffrey
- Contribution from the Institut de Biologie Structurale “Jean-Pierre Ebel” (CEA-CNRS), 41 Avenue des Martyrs, 38027 Grenoble Cedex, France, DRFMC-SCIB-SCPM, 85X, CEN-Grenoble, 38041 Grenoble Cedex, France, and Department of Biochemistry, University of Arizona, Tucson, Arizona 85721
| | - Max Lawson Daku
- Contribution from the Institut de Biologie Structurale “Jean-Pierre Ebel” (CEA-CNRS), 41 Avenue des Martyrs, 38027 Grenoble Cedex, France, DRFMC-SCIB-SCPM, 85X, CEN-Grenoble, 38041 Grenoble Cedex, France, and Department of Biochemistry, University of Arizona, Tucson, Arizona 85721
| | - Michael Cusanovich
- Contribution from the Institut de Biologie Structurale “Jean-Pierre Ebel” (CEA-CNRS), 41 Avenue des Martyrs, 38027 Grenoble Cedex, France, DRFMC-SCIB-SCPM, 85X, CEN-Grenoble, 38041 Grenoble Cedex, France, and Department of Biochemistry, University of Arizona, Tucson, Arizona 85721
| | - Dominique Marion
- Contribution from the Institut de Biologie Structurale “Jean-Pierre Ebel” (CEA-CNRS), 41 Avenue des Martyrs, 38027 Grenoble Cedex, France, DRFMC-SCIB-SCPM, 85X, CEN-Grenoble, 38041 Grenoble Cedex, France, and Department of Biochemistry, University of Arizona, Tucson, Arizona 85721
| | - Pierre Gans
- Contribution from the Institut de Biologie Structurale “Jean-Pierre Ebel” (CEA-CNRS), 41 Avenue des Martyrs, 38027 Grenoble Cedex, France, DRFMC-SCIB-SCPM, 85X, CEN-Grenoble, 38041 Grenoble Cedex, France, and Department of Biochemistry, University of Arizona, Tucson, Arizona 85721
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34
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Moir JW. Cytochrome c' from Paracoccus denitrificans: spectroscopic studies consistent with a role for the protein in nitric oxide metabolism. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1430:65-72. [PMID: 10082934 DOI: 10.1016/s0167-4838(98)00276-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytochrome c' was purified from the denitrifying bacterium Paracoccus denitrificans and the interaction of the protein with nitric oxide was examined spectroscopically. Two distinct types of haem-nitrosyl electronic absorption spectrum were observed, which were dependent upon [NO]. When cytochrome c' was saturated with NO, alpha and beta bands were centred at 562 nm and 530 nm, whereas with sub-saturating concentrations of NO the alpha and beta bands were red-shifted to 578 nm and 542 nm respectively. Further spectroscopic analysis showed that purified cytochrome c', added to suspensions of P. denitrificans, is able to complex with the NO which is formed as a freely diffusible intermediate of denitrification. In the presence of added NO-3 or NO-2, 40-60% of Fe(II)-cytochrome c' forms a 6-coordinate haem-nitrosyl complex. In the absence of nitrogen oxyanions or NO whole denitrifying cells are able to remove the NO from a Fe(II)-cytochrome c'-NO complex. These findings support the hypothesis that the physiological function of this enigmatic cytochrome involves the reversible binding of nitric oxide.
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Affiliation(s)
- J W Moir
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
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35
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Page MD, Sockett RE. 13 Molecular Genetic Methods in Paracoccus and Rhodobacter with Particular Reference to the Analysis of Respiration and Photosynthesis. METHODS IN MICROBIOLOGY 1999. [DOI: 10.1016/s0580-9517(08)70124-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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36
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Shibata N, Iba S, Misaki S, Meyer TE, Bartsch RG, Cusanovich MA, Morimoto Y, Higuchi Y, Yasuoka N. Basis for monomer stabilization in Rhodopseudomonas palustris cytochrome c' derived from the crystal structure. J Mol Biol 1998; 284:751-60. [PMID: 9826513 DOI: 10.1006/jmbi.1998.2190] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crystal structure of an unusual monomeric cytochrome c' from Rhodopseudomonas palustris (RPCP) has been determined at 2.3 A resolution. RPCP has the four-helix (helices A, B, C and D) bundle structure similar to dimeric cytochromes c'. However the amino acid composition of the surface of helices A and B in RPCP is remarkably different from that of the dimeric cytochromes c'. This surface forms the dimer interface in the latter proteins. RPCP has seven charged residues on this surface contrary to the dimeric cytochromes c', which have only two or three charged groups on the corresponding surface. Moreover, hydrophobic residues on this surface of RPCP are two to three times fewer than in dimeric cytochromes c'. As a result of the difference in amino acid composition, the A-B surface of RPCP is rather hydrophilic compared with dimeric cytochromes c'. We thus suggest that RPCP is monomeric in solution because of the hydrophilic nature of the A-B surface. The amino acid composition of the A-B surface is similar to that of Rhodobacter capsulatus cytochrome c' (RCCP), which is an equilibrium admixture of monomer and dimer. The charge distribution of the A-B surface in RCCP, however, is considerably different from that of RPCP. Due to the difference, RCCP can form dimers by both ionic and hydrophobic interactions. These dimers are quite different from those in proteins which form strong dimers such as in Chromatium vinosum, Rhodospirillum rubrum, Rhodospirillum molischianum and Alcaligenes. Cytochrome c' can be classified into two types. Type 1 cytochromes c' have hydrophobic A-B surfaces and they are globular. The A-B surface of type 2 cytochromes c' is hydrophilic and they take a monomeric or flattened dimeric form.
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Affiliation(s)
- N Shibata
- Faculty of Science, Himeji Institute of Technology, Hyogo, 678-1297, Japan
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37
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Bertini I, Dikiy A, Luchinat C, Macinai R, Viezzoli MS. 1H NMR Study of the Reduced Cytochrome c' from Rhodopseudomonas palustris Containing a High-Spin Iron(II) Heme Moiety. Inorg Chem 1998; 37:4814-4821. [PMID: 11670644 DOI: 10.1021/ic980531c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The assignment of the hyperfine shifted signals of the reduced cytochrome c' from Rhodopseudomonas palustris has been obtained through saturation transfer experiments with assigned signals of the high-spin oxidized protein and through tailored experiments to reveal proton-proton dipolar connectivities in paramagnetic molecules. The peculiar shift pattern consisting of the 1-, 8-, and 5-methyl signals shifted upfield and the 3-methyl signal downfield, which is shared by all cytochromes c' so far described, has been semiquantitatively related to the orientation of the histidine plane with respect to the iron-heme nitrogen axes. The research is meaningful with respect to the use of paramagnetic NMR as a tool to obtain direct structural information on all high spin iron(II) heme containing systems, including deoxyglobins.
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Affiliation(s)
- Ivano Bertini
- Department of Chemistry, University of Florence, Via Gino Capponi 7, 50121 Florence, Italy, and Department of Soil Science and Plant Nutrition, University of Florence, P. le delle Cascine 28, 50144 Florence, Italy
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