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Patila M, Pavlidis IV, Diamanti EK, Katapodis P, Gournis D, Stamatis H. Enhancement of cytochrome c catalytic behaviour by affecting the heme environment using functionalized carbon-based nanomaterials. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.04.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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2
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Wei W, Danielson ND. Fluorescence and circular dichroism spectroscopy of cytochrome c in alkylammonium formate ionic liquids. Biomacromolecules 2011; 12:290-7. [PMID: 21210672 DOI: 10.1021/bm1008052] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural stability of cytochrome c has been studied in alkylammonium formate (AAF) ionic liquids such as methylammonium formate (MAF) and ethylammonium formate (EAF) by fluorescence and circular dichroism (CD) spectroscopy. At room temperature, the native structure of cytochrome c is maintained in relatively high ionic liquid concentrations (50-70% AAF/water or AAF/phosphate buffer pH 7.0) in contrast with denaturation of cytochrome c in similar solutions of methanol or acetonitrile with water or buffer cosolvents. Fluorescence and CD spectra indicate that the conformation of cytochrome c is maintained in 20% AAF-80% water from 30 to 50 °C. No such temperature stability is found in 80% AAF-20% water. About one-third of the enzyme activity of cytochrome c in 80% AAF-20% water can be maintained as compared with phosphate buffer, and this is greater than the activities measured in corresponding methanol and acetonitrile aqueous solutions. This biophysical study shows that AAFs have potential application as organic solvent replacements at moderate temperature in the mobile phase for the separation of proteins in their native form by reversed phase liquid chromatography.
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Affiliation(s)
- Wenjun Wei
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
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3
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Arutyunyan AM, Borisov VB, Novoderezhkin VI, Ghaim J, Zhang J, Gennis RB, Konstantinov AA. Strong Excitonic Interactions in the Oxygen-Reducing Site of bd-Type Oxidase: The Fe-to-Fe Distance between Hemes d and b595 is 10 Å. Biochemistry 2008; 47:1752-9. [DOI: 10.1021/bi701884g] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander M. Arutyunyan
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, and Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, Illinois 61801
| | - Vitaliy B. Borisov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, and Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, Illinois 61801
| | - Vladimir I. Novoderezhkin
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, and Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, Illinois 61801
| | - Josh Ghaim
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, and Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, Illinois 61801
| | - Jie Zhang
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, and Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, Illinois 61801
| | - Robert B. Gennis
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, and Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, Illinois 61801
| | - Alexander A. Konstantinov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia, and Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, Illinois 61801
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4
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Olteanu A, Patel CN, Dedmon MM, Kennedy S, Linhoff MW, Minder CM, Potts PR, Deshmukh M, Pielak GJ. Stability and apoptotic activity of recombinant human cytochrome c. Biochem Biophys Res Commun 2004; 312:733-40. [PMID: 14680826 DOI: 10.1016/j.bbrc.2003.10.182] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2003] [Indexed: 10/26/2022]
Abstract
An efficient system for producing human cytochrome c variants is important to help us understand the roles of this protein in biological processes relevant to human diseases including apoptosis and oxidative stress. Here, we describe an Escherichia coli expression system for producing recombinant human cytochrome c. We also characterize the structure, stability, and function of the protein and show its utility for studying apoptosis. Yields of greater than 8 mg of pure protein per liter culture were attained. Circular dichroism spectropolarimetry studies show that the secondary and tertiary structures of the human protein are nearly identical to those of the horse protein, but the human protein is more stable than other eukaryotic cytochromes c. Furthermore, recombinant human cytochrome c is capable of inducing caspase-3 activity in a cell-free caspase activation assay. We use data from this assay along with data from the literature to define the apaf-1 binding site on human cytochrome c.
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Affiliation(s)
- Alina Olteanu
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
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5
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Dadák V, Janiczek O, Vrána O. Cytochrome c forms complexes and is partly reduced at interaction with GPI-anchored alkaline phosphatase. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1570:9-18. [PMID: 11960683 DOI: 10.1016/s0304-4165(02)00145-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cytochrome (cyt) c forms complexes, undergoes a conformational change and becomes partly reduced at interaction with membrane anchored alkaline phosphatase (AP), a glycoprotein which is released into the body fluid in forms differing in hydrophobicity. The proportion of products formed in the mixtures depends on pH, ionic strength, temperature and the buffer composition. The reaction terminates in an equilibrium between cyt c(FeII) and other cyt c conformers. Optimal conditions for the rate of the reaction are 100 mM glycine/NaOH, pH 9.7-9.9, at which 68-74% of cyt c is found in the reduced state. The interaction affects compactness of the haem cleft as shown by changes induced in CD spectra of the Soret region and changes in optical characteristics of phenylalanine, tyrosine and tryptophan residues. Differential scanning calorimetry of AP+cyt c mixtures revealed a creation of at least two types of complexes. A complex formed by non-coulombic binding prevails at substoichiometric AP/cyt c ratios, at higher ratios more electrostatic attraction is involved and at 1:1 molar ratio an apparent complexity of binding forces occurs. The rapid phase of the cyt c(FeII) formation depends on the presence of the hydrophobic alkylacylphosphoinositol (glycosylphosphatidylinositol) moiety, the protein part of the enzyme participates in an electrostatic and much slower phase of cyt c(FeII) creation. The results show that non-coulombic interaction may participate at interaction of cyt c with cellular proteins.
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Affiliation(s)
- Vladimír Dadák
- Department of Biochemistry, Faculty of Science, Masaryk University, 61137, Brno, Czech Republic
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6
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Unfolding pathway of cytochromec oxidase induced by ionic surfactants: Circular dichroism and picosecond time-resolved fluorescence studies. J CHEM SCI 1998. [DOI: 10.1007/bf02871280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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7
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Karlsson JJ, Nielsen MF, Thuesen MH, Ulstrup J. Electrochemistry of Cytochrome c4 from Pseudomonas stutzeri. J Phys Chem B 1997. [DOI: 10.1021/jp962725o] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jens-J. Karlsson
- Department of Chemistry, Building 207, Technical University of Denmark, DK-2800 Lyngby, Denmark, and Department of Chemistry, Symbion Science Park, University of Copenhagen, Fruebjergvej 3, DK-2100 Copenhagen Ø, Denmark
| | - Merete F. Nielsen
- Department of Chemistry, Building 207, Technical University of Denmark, DK-2800 Lyngby, Denmark, and Department of Chemistry, Symbion Science Park, University of Copenhagen, Fruebjergvej 3, DK-2100 Copenhagen Ø, Denmark
| | - Marianne H. Thuesen
- Department of Chemistry, Building 207, Technical University of Denmark, DK-2800 Lyngby, Denmark, and Department of Chemistry, Symbion Science Park, University of Copenhagen, Fruebjergvej 3, DK-2100 Copenhagen Ø, Denmark
| | - Jens Ulstrup
- Department of Chemistry, Building 207, Technical University of Denmark, DK-2800 Lyngby, Denmark, and Department of Chemistry, Symbion Science Park, University of Copenhagen, Fruebjergvej 3, DK-2100 Copenhagen Ø, Denmark
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8
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Qu K, Vaughn JL, Sienkiewicz A, Scholes CP, Fetrow JS. Kinetics and motional dynamics of spin-labeled yeast iso-1-cytochrome c: 1. Stopped-flow electron paramagnetic resonance as a probe for protein folding/unfolding of the C-terminal helix spin-labeled at cysteine 102. Biochemistry 1997; 36:2884-97. [PMID: 9062118 DOI: 10.1021/bi962155i] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The kinetics of chemically induced folding and unfolding processes in spin-labeled yeast iso-1-cytochrome c were measured by stopped-flow electron paramagnetic resonance (EPR). Stopped-flow EPR, based on a new dielectric resonator structure [Sienkiewicz, A., Qu, K., & Scholes, C. P. (1994) Rev. Sci. Instrum. 65, 68-74], gives a new temporal component to probing nanosecond molecular tumbling motions that are modulated by macromolecular processes requiring time resolution of milliseconds to seconds. The stopped-flow EPR technique presented in this work is a kinetic technique that has not been previously used with such a time resolution on spin-labeled systems, and it has the potential for application to numerous spin-labeled sites in this and other proteins. The cysteine-specific spin-label, methanethiosulfonate spin-label (MTSSL), was attached to yeast iso-1-cytochrome c at the single naturally occurring cysteine102, and the emphasis for this work was on this disulfide-attached spin-labeled prototype. This probe has the advantage of reflecting the protein tertiary fold, as shown by recent, systematic site-directed spin labeling of T4 lysozyme [Mchaourab, H. S. Lietzow, M. A., Hideg, K., & Hubbell, W. L. (1996) Biochemistry 35, 7692-7704], and protein backbone dynamics, as also shown by model peptide studies [Todd, A. P., & Millhauser, G. L. (1991) Biochemistry 30, 5515-5523]. The C-terminal cytochrome c helix where the label is attached is thought to be critical in the initial steps of protein folding and unfolding. Stopped-flow EPR resolved the monoexponential, guanidinium-induced unfolding process at pH 6.5 with an approximately 20 ms time constant; this experiment required less than 150 microL of 80 microM spin-labeled protein. We observed an approximately 50-fold decrease of this unfolding time from the 1 s range to the 20 ms time range as the guanidinium denaturant concentration was increased from 0.6 to 2.0 M. The more complex refolding kinetics of our labeled cytochrome were studied by stopped-flow EPR at pH 5.0 and 6.5. The spin probe showed a fast kinetic process compatible with the time range over which hydrogen/deuterium amide protection indicates helix formation; this process was monoexponential at pH 5.0. At pH 6.5, there was evidence of an additional slower kinetic phase resolved by stopped-flow EPR and by heme-ligation-sensitive UV-Vis that indicated a slower folding where heme misligation may be involved. Since the disulfide-attached probe has reported folding and backbone dynamics in other systems, the implication is that our kinetic experiments were directly sensing events of the C-terminal helix formation and possibly the N- and C-terminal helical interaction. The cysteine-labeled protein was also studied under equilibrium conditions to characterize probe mobility and the effect of the probe on protein thermodynamics. The difference in spin probe mobility between folded and denatured protein was marked, and in the folded protein, the motion of the probe was anisotropically restricted. The motion of the attached nitroxide in the folded protein appears to be restricted about the carbon and sulfur bonds which tether it to the cysteine. The original point of cysteine sulfur attachment is approximately 11 A from the heme iron within the C-terminal helix near its interface with the N-terminal helix, but the low-temperature EPR spin probe line width showed that the probe lies more distant (> 15 A) from the heme iron. By all physical evidence, the protein labeled at cysteine102 folded, but the spin probe in this prototype system perturbed packing which lowered the thermal melting temperature, the free energy of folding, the guanidinium concentration at the midpoint of the unfolding transition, the m parameter of the denaturant, and the helical CD signature. This study prepares the way for study of protein folding/unfolding kinetics using EPR spectroscopy of spin-labels placed at specific cysteine-mutated sites within
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Affiliation(s)
- K Qu
- Department of Chemistry, State University of New York at Albany, 12222, USA
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9
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Shen C, Kostić NM. Kinetics of Photoinduced Electron-Transfer Reactions within Sol-Gel Silica Glass Doped with Zinc Cytochrome c. Study of Electrostatic Effects in Confined Liquids. J Am Chem Soc 1997. [DOI: 10.1021/ja961867t] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chengyu Shen
- Contribution from the Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Nenad M. Kostić
- Contribution from the Department of Chemistry, Iowa State University, Ames, Iowa 50011
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10
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Fetrow JS, Horner SR, Oehrl W, Schaak DL, Boose TL, Burton RE. Analysis of the structure and stability of omega loop A replacements in yeast iso-1-cytochrome c. Protein Sci 1997; 6:197-210. [PMID: 9007992 PMCID: PMC2143502 DOI: 10.1002/pro.5560060122] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Omega (omega)-loop A, residues 18-32 in wild-type yeast iso-1-cytochrome c, has been deleted and replaced with loop sequences from three other cytochromes c and one from esterase. Yeast expressing a partial loop deletion do not contain perceptible amounts of holoprotein as measured by low-temperature spectroscopy and cannot grow on nonfermentable media. Strains expressing loop replacement mutations accumulate holoprotein in vivo, but the protein function varies depending on the sequence and length of the replacement loop; in vivo expression levels do not correlate with their thermal denaturation temperatures. In vitro spectroscopic studies of the loop replacement proteins indicate that all fold into a native-like cytochrome c conformation, but are less stable than the wild-type protein. Decreases in thermal stability are caused by perturbation of loop C backbone in one case and a slight reorganization of the protein hydrophobic core in another case, rather than rearrangement of the loop A backbone. A single-site mutation in one of the replacement mutants designed to relieve inefficient hydrophobic core packing caused by the new loop recovers some, but not all, of the lost stability.
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Affiliation(s)
- J S Fetrow
- Department of Biological Sciences, University at Albany, SUNY 12222, USA.
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11
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Conrad LS, Karlsson JJ, Ulstrup J. Electron transfer and spectral alpha-band properties of the di-heme protein cytochrome c4 from Pseudomonas stutzeri. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 231:133-41. [PMID: 7628463 DOI: 10.1111/j.1432-1033.1995.0133f.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: 01/26/2023]
Abstract
Cytochrome c4 is a 190-residue protein active in the aerobic and anaerobic respiration of several bacteria. We have isolated Pseudomonas stutzeri (ATCC no. 11607) cytochrome c4 by an optimized growth procedure following factorial design. The ultraviolet/visible spectra of reduced cytochrome c4 have a composite alpha/beta band which can be resolved into six components. One of these seems to be specific for the high-potential heme group. The kinetics for full oxidation and reduction with the two inorganic redox couples, [Co(terpy)2]2+/3+ and [Co(bipy)3]2+/3+, is formally compatible with either bi- or tri-exponential kinetics. The former would be in line with weak interaction between the heme groups, the latter with notable interaction effects. Arguments in favour of the latter and a cooperative two-electron transfer pattern are given. All phases are approximately proportional to the Co-complex concentration, implying that intramolecular electron transfer in this time range is unlikely. The rate constants are in the range (0.7-80) x 10(4) M-1 s-1 at pH = 7.6 (Tris) and 0.1 M NaCl and very little dependent on the ionic strength in the range 0.1-0.3 M. The reduction potentials could be calculated from the forward and reverse rate constant ratios. The values are 241 +/- 5 and 328 +/- 2 mV (Nernst hydrogen electrode) if bi-exponential kinetics is used and interaction between the heme groups disregarded. The intrinsic microscopic reduction potential values are closer when the tri-exponential, cooperative model is used as this model transfers 30-40 mV to electrostatically dominated interaction potentials. The overall electron transfer pattern can be related to the recently determined crystal structure of the P. stutzeri cytochrome c4.
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Affiliation(s)
- L S Conrad
- Chemistry Department A, Technical University of Denmark, Lyngby
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12
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Affiliation(s)
- R W Woody
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523, USA
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13
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Palmer G, Degli Esposti M. Application of exciton coupling theory to the structure of mitochondrial cytochrome b. Biochemistry 1994; 33:176-85. [PMID: 8286337 DOI: 10.1021/bi00167a023] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The circular dichroism of the reduced bis-heme mitochondrial cytochrome b in the Soret region has been analyzed using exciton theory. The theory was applied to a geometric model that reflects the current consensus of the structure of this membrane protein [Degli Esposti, M., De Vries, S., Crimi, M., Ghelli, A., Patarnello, T., & Meyer, A. (1993) Biochim. Biophys. Acta 1143, 243-271]. The analysis suggests that the iron-iron distance is about 19.5 A, with a possible range of 17-23 A; the two hemes appear to be canted at 45 degrees with respect to one another. It appears that the two hemes undergo a relative angular displacement upon reduction, suggesting some flexibility in the protein structure. Some applications of this analysis to other bis-heme proteins are considered.
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Affiliation(s)
- G Palmer
- Department of Biochemistry & Cell Biology, Rice University, Houston, Texas 77251-1892
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14
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Lou BS, Hobbs JD, Chen YR, Yu L, Yu CA, Ondrias MR. Structural characterization of isolated mitochondrial cytochrome c1. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1144:403-10. [PMID: 8399285 DOI: 10.1016/0005-2728(93)90127-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Resonance Raman spectroscopy (RRS) has been employed to characterize cytochromes c1 isolated from bc1 complexes of beef heart mitochondria and Rhodopseudomonas sphaeroides. The data obtained in this study extend the physical characterization of cytochromes c1 and focus on the effects of the local protein environment on the heme active site. While the general characteristics of the cytochromes c1 are similar to those of smaller soluble cytochromes c, the behavior of several core-size and ligation-sensitive heme modes reveal that significant systematic differences exist between those species. These, most likely, result from changes in the heme axial-ligand interactions.
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Affiliation(s)
- B S Lou
- Department of Chemistry, University of New Mexico, Albuquerque 87131
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15
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Wang J, Zhu H, Ondrias MR. Protein conformational perturbations affect the photoreduction of native cytochrome c peroxidase (III) at alkaline pH. Biochemistry 1992; 31:12847-54. [PMID: 1334434 DOI: 10.1021/bi00166a020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ferric cytochrome c peroxidase (CCP) undergoes a ligation-state transition from a pentacoordinate, high-spin (5c/hs) heme to a hexacoordinate, low-spin (6c/1s) heme when titrated over a pH range of 7.30-9.70. This behavior is similar to that exhibited by the ferrous form of the enzyme. However, the photodissociation of the low-spin, axial ligand, exhibited by ferrous CCP at alkaline pH, is not observed for ferric CCP. Instead, a photoinduced reduction of the ferric heme is apparent in the pH range 7.90-9.70. In the absence of O2 and redox mediators such as methyl viologen (MV2+), the reoxidation of the photoreduced enzyme is very slow (tau 1/2 approximately 3 min). F(-)-bound CCP(III) (6c/hs) displays similar pH-dependent photoreduction. Horseradish peroxidase, however, does not. The formation of 6c/1s heme coincides with the onset of appreciable photoreduction (between laser pulses, > 60 ms) of CCP (III) at alkaline pH, suggesting a global protein conformational rearrangement within or around its heme pocket. Photoreduction of alkaline CCP(III) most likely involves intramolecular electron transfer (ET) from the aromatic residue in the proximal heme pocket to the photoexcited heme. We speculate that the kinetics of electron transfer are affected by changes in the orientation of Trp-191.
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Affiliation(s)
- J Wang
- Department of Chemistry, University of New Mexico, Albuquerque 87131
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16
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Frauenhoff MM, Scott RA. The role of tyrosine 67 in the cytochrome c heme crevice structure studied by semisynthesis. Proteins 1992; 14:202-12. [PMID: 1329082 DOI: 10.1002/prot.340140207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Tyr-67 of mitochondrial cytochrome c is thought to be involved in important hydrogen bonding interactions in the hydrophobic heme pocket of the protein (Takano, T., Dickerson, R. E. (1981) J. Mol. Biol. 153:95-115). The role of this highly conserved residue in heme pocket stability was studied by comparing properties of semisynthetic (Phe-67) and (p-F-Phe-67) analogs with those of native cytochrome c and a "control" analog, (Hse-65)cytochrome c. The (Phe-67) and (p-F-Phe-67) analogs have well-developed 695-nm visible absorption bands and are active in a cytochrome c oxidase assay. The reduction potentials of both analogs are lower than the native protein by approximately 50 mV. Although both analogs bind imidazole with higher affinity than the native protein, only the (p-F-Phe-67) analog has a 3- to 5-fold lower binding constant for cyanide. Only the (Phe-67) analog was significantly more stable toward alkaline isomerization. These results are not consistent with stabilization of the native protein heme pocket via hydrogen bonding of Tyr-67 to Met-80. An alternative steric role for Tyr-67 is proposed in which the residue controls the heme reduction potential by limiting the number of internal H2O molecules in the heme pocket.
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Affiliation(s)
- M M Frauenhoff
- Department of Chemistry, University of Georgia, Athens 30602
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17
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The structure of the dihaem cytochrome b of fumarate reductase in Wolinella succinogenes: circular dichroism and sequence analysis studies. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1056:243-9. [PMID: 2001380 DOI: 10.1016/s0005-2728(05)80055-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The fumarate reductase from Wolinella succinogenes contains two haem groups with markedly different midpoint potentials (-20 mV and -200 mV). The enzyme is made up of three subunits, the lipophilic one of which (cytochrome b) ligates the haems. Circular dichroism (CD) spectroscopy has been applied to the reductase in order to obtain information on the structure of the haems and of their environment. This approach is integrated with amino acid sequence comparison of the cytochrome b with other quinone-reacting membrane haemoproteins for predicting the axial ligands of the haems as well as their location relative to the membrane. The following results have been obtained: (1) the CD spectra in the Soret region show exciton coupling indicating haem-haem interaction, which is particularly evident in the reduced state and disappears upon denaturation of the enzyme; (2) The apoprotein of cytochrome b is predicted to consist of five hydrophobic helices (helices A-D and cd), four of which should span the membrane. Helices A, B, C and cd contain a histidine residue each which possibly forms one of the ligands of the haems. It is proposed that haem b (-20 mV) is ligated by H44 and H93, and haem b (-200 mV) by H143 and H182.
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18
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Esposti MD. Prediction and comparison of the haem-binding sites in membrane haemoproteins. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 977:249-65. [PMID: 2686753 DOI: 10.1016/s0005-2728(89)80079-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This article contains a comparative review of the structural properties of membrane haemoproteins, with particular emphasis on the possible similarities of the haem-binding peptides. A procedure is suggested for identifying the peptides which may bind membrane-buried haems on the basis of the primary sequences of the proteins. The integration of this procedure with the information deduced by refined hydropathy analysis indicates that the basic structural model for the haemoproteins which interact with quinones may be a transmembrane helical bundle containing the haem(s) at its centre. Structural similarities exist in the sequence of hydrophobic segments that are predicted to bind the membrane-buried haems of b-cytochromes which interact with quinones. The predicted haem-binding sites show similarities also with the peptides that bind the non-haem iron in the bacterial reaction centres, and this may be correlated to the common function of interacting with quinones and their intermediates. The analysis of the amino-acid composition of the proposed ligand peptides in the membrane haemoproteins examined has provided a molecular rationale for explaining the highly anisotropic low-spin EPR signal which is characteristic of many membrane-bound b-cytochromes.
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Affiliation(s)
- M D Esposti
- Department of Biology, University of Bologna, Italy
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19
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Degli Esposti M, Kamensky YuA, Arutjunjan AM, Konstantinov AA. A model for the molecular organization of cytochrome beta-561 in chromaffin granule membranes. FEBS Lett 1989; 254:74-8. [PMID: 2776888 DOI: 10.1016/0014-5793(89)81012-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The CD spectrum of reduced cytochrome (cyt.) beta-561 in chromaffin granule membranes resembles that of mitochondrial cyt. beta 1 and indicates possible heme-heme interaction in the protein. Based on spectroscopic data and analysis of the amino acid sequence, a model of cyt. beta-561 is suggested, in which the protein carries two transmembrane-localized hemes, each coordinated by two histidines. The model accounts for the presence of two different forms of cyt. beta-561 in chromaffin granule membranes and provides a mechanism of transmembrane electron transfer by this hemoprotein.
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20
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Degli Esposti M, Palmer G, Lenaz G. Circular dichroic spectroscopy of membrane haemoproteins. The molecular determinants of the dichroic properties of the b cytochromes in various ubiquinol:cytochrome c reductases. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 182:27-36. [PMID: 2543573 DOI: 10.1111/j.1432-1033.1989.tb14796.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The circular dichroism (CD) of dihaem cytochrome b from mitochondrial and bacterial ubiquinol:cytochrome-c reductase (bc1 complex) has been characterized. The dichroic properties of the yeast purified cyt b are very similar to those of the native cyt b within the mitochondrial bc1 complex. The CD spectra in the Soret region of the native cytochrome b present in all species studied show an intense bisignate Cotton effect having a zero-crossing wavelength close to the absorbance maximum. In preparations partially or completely depleted of the low-potential b haem (b1) the CD spectra exhibit a single positive Cotton effect resembling the corresponding absorption spectrum. This is particularly evident in the purified cytochrome b-562 from Rhodobacter sphaeroides R26, which contains only the high-potential b haem (bh). These spectral features together with the reconstitution of the cytochrome b1 haem have been used to resolve the CD contribution of each haem to the CD spectra of cytochrome b. The mechanisms which might be responsible for the optical activity have been examined. It appears that the CD spectra of cytochrome b derive from both the mutual interaction of its two haems (giving rise to exciton coupling) and to the interaction of each haem with nearby aromatic residues, other than the pairs of histidines which coordinate the iron. The dipole coupling between haem and aromatic residues appears to be more important than exciton coupling in the CD spectra of oxidized b cytochromes and correlations have been made between the CD features and the proposed structure of cytochrome b.
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Manning MC. Underlying assumptions in the estimation of secondary structure content in proteins by circular dichroism spectroscopy--a critical review. J Pharm Biomed Anal 1989; 7:1103-19. [PMID: 2490370 DOI: 10.1016/0731-7085(89)80049-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Recombinant DNA technology has made possible the large-scale production of proteins for pharmaceutical applications. As a result, there has been a renaissance in methodology which can provide information on the structural stability and character of these materials. Circular dichroism (CD) spectroscopy, with its sensitivity to the secondary structure adopted by the polypeptide chain, is a powerful tool in this regard. Quantitative analysis of the CD spectra of proteins is now wide-spread, aided by the availability of such algorithms on commercial instrumentation. However, there are basic assumptions made when conducting these calculations, many of which have not been addressed or summarized. Some of these assumptions are independent of the selection of basis spectra and the algorithm employed. These assumptions are listed and the available data concerning their validity is presented and discussed.
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Affiliation(s)
- M C Manning
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence 66045
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Yamaguchi T, Hayakawa T, Kaneda M, Kakinuma K, Yoshikawa A. Purification and some properties of the small subunit of cytochrome b558 from human neutrophils. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(17)31230-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Degli Esposti M, Crimi M, Samworth CM, Solaini G, Lenaz G. Resolution of the circular dichroism spectra of the mitochondrial cytochrome bc1 complex. BIOCHIMICA ET BIOPHYSICA ACTA 1987; 892:245-52. [PMID: 3036219 DOI: 10.1016/0005-2728(87)90228-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The circular dichroic spectrum of the mitochondrial cytochrome bc1 complex isolated from bovine heart has been resolved into the contributions from the prosthetic groups: cytochrome c1, the 'Rieske' iron-sulphur centre and the two b cytochromes. It is apparent that firstly, the circular dichroism (CD) properties of cytochrome c1 within the bc1 complex differ from those found in the isolated cytochrome c1 and secondly, both the oxidized and reduced b cytochromes exhibit an intense spectrum of bilobic shape, with the wavelengths of the cross-over points closely corresponding to those of the maxima in the optical absorbance spectra. These latter CD features are discussed in relation to the proposed structure of cytochrome b.
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