101
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Electrochemical properties of pyrolytic graphite electrodes modified through adsorbed proteins. Electrochim Acta 1990. [DOI: 10.1016/0013-4686(90)85056-s] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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102
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Louie GV, Brayer GD. A polypeptide chain-refolding event occurs in the Gly82 variant of yeast iso-1-cytochrome c. J Mol Biol 1989; 210:313-22. [PMID: 2557455 DOI: 10.1016/0022-2836(89)90333-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The replacement of Phe82 in yeast iso-1-cytochrome c by a glycine residue substantially alters both the tertiary structure and electron transfer properties of this protein. The largest structural change involves a polypeptide chain refolding of residues 79 through 85. Refolding places glycines 82, 83 and 84 immediately adjacent to the plane of the heme group in a spatial positioning comparable to that of the phenyl ring of Phe82 in the wild-type protein. Despite this perturbation in structure, solvent accessibility computations show that heme solvent exposure has not increased in the Gly82 variant protein. However, refolding does result in the introduction of a number of polar groups into the hydrophobic heme pocket. This appears to be responsible for the decreased reduction potential of the heme in this protein. The present study, along with that of the Ser82 variant protein (Louie et al., 1988b), clearly establishes the link between dielectric constant within the heme crevice and reduction potential. The further anomalously low electron transfer activity of the Gly82 variant protein would appear to arise from two factors. First, the polypeptide chain medium now adjacent to the heme is unable to facilitate electron transfer in a manner similar to that of the aromatic side-chain of Phe82. Second, polypeptide chain refolding significantly alters the surface contour of the Gly82 protein rendering it less suitable to interact with the corresponding complementary surfaces of redox partners. Our data support the conclusion that Phe82 plays a number of roles in the electron transfer process mediated by yeast iso-1-cytochrome c. These include the maintenance of the heme environment, provision of an optimal medium along the path of electron transfer and formation of interactions at the contact interface in complexes with redox partners.
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Affiliation(s)
- G V Louie
- Department of Biochemistry, University of British Columbia, Vancouver, Canada
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103
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Hill HO, Lawrance GA. Some consequences of mixed and dilute surface modification of gold electrodes for protein electrochemistry. ACTA ACUST UNITED AC 1989. [DOI: 10.1016/0022-0728(89)85045-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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104
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Wallace CJA, Mascagni P, Chait BT, Collawn JF, Paterson Y, Proudfoot AEI, Kent SBH. Substitutions engineered by chemical synthesis at three conserved sites in mitochondrial cytochrome c. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(19)84810-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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105
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Kipke CA, Enemark JH, Sunde RA. Purification of prosthetically intact sulfite oxidase from chicken liver using a modified procedure. Arch Biochem Biophys 1989; 270:383-90. [PMID: 2930196 DOI: 10.1016/0003-9861(89)90041-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A modified procedure was used to purify sulfite oxidase (sulfite:O2 oxidoreductase; EC 1.8.3.1) from chicken liver in high yield. The modifications included dialysis of the enzyme against a buffered solution containing sodium molybdate (prior to ion-exchange chromatography), which apparently reconstituted any demolybdo enzyme present in the extract, and phenyl-Sepharose column chromatography. Analysis showed that the purified enzyme contained Mo and heme in a 1.03:1.00 ratio, indicating that the enzyme was prosthetically intact; exogenous heme and other colored proteins were absent from the final pool. Treatment of the sulfite-reduced enzyme with 50 mM cyanide at pH 8.5 resulted in a gradual loss of catalytic activity with a half-life of 19.7 min. Analysis of the cyanide-inactivated enzyme gave a Mo:heme ratio of 1.02:1.00, providing the first direct evidence that the enzyme does not lose molybdenum when inactivated with cyanide. This modified purification procedure provides enzyme in high yield which is well-suited for experiments requiring prosthetically intact enzyme and which is not contaminated with extraneous heme or with other redox active proteins.
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Affiliation(s)
- C A Kipke
- Department of Chemistry, University of Arizona, Tucson 85721
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106
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Evans MJ, Scarpulla RC. The human somatic cytochrome c gene: two classes of processed pseudogenes demarcate a period of rapid molecular evolution. Proc Natl Acad Sci U S A 1988; 85:9625-9. [PMID: 2849112 PMCID: PMC282819 DOI: 10.1073/pnas.85.24.9625] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have isolated and determined the DNA sequences of the human somatic cytochrome c gene (HCS) and 11 processed pseudogenes. HCS is the functional homologue to the previously characterized rat somatic gene because it correctly encodes the human heart protein, is present in single copy in the human genome, is nearly identical in both size and intron/exon structure to rodent somatic genes, and shares a high degree of sequence homology with its rat counterpart including a well-conserved promoter region (77% over 250 nucleotides). In contrast to the rodent system, however, where the known pseudogenes all originated from a locus encoding the present day cytochrome c, the human pseudogenes are of two types. A predominant class of older pseudogenes came from a progenitor of HCS that encoded an ancestral form of the protein, while a second group of only a few young pseudogenes originated from a recent parent of HCS that encoded the current cytochrome c polypeptide. These two distinct classes of human pseudogenes provide a molecular record of the history of cytochrome c evolution in primates and demarcate a short period of rapid evolution of the functional gene.
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Affiliation(s)
- M J Evans
- Department of Molecular Biology, Northwestern University Medical School, Chicago, IL 60611
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107
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Ligand Binding to cytochrome c and other related haem proteins and peptides. Part II. Kinetic studies. Inorganica Chim Acta 1988. [DOI: 10.1016/s0020-1693(00)83866-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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108
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Corthésy BE, Wallace CJ. The oxidation-state-dependent ATP-binding site of cytochrome c. Implication of an essential arginine residue and the effect of occupancy on the oxidation-reduction potential. Biochem J 1988; 252:349-55. [PMID: 2843168 PMCID: PMC1149151 DOI: 10.1042/bj2520349] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Arg-91 is not part of the active site of cytochrome c that mediates binding and electron transfer, yet it is absolutely conserved in eukaryotic cytochromes c, indicating a special function. The physicochemical properties of analogues are unaffected by the modification of this residue, so they can be used with confidence to study the role of Arg-91. We have established limiting conditions under which this residue alone is specifically modified by cyclohexane-1,2-dione, and have subsequently shown that ATP, and to a lesser extent ADP or Pi, protects it from the action of the reagent in an oxidation-state-dependent manner. These observations strongly support the idea that this site exerts a controlling influence on cytochrome c activity in the electron transport or other cellular redox systems, and we have commenced a study of how that influence might operate. We find that the redox potentials of both cytochrome c and analogue are little affected by changing ATP or Pi concentrations.
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Affiliation(s)
- B E Corthésy
- Département de Biochimie Médicale, Centre Médical Universitaire, Genève, Switzerland
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109
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110
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Louie GV, Hutcheon WL, Brayer GD. Yeast iso-1-cytochrome c. A 2.8 A resolution three-dimensional structure determination. J Mol Biol 1988; 199:295-314. [PMID: 2832611 DOI: 10.1016/0022-2836(88)90315-4] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A molecular replacement approach, augmented with the results of predictive modeling procedures, solvent accessibility studies, packing analyses and translational coefficient searches, has been used to elucidate the 2.8 A (1 A = 0.1 nm) resolution structure of yeast iso-1-cytochrome c. An examination of the polypeptide chain folding of this protein shows it to have unique conformations in three regions, upon comparison with the structures of other eukaryotic cytochromes c. These include: residues -5 to +1 at the N-terminal end of the polypeptide chain, which are in an extended conformation and project in large part off the surface of the protein; residues 19 to 26, which form a surface beta-loop on the His18 ligand side of the central heme group; and, the C-terminal end of the helical segment composed of residues 49 to 56, which serves to form a part of the heme pocket. Structural studies also show that the highly reactive sulfhydryl group of Cys102 is buried within a hydrophobic region in the monomer form of yeast iso-1-cytochrome c. Dimerization of yeast iso-1-cytochrome c through disulfide bond formation between two such residues would require a substantial conformational change in the C-terminal helix of this protein. Another unique structural feature, the trimethylated side-chain of Lys72, is located on the surface of yeast iso-1-cytochrome c near the solvent-exposed edge of the bound heme prosthetic group. On the basis of the results of these and other structural studies, an analysis of the spatial conservation of structural features in the heme pocket of eukaryotic cytochromes c has been conducted. It was found that the residues involved could be divided into three general classes. The current structural analyses and additional modeling studies have also been used to explain the altered functional properties observed for mutant yeast iso-1-cytochrome c proteins.
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Affiliation(s)
- G V Louie
- Department of Biochemistry, University of British Columbia, Vancouver, Canada
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111
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112
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Gadsby PM, Peterson J, Foote N, Greenwood C, Thomson AJ. Identification of the ligand-exchange process in the alkaline transition of horse heart cytochrome c. Biochem J 1987; 246:43-54. [PMID: 2823795 PMCID: PMC1148238 DOI: 10.1042/bj2460043] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Magnetic-circular-dichroism (m.c.d.) spectra over the wavelength range 300-2000 nm at room temperature and at 4.2K of horse heart cytochrome c are reported at a series of pH values between 7.8 and 11.0, encompassing the alkaline transition. The effect of glassing agents on the e.p.r. spectrum at various pH values is also reported. Comparison of these results with spectra obtained for the n-butylamine adduct of soybean leghaemoglobin support the hypothesis that lysine is the sixth ligand in the alkaline form of horse heart cytochrome c. The m.c.d. and e.p.r. spectra of horse heart cytochrome c in the presence of 1-methylimidazole have also been examined. These studies strongly suggest that histidine-18, the proximal ligand of the haem, is the ionizing group that triggers the alkaline transition. Low-temperature m.c.d. and e.p.r. spectra are also reported for Pseudomonas aeruginosa cytochrome c551. It is shown that no ligand exchange takes place at the haem in this species over the pH range 6.0-11.3.
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Affiliation(s)
- P M Gadsby
- School of Chemical Sciences, University of East Anglia, Norwich, U.K
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113
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Liang N, Pielak GJ, Mauk AG, Smith M, Hoffman BM. Yeast cytochrome c with phenylalanine or tyrosine at position 87 transfers electrons to (zinc cytochrome c peroxidase)+ at a rate ten thousand times that of the serine-87 or glycine-87 variants. Proc Natl Acad Sci U S A 1987; 84:1249-52. [PMID: 3029774 PMCID: PMC304404 DOI: 10.1073/pnas.84.5.1249] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Of the many factors known to influence the rate of electron transfer between two metalloproteins, it is particularly difficult to assess the role of the polypeptide matrix intervening between the donor and acceptor sites. To determine whether the phylogenetically conserved Phe-87 of yeast iso-1-cytochrome c helps to mediate electron transfer between cytochrome c and cytochrome c peroxidase, we have constructed mutants of cytochrome c that are altered at this position and now have studied the kinetics of long-range electron transfer within their complexes with zinc-substituted cytochrome c peroxidase. We find that the rate of electron transfer from reduced cytochrome c to the zinc cytochrome c peroxidase pi-cation radical is four orders of magnitude greater when phenylalanine or tyrosine is present at position 87 than when serine or glycine is present.
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114
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Armstrong FA, Anthony Cox P, Hill HO, Lowe VJ, Nigel Oliver B. Metal ions and complexes as modulators of protein-interfacial electron transport at graphite electrodes. ACTA ACUST UNITED AC 1987. [DOI: 10.1016/0022-0728(87)80228-0] [Citation(s) in RCA: 114] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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115
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Poerio E, Parr GR, Taniuchi H. A study of roles of evolutionarily invariant proline 30 and glycine 34 of cytochrome c. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67336-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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116
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Bechtold R, Kuehn C, Lepre C, Isied SS. Directional electron transfer in ruthenium-modified horse heart cytochrome c. Nature 1986; 322:286-8. [PMID: 3016549 DOI: 10.1038/322286a0] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cytochrome c can be modified by [(NH3)5RuII/III-] specifically at the imidazole moiety of histidine 33, and we have recently discussed the thermodynamics and kinetics of electron transfer within this modified protein. X-ray crystal structures of the oxidized and reduced forms of tuna cytochrome c indicate that the separation between the haem group of cytochrome c and the ruthenium label is 12-16 A. Internal electron transfer from the [(NH3)5RuII-] centre to the Fe(III) haem centre occurs with a rate constant k congruent to 53 s-1 (25 degrees C) (delta H = 3.5 kcal mol-1, delta S = -39 EU), as measured by pulse radiolysis. The measured unimolecular rate constant, k congruent to 53 s-1, is on the same timescale as a number of conformational changes that occur within the cytochrome c molecule. These results raise the question of whether electron transfer or protein conformational change is the rate limiting step in this process. We describe here an experiment that probes this intramolecular electron transfer step further. It involves reversing the direction of electron transfer by changing the redox potential of the ruthenium label. Electron transfer in the new ruthenium-cytochrome c derivative described here is from haem(II) to the Ru(III) label, whereas in (NH3)5Ru-cytochrome c the electron transfer is from Ru(II) to haem(III). Intramolecular electron transfer from haem(II) to Ru(III) in the new ruthenium-cytochrome c described here proceeds much slower (greater than 10(5) times) than the electron transfer from Ru(II) to haem(III) in the (NH3)5Ru-cytochrome c. We therefore conclude that electron transfer in cytochrome c is directional, with the protein envelope presumably involved in this directionality.
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117
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Churg AK, Warshel A. Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins. Biochemistry 1986; 25:1675-81. [PMID: 3011070 DOI: 10.1021/bi00355a035] [Citation(s) in RCA: 194] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
X-ray structural information provides the opportunity to explore quantitatively the relation between the microenvironments of heme proteins and their redox potentials. This can be done by considering the protein as a "solvent" for its redox center and calculating the difference between the electrostatic energy of the reduced and oxidized heme. Such calculations are presented here, applying the protein dipoles-Langevin dipoles (PDLD) model to cytochrome c. The calculations focus on an evaluation of the difference between the redox potentials of cytochrome c and the octapeptide-methionine complex formed by hydrolysis of cytochrome c. The corresponding difference (approximately 7 kcal/mol) is accounted for by the PDLD calculations. It is found that the protein provides basically a low dielectric environment for the heme, which destabilizes the oxidized heme (relative to its energy in water). The effect of the charged propionic acids on the heme is examined in a preliminary way. It is found that the negative charges of these groups are in a hydrophilic rather than a hydrophobic environment and that the protein-water system provides an effective high dielectric constant for their interaction with the heme. The dual nature of the dielectric effect of the cytochrome (a low dielectric constant for the self-energy of the heme and a high dielectric constant for charge-charge interactions) is discussed. The findings of this work are consistent with the difference between the folding energies of the reduced and oxidized cytochrome c.
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118
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Sherwood C, Brayer GD. Crystallization and preliminary diffraction data for iso-1-cytochrome c from yeast. J Mol Biol 1985; 185:209-10. [PMID: 2995685 DOI: 10.1016/0022-2836(85)90192-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Deep red crystals of the electron transfer protein, iso-1-cytochrome c from yeast (Saccharomyces cerevisiae), have been obtained from a 90% saturated solution of (NH4)2SO4 containing 2 mg protein/ml, 0.1 M-sodium phosphate and adjusted to pH 6.7. The space group is P4(1)2(1)2 (or P4(3)2(1)2) with a = b = 36.4 A, c = 136.8 A and Z = 8. Crystals are stable for at least ten days in the X-ray beam and diffract to better than 2.0 A resolution. Comparable and morphologically similar crystal forms of three iso-1-cytochrome c mutants at Phe87, a pivotal residue in the electron transport chain, have also been obtained.
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119
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MacNaughtan W, Snook KA, Caspi E, Franks NP. An X-ray diffraction analysis of oriented lipid multilayers containing basic proteins. BIOCHIMICA ET BIOPHYSICA ACTA 1985; 818:132-48. [PMID: 2411290 DOI: 10.1016/0005-2736(85)90556-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
X-ray diffraction techniques have been used to study the structures of lipid bilayers containing basic proteins. Highly ordered multilayer specimens have been formed by using the Langmuir-Blodgett method in which a solid support is passed through a lipid monolayer held at constant surface pressure at an air/water interface. If the lipid monolayer contains acidic lipids then basic proteins in the aqueous subphase are transferred with the monolayer and incorporated into the multi-membrane stack. X-ray diffraction patterns have been recorded from multilayers of cerebroside sulphate and 40% (molar) cholesterol both with and without polylysine, cytochrome c and the basic protein from central nervous system myelin. Electron density profiles across the membranes have been derived at between 6 A and 12 A resolution. All of the membrane profiles have been placed on an absolute scale of electron density by the isomorphous exchange of cholesterol with a brominated cholesterol analog. The distributions and conformations of the various basic proteins incorporated within the cerebroside sulphate/cholesterol bilayer are very different. Polylysine attaches to the surface of the lipid bilayer as a fully extended chain while cytochrome c maintains its native structure and attaches to the bilayer surface with its short axis approximately perpendicular to the membrane plane. The myelin basic protein associates intimately with the lipid headgroups in the form of an extended molecule, yet its dimension perpendicular to the plane of the membrane of approx. 15 A is consistent with the considerable degree of secondary structure found in solution. In the membrane plane, the myelin basic protein extends to cover an area of about 2500 A2. There is no significant penetration of the protein into the hydrocarbon region of the bilayer or, indeed, beyond the position of the sulphate group of the cerebroside sulphate molecule.
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120
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Katayama-Yoshida H, Zunger A. Calculation of the spin-polarized electronic structure of an interstitial iron impurity in silicon. PHYSICAL REVIEW. B, CONDENSED MATTER 1985; 31:7877-7899. [PMID: 9935733 DOI: 10.1103/physrevb.31.7877] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
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121
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Solution structure of mitochondrial cytochrome c. I. 1H nuclear magnetic resonance of ferricytochrome c. J Mol Biol 1985; 183:409-28. [PMID: 2991531 DOI: 10.1016/0022-2836(85)90011-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The 1H nuclear magnetic resonance spectra of tuna and horse ferricytochromes c have been investigated and the resonances of all amino acid methyl groups have been assigned to specific absorption lines. The assignment procedure involves principally the comparison of one-dimensional nuclear magnetic resonance spectra from a range of homologous ferricytochromes c and does not require a prior knowledge of the secondary or tertiary protein structure. Of the 49 methyl groups of tuna cytochrome c, the assignment of 33 is made without reference to the X-ray crystal structure. The method should therefore be applicable to other proteins of similar size where X-ray structures are unavailable. The assignments will be used to investigate the structure of cytochrome c in solution.
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122
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Processed pseudogenes for rat cytochrome c are preferentially derived from one of three alternate mRNAs. Mol Cell Biol 1985. [PMID: 6096691 DOI: 10.1128/mcb.4.11.2279] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Three cytochrome c mRNAs (1,400, 1,100 and 700 nucleotides) are colinear with RC4, a gene that has introns and correctly encodes cytochrome c. A comparison of RC4 to six nonallelic clones isolated from the rat cytochrome c multigene family demonstrates that all three mRNAs are represented in the genome as processed pseudogenes. Four of the six pseudogenes are derived from the 1,100-nucleotide mRNA, and genomic hybridizations further establish that nearly all of the 30 or so gene family members are also genomic copies of this mRNA despite the equimolar ratio of the three messages in rat tissues. Thus, the surprising multiplicity of cytochrome c sequences in the rat genome is mainly accounted for by the selective use of the 1,100-nucleotide mRNA for the formation of processed pseudogenes. In contrast to 700- and 1,400-nucleotide species which are polyadenylated downstream from AAGUAAA and AAUUAAA, respectively, the 1,100-nucleotide mRNA uses the ubiquitous AAUAAA and also displays a unique stem and loop structure (delta G = -59.4 kJ) centered 37 base pairs upstream from this sequence.
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123
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Limbach KJ, Wu R. Characterization of two Drosophila melanogaster cytochrome c genes and their transcripts. Nucleic Acids Res 1985; 13:631-44. [PMID: 2987802 PMCID: PMC341020 DOI: 10.1093/nar/13.2.631] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Analysis of total Drosophila melanogaster DNA by genomic blot hybridization indicates that two cytochrome c-like sequences exist in the Drosophila genome. These two sequences, DC3 and DC4, have been isolated from a Charon 4A-D. melanogaster genomic library. DC3 and DC4 are located within a 4 kb region of DNA, at position 36A 10-11, on the left arm of chromosome 2. The nucleotide sequence of these two clones has been determined. Both DC3 and DC4 can encode functional cytochrome c proteins. The polypeptide sequences predicted by these two genes, however, differ at 32 amino acid residues. DC4 is expressed at varying, but relatively high levels throughout Drosophila development. In contrast, DC3 is expressed at constant, but relatively low levels throughout development.
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124
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Limbach KJ, Wu R. Characterization of a mouse somatic cytochrome c gene and three cytochrome c pseudogenes. Nucleic Acids Res 1985; 13:617-30. [PMID: 2987801 PMCID: PMC341019 DOI: 10.1093/nar/13.2.617] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Mouse contains two functional, but differentially expressed, cytochrome c genes. One of these genes is expressed in all somatic tissues so far examined. The other gene is expressed only in testis and is assumed to be spermatogenesis-specific. The nucleotide sequence of four mouse cytochrome c-like genes has been determined. One of these genes (MC1) contains an intron and encodes a polypeptide sequence identical to the published mouse somatic cytochrome c amino acid sequence. The other three genes can not properly encode a mouse cytochrome c protein and appear to be pseudogenes which have arisen via an insertion into the mouse genome of a cDNA copy of a cytochrome c mRNA molecule.
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125
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Scarpulla RC. Processed pseudogenes for rat cytochrome c are preferentially derived from one of three alternate mRNAs. Mol Cell Biol 1984; 4:2279-88. [PMID: 6096691 PMCID: PMC369056 DOI: 10.1128/mcb.4.11.2279-2288.1984] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Three cytochrome c mRNAs (1,400, 1,100 and 700 nucleotides) are colinear with RC4, a gene that has introns and correctly encodes cytochrome c. A comparison of RC4 to six nonallelic clones isolated from the rat cytochrome c multigene family demonstrates that all three mRNAs are represented in the genome as processed pseudogenes. Four of the six pseudogenes are derived from the 1,100-nucleotide mRNA, and genomic hybridizations further establish that nearly all of the 30 or so gene family members are also genomic copies of this mRNA despite the equimolar ratio of the three messages in rat tissues. Thus, the surprising multiplicity of cytochrome c sequences in the rat genome is mainly accounted for by the selective use of the 1,100-nucleotide mRNA for the formation of processed pseudogenes. In contrast to 700- and 1,400-nucleotide species which are polyadenylated downstream from AAGUAAA and AAUUAAA, respectively, the 1,100-nucleotide mRNA uses the ubiquitous AAUAAA and also displays a unique stem and loop structure (delta G = -59.4 kJ) centered 37 base pairs upstream from this sequence.
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126
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The functional and physical form of mammalian cytochrome c oxidase determined by gel filtration, radiation inactivation, and sedimentation equilibrium analysis. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(18)89815-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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127
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Dowe RJ, Vitello LB, Erman JE. Sedimentation equilibrium studies on the interaction between cytochrome c and cytochrome c peroxidase. Arch Biochem Biophys 1984; 232:566-73. [PMID: 6087732 DOI: 10.1016/0003-9861(84)90574-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The interaction between cytochrome c and cytochrome c peroxidase was investigated using sedimentation equilibrium at pH 6,20 degrees C, in a number of buffer systems varying in ionic strength between 1 and 100 mM. Between 10 and 100 mM ionic strengths, the sedimentation of the individual proteins was essentially ideal, and sedimentation equilibrium experiments on mixtures of the two proteins were analyzed assuming ideal solution behavior. Analysis of the distribution of mixtures of cytochrome c and cytochrome c peroxidase in the ultracentrifuge cell based on a model involving the formation of a 1:1 cytochrome c-cytochrome c peroxidase complex gave values of the equilibrium dissociation constant ranging from 2.3 +/- 2.7 microM at 10 mM ionic strength to infinity (no detectable interaction) at 100 mM ionic strength. Attempts to determine the presence of complexes involving two cytochrome c molecules bound to cytochrome c peroxidase were inconclusive.
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128
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Lundell DJ, Glazer AN, DeLange RJ, Brown DM. Bilin attachment sites in the alpha and beta subunits of B-phycoerythrin. Amino acid sequence studies. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(18)91035-5] [Citation(s) in RCA: 33] [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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129
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130
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Characterization of cytochrome c accumulation in white and pink strains ofUstilago violacea using low-temperature spectroscopy and amino acid analysis. Curr Microbiol 1984. [DOI: 10.1007/bf01576039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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131
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Limbach KJ, Wu R. Isolation and characterization of two alleles of the chicken cytochrome c gene. Nucleic Acids Res 1983; 11:8931-50. [PMID: 6324108 PMCID: PMC326635 DOI: 10.1093/nar/11.24.8931] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Analysis of total chicken DNA by genomic blot hybridization indicates that only one cytochrome c gene exists in the chicken genome. The two alleles of this single cytochrome c gene have been isolated from a Charon 4A-chicken genomic library. This isolation made use of the yeast CYC1 cytochrome c gene as a specific hybridization probe. The 2 chicken alleles, CC9 and CC10, have been sequenced. The amino acid sequence predicted by these 2 alleles is identical, and agrees with the published chicken cytochrome c protein sequence. The flanking regions of these 2 alleles exhibit approximately 1% divergence, indicating a very limited polymorphism. Comparative sequence analysis with the flanking regions of previously isolated cytochrome c genes (yeast and rat) indicate no significant regions of homology. The presence of only one cytochrome c-like sequence in the chicken genome is in striking contrast with mammalian genomes, which contain as many as 20-30 cytochrome c-like sequences.
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132
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A mitochondrial protein essential for the formation of the cytochrome c1-c complex. Isolation, purification, and properties. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)43948-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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133
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Abstract
An assessment is made of the proposal: electrostatic interactions between the ferric ion of oxidised cytochrome c and its haem propionate sidechains assists in determining the value of the redox potential and plays an important role in the redox state conformation change. Differences between the properties of homologous cytochromes are proposed to be due to differences associated with the charge on their haem propionates.
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134
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Robinson MN, Boswell AP, Huang ZX, Eley CG, Moore GR. The conformation of eukaryotic cytochrome c around residues 39, 57, 59 and 74. Biochem J 1983; 213:687-700. [PMID: 6311172 PMCID: PMC1152184 DOI: 10.1042/bj2130687] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
1H-n.m.r. studies of horse, tuna, Candida krusei and Saccharomyces cerevisiae cytochromes c showed that each of the proteins contains a similar cluster of residues at the bottom of the protein that assists in shielding the haem from the solvent. The relative positions of the residues forming these clusters vary continuously with temperature, and they change with the change in protein redox state. This conformational heterogeneity is discussed with reference to the conformational flexibility of cytochrome c around residues 57, 59 and 74. Spectroscopic measurements of pKa values for Lys-55 (horse and tuna cytochromes c) and His-33 and His-39 (C. krusei and S. cerevisiae cytochromes c) are in excellent agreement with expectations based on chemical-modification studies of horse cytochrome c. [Bosshard & Zürrer (1980) J. Biol. Chem. 255, 6694-6699] and on the X-ray-crystallographic structure of tuna cytochrome c [Takano & Dickerson (1981) J. Mol. Biol. 153, 79-94, 95-115].
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135
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136
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Evidence for formation of two thioether bonds to link heme to apocytochrome c by partially purified cytochrome c synthetase. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44371-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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137
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Osheroff N, Speck SH, Margoliash E, Veerman EC, Wilms J, König BW, Muijsers AO. The reaction of primate cytochromes c with cytochrome c oxidase. Analysis of the polarographic assay. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(20)81954-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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138
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Butler J, Chapman SK, Davies DM, Sykes AG, Speck SH, Osheroff N, Margoliash E. Preferred sites for electron transfer between cytochrome c and iron and cobalt complexes. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32423-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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139
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Augustin MA, Chapman SK, Davies DM, Sykes AG, Speck SH, Margoliash E. Interaction of cytochrome c with the blue copper proteins, plastocyanin and azurin. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32424-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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140
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Voellmy R, Bromley P, Kocher HP. Structural similarities between corresponding heat-shock proteins from different eucaryotic cells. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32692-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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141
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Kato Y, Hashimoto T. Solute-support interactions in high performance gel filtration of proteins on TSK-GEL SW type column. ACTA ACUST UNITED AC 1983. [DOI: 10.1002/jhrc.1240060113] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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142
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143
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Capeillere-Blandin C. Transient kinetics of the one-electron transfer reaction between reduced flavocytochrome b2 and oxidized cytochrome c. Evidence for the existence of a protein complex in the reaction. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 128:533-42. [PMID: 6295760 DOI: 10.1111/j.1432-1033.1982.tb06998.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The one-electron transfer reaction from reduced flavocytochrome b2 (fully reduced by three electron equivalents) to ferricytochrome c, both purified from the yeast Hansenula anomala, has been studied using stopped-flow spectrophotometry in the course of a single turnover, for reactants initially mixed in a heme molar ratio equal to one. The cytochrome c reduction proceeded to completion through an apparently first-order process. Depending on the experimental conditions (concentrations and or ionic strength), the reduction is of second-order or first-order character. To interpret these kinetic results computer simulation studies have been performed based on a kinetic scheme involving, besides the formation of a complex before the electron transfer step, intramolecular electron transfer steps within flavocytochrome b2 to maintain the concentration of the specific electron donor center, the reduced cytochrome b2. As far as the cytochrome c reduction rate constant, ka, and its variations were concerned the simulated data showed that this complicated scheme could approximate a mechanism which is by far the simplest, involving only the two former steps. Such a scheme accounts firstly for the hyperbolic dependence of the rate of reduction of cytochrome c, ka, upon reductant concentrations which had provided clear evidence for the kinetic existence of a complex in the reaction pathway. At 5 degrees C the rate constant for the electron transfer is 380 s-1 with an activation energy of 13.8kJ mol-1 (3.3 kcal mol-1). Secondly it predicts the observed variations of ka with ionic strength and provides estimates of the rate constants of the binding step.
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144
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The cytochrome c peroxidase-catalyzed oxidation of ferrocytochrome c by hydrogen peroxide. Steady state kinetic mechanism. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33580-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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145
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Buchmüller Y, Corradin G. Lymphocyte specificity to protein antigens. V. Conformational dependence of activation of cytochrome c-specific T cells. Eur J Immunol 1982; 12:412-6. [PMID: 6178609 DOI: 10.1002/eji.1830120510] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Variations in the immunogenic and antigenic properties of native and denatured forms of cytochrome c were observed depending on the strain of mouse tested. In C57BL/6 and (C57BL/6 X DBA/2)F1 (BDF1) mice, priming with either native or denatured cytochrome c (apocytochrome c) gave rise to T cell blasts responding in a similar fashion to the two forms of the antigen and to different peptides derived from CNBr cleavage of the protein when tested for proliferation in the presence of C57BL/6 or BDF1 accessory cells. A different pattern of proliferation was observed when apocytochrome c-specific DBA/2 or BDF1 T cell blasts were tested with DBA/2 accessory cells. In this case, no response was obtained to heme peptide 1-65. This was not due to an inability of DBA/2 macrophages to process and present heme peptide 1-65, as they were able to present this antigen to native cytochrome c-specific BDF1 T cell blasts. Thus, it seems that different sets of clones are generated upon priming BDF1 mice with denatured cytochrome c which are able to recognize different sets of peptides depending on the nature of the accessory cells. The results obtained are consistent with the hypothesis that degradation and presentation of native and denatured cytochrome c by macrophages is dependent on the three-dimensional conformation of the protein.
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146
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Nemat-Gorgani M, Karimian K. Non-ionic adsorptive immobilization of proteins to palmityl-substituted Sepharose 4B. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 123:601-10. [PMID: 7075604 DOI: 10.1111/j.1432-1033.1982.tb06575.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
1. Palmityl-substituted Sepharose 4B prepared by the glycidyl ether method of S. Hjertén et al. [J. Chromatogr. (1974) 101, 281-288] has been used as a non-ionic matrix for protein adsorption. A number of proteins, some of which are catalytically active, may be immobilized on this adsorbent in the form of suspension or column. 2. Of the proteins examined, bovine serum albumin, hemoglobin, myoglobin, lysozyme, glutamate dehydrogenase, and beta-galactosidase were immobilized on the adsorbent irrespective of NaCl concentration. Trypsin, alpha-chymotrypsin, papain, pepsin, and amyloglucosidase were totally adsorbed either in the absence of any additional salt or at high salt concentrations. Cytochrome c, used as a model protein, was totally immobilized only at high ionic strength and low pH. 3. Immobilization normally took place with an apparent increase in initial activity rates. In the case of trypsin using N alpha-benzoyl-DL-arginine p-nitroanilide as substrate, adsorption resulted in an increase in V (app). 4. Beef-liver glutamate dehydrogenase, used as a model allosteric enzyme, was found to retain its allosteric properties towards ADP and GTP after immobilization. 5. Results are discussed in terms of specific interactions involving a smaller number of binding sites in protein molecules as compared to the multiple attachment to highly substituted adsorbents prepared with shorter ligands. Retention of the essential properties of the proteins examined in this study are ascribed to these characteristics of the adsorbent and to its non-ionic nature. Relevance of these observations to in vivo processes and the potential use of the adsorbent for enzyme immobilization are also discussed.
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147
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148
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Haladjian J, Pilard R, Bianco P, Serre PA. 455 — Effect of pH on the electroactivity of horse heart cytochrome c. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/0022-0728(82)85194-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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149
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Scarpulla RC, Agne KM, Wu R. Cytochrome c gene-related sequences in mammalian genomes. Proc Natl Acad Sci U S A 1982; 79:739-43. [PMID: 6278493 PMCID: PMC345827 DOI: 10.1073/pnas.79.3.739] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We use a rat cytochrome c gene that we previously isolated and determined the sequence of to estimate the number of related sequences present in the rat genome. Approximately 25 different EcoRI restriction endonuclease fragments from total rat DNA hybridize to the gene of known structure. Four of these correspond to homologous sequences present in four different lambda Charon 4A-rat cytochrome c recombinants previously isolated. Intact or nearly intact genes appear to reside on almost all of the genomic fragments, because they hybridize strongly to gene subfragments representing both 5' and 3' portions of the coding sequence as well as to 3' noncoding DNA that is found specifically associated with the coding region. A subgroup of about six of the fragments also shares homology within the 73 nucleotides immediately preceding the AUG codon. An intron-specific probe reveals only the EcoRI fragment from which it was derived and one other genomic fragment. On the basis of the temperature of complete dissociation of the coding region probe in 0.75 M NaCl/0.075 M Na3 citrate/50% (vol/vol) formamide, the 25 fragments are separable into three stringency classes of 40-50 degrees C, 50-55 degrees C, and 55-60 degrees C. The latter, high-stringency group of about seven fragments includes those cloned in the recombinant phage isolates, whose regions homologous to cytochrome c are shown to differ from the purified gene of known sequence by an amount equivalent to about 2% mismatched bases. Families of cytochrome c gene-related sequences are also found in the genomes of several other mammals, including humans.
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150
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Eden D, Matthew JB, Rosa JJ, Richards FM. Increase in apparent compressibility of cytochrome c upon oxidation. Proc Natl Acad Sci U S A 1982; 79:815-9. [PMID: 6278497 PMCID: PMC345843 DOI: 10.1073/pnas.79.3.815] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The apparent molal adiabatic compressibilities of ferri- and ferrocytochrome c have been determined from measurements of density and sound velocity. The values found were +2.99 X 10(-8) and -2.40 X 10(-8) cm5 mol-1 dyne-1 for the ferri and ferro forms, respectively. Experiments were performed on identical solutions containing either the oxidized or reduced form of protein. Solutions of ferricytochrome c were found to have significantly greater adiabatic compressibility than equivalent solutions of ferrocytochrome c at 25 degrees C and pH 7.15. The remarkable similarity of the three-dimensional structures of the ferri and ferro proteins [Takano, T. & Dickerson, R.E. (1980) Proc. Natl. Acad. Sci. USA 77, 6371-6375] strongly suggests that this difference in compressibility is due to an increase in volume fluctuations within ferricytochrome c relative to the ferro form rather than a change in equilibrium structure or hydration. Such a difference in the dynamic properties of the structures is consistent with both the crystallographic thermal B factors and the observed increase in amide hydrogen exchange kinetics when ferrocytochrome c is oxidized. The relative magnitude of the root mean square volume fluctuations is approximated from an ideal solution treatment of the compressibility data and yields a ratio of delta Vrms (ferri cyt c)/ delta Vrms (ferro cyt c) = 1.3.
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