201
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Brautigan DL, Ferguson-Miller S, Margoliash E. Mitochondrial cytochrome c: preparation and activity of native and chemically modified cytochromes c. Methods Enzymol 1978; 53:128-64. [PMID: 213675 DOI: 10.1016/s0076-6879(78)53021-8] [Citation(s) in RCA: 313] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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202
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Abstract
A search for derivatized amino acids in proteins has shown that the extent of posttranslational modification of proteins is quite substantial. While only 20 primary amino acids are specified in the genetic code and are involved as monomer building blocks in the assembly of the polypeptide chain, about 140 amino acids and amino acid derivatives have been identified as constituents of different proteins in different organisms. A brief consideration of the questions about where and when the derivatization reactions occur, how the specificity of the reactions is established, and how the posttranslational modifications can facilitate biological processes, reveal a need for more information on all these points. Answers to these questions should represent significant contributions to our understanding of biochemistry and cell biology.
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203
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Osheroff N, Feinberg B, Margoliash E, Morrison M. Lactoperoxidase-catalyzed iodination of horse cytochrome c:monoiodotyrosyl 74 cytochrome c. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)41031-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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204
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Roberts H, Hess B. Kinetics of cytochrome c oxidase from yeast. Membrane-facilitated electrostatic binding of cytochrone c showing a specific interaction with cytochrome c oxidase and inhibition by ATP. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 462:215-34. [PMID: 20949 DOI: 10.1016/0005-2728(77)90204-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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205
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206
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Moore GR, Pitt RC, Williams RJ. Nuclear-magnetic-resonance studies of Pseudomonas aeruginosa cytochrome c-551. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 77:53-60. [PMID: 198212 DOI: 10.1111/j.1432-1033.1977.tb11640.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy was used to study Pseudomonas aeruginosa cytochrome c-551. Assignments of resonances to specific residues have been made. A low-resolution X-ray structure was used to aid assignments. A structural comparison was made between P. aeruginosa cytochrome c-551 and mammalian cytochrome c, based on comparisons of NMR data.
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207
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Jones HP, Johnson JL, Rajagopalan KV. In vitro reconstitution of demolybdosulfite oxidase by molybdate. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)40150-5] [Citation(s) in RCA: 16] [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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208
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Slama JT, Willson CG, Grimshaw CE, Rapoport H. Stereochemistry of the porphyrin-protein bond of cytochrome c. Stereochemical comparison of Rhodospirillum rubrum, yeast, and horse heart porphyrins c. Biochemistry 1977; 16:1750-4. [PMID: 192273 DOI: 10.1021/bi00627a036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Porphyrins c have been obtained from Rhodospirillum rubrum cytochrome c2, yeast cytochrome c, and horse heart cytochrome c and compared using proton magnetic resonance and circular dichroism. Identity of the spectra establishes that chemically and stereochemically the three porphyrins c are identical. Since the stereochemistry of the porphyrin alpha-thioether linkage is not affected in the conversion to porphyrin c, the stereochemistry at the porphyrin alpha-thioether bonds among the corresponding cytochromes c also must be the same. Differences between the proton magnetic resonance of R. rubrum cytochrome c2 and horse heart cytochrome c which were rationalized by invoking an opposite stereochemistry at these condensation sites (Smith, G. M., and Kamen, M. D. (1974), Proc. Natl. Acad. Sci. U.S.A. 71, 4303) must therefore be attributed to other factors.
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209
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Butler J, De Kok J, De Weille JR, Koppenol WH, Braams R. Mechanism of the reaction of hydrated electrons with ferrocytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 459:207-15. [PMID: 13826 DOI: 10.1016/0005-2728(77)90022-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
1. The hydrated electron reacts with ferrocytochrome c to form an unstable intermediate. This intermediate decays in a first-order manner to give, in the first instance, a product which has a similar absorption spectrum in the range 400-610 nm as normal ferricytochrome c. 2. At 21 degrees C the rate constant for the reaction of hydrated electrons with ferrocytochrome c at pH 7.4 (2 mM phosphate buffer) is (3.0 +/- 0.3) = 10(10) M-1 - S-1. As the pH is increased above pH 8.0 the rate constant steadily decreases. The dependence of the rate constant on pH can be explained if ferrocytochrome c has a pK of around 9.2. 3. At 21 degrees C and pH 7.4, the rate constant for the decay of the intermediate is (1.40 +/- 0.15) - 10(5) S-1. This reaction shows no pH dependence in the range 6-2-11.0. 4. A mechanism is proposed whereby the central metal atom of the ferrocytochrome c is oxidased and a thioether bond is reduced. The resulting ferricytochrome c species then slowly develops an absorbance at 606 nm due to the attack of the sulfhydryl group on the haem.
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210
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Herskovits TT, Behrens CF, Siuta PB, Pandolfelli ER. Solvent denaturation of globular proteins: unfolding by the monoalkyl- and dialkyl-substituted formamides and ureas. BIOCHIMICA ET BIOPHYSICA ACTA 1977; 490:192-9. [PMID: 189823 DOI: 10.1016/0005-2795(77)90119-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The effects of the monoalkyl and dialkyl-substituted formamide series of denaturants on the native conformation of sperm whale myoglobin, horse heart cytochrome c, and Glycera dibranciata (single chain) hemoglobin have been investigated by spectral measurements in the Soret region (409 and 422 nm) and optical rotation measurements (265nm). The effectiveness of these two classes of protein denaturants is similar to the other straight-chain compounds of the urea, amide, and alcohol classes, examined in previous investigations from our laboratory. Their denaturing effectiveness is found to increase with increasing chain length or hydrocarbon content of the substituent alkyl groups. Application of the Peller and Flory equation to the denaturation data of the formamides shows that both the polar and the nonpolar group contributions to the protein-denaturant interactions have to be taken into account in order to correctly predict the observed denaturation midpoints. Additivity of the hydrophobic, KHø, and the polar, Kp, group contributions to the binding constants, KB = nKHø + Kp, with n = 1 or 2 for the mono- of the di-alkyl substituted denaturants gave best account of the experimental data. The KHø values used were based on free energy transfer data of various alkyl groups or the Scheraga-Nemethy theory of hydrophobic bonding. The assumption of group contributions of the denaturant to KB were also applied to the denaturation data of the unsubstituted amides and some examples of the monoalkyl and symmetrically substituted dialkyl ureas, taken from the literature.
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211
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Weathers PJ, Jost M, Lamport DT. The gas vacuole membrane of Microcystis aeruginosa. A partial amino acid sequence. Arch Biochem Biophys 1977; 178:226-44. [PMID: 402115 DOI: 10.1016/0003-9861(77)90188-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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212
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213
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Brautigan DL, Feinberg BA, Hoffman BM, Margoliash E, Preisach J, Blumberg WE. Multiple low spin forms of the cytochrome c ferrihemochrome. EPR spectra of various eukaryotic and prokaryotic cytochromes c. J Biol Chem 1977. [DOI: 10.1016/s0021-9258(17)32756-4] [Citation(s) in RCA: 176] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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214
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Goldkorn T, Schejter A. The redox potential of cytochrome c-552 from Euglena gracillis: a thermodynamic study. Arch Biochem Biophys 1976; 177:39-45. [PMID: 187126 DOI: 10.1016/0003-9861(76)90413-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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215
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Zitomer RS, Hall BD. Yeast cytochrome c messenger RNA. In vitro translation and specific immunoprecipitation of the CYC1 gene product. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(20)81862-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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216
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Looze Y, Polastro E, Gielens C, Léonis J. Iso-cytochrome c species from baker's yeast. Analysis of their circular-dichroism spectra. Biochem J 1976; 157:773-5. [PMID: 186031 PMCID: PMC1163921 DOI: 10.1042/bj1570773] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The circular-dichroism spectra of baker's-yeast iso-1- (methylated and unmethylated forms) and iso-2-cytochrome c species were examined between 200 and 600nm. In the visible region the yeast haemoproteins have characteristics nearly indistinguishable from those of horse heart cytochrome c. From the spectra in the u.v. region the latter appears, however, to be more helical. It is proposed that the likely element of non-helical structure in iso-1-cytochrome c is residues 62-70.
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217
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Johnson JL, Rajagopalan KV. Purification and properties of sulfite oxidase from human liver. J Clin Invest 1976; 58:543-50. [PMID: 956383 PMCID: PMC333211 DOI: 10.1172/jci108499] [Citation(s) in RCA: 92] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Sulfite oxidase has been purified to near homogeneity from human liver. Properties of the molecule have been investigated and compared to those of the rat liver enzyme which has been isolated in a pure form. Both proteins exist as dimeric molecules with one molybdenum and one cytochrome b5-type heme per sub-unit. The human enzyme has a slightly larger subunit molecular weight (61,100 vs. 57,200 daltons) and is a more negatively charged molecule. Decreased reactivity of the human enzyme with various electron acceptors suggests the presence of nonfunctional molybdenum centers in a portion of the molecules isolated. Human liver sulfite oxidase cross-reacts strongly with antibody prepared against the rat liver enzyme. Human enzyme activity is precipitated by antibody at concentrations about twofold greater than required for comparable complexation of rat sulfite oxidase.
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218
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Hurrell JG, Nicola NA, Broughton WJ, Dilworth MJ, Minasian E, Leach SJ. Comparative structural and immunochemical properties of leghaemoglobins. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 66:389-99. [PMID: 820557 DOI: 10.1111/j.1432-1033.1976.tb10528.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Circular dichroism studies on leghaemoglobins from snake bean, lupin, serradella and other plants show that, in common with soybean (reported earlier) they have a similar overall polypeptide chain conformation and haem environment and orientation. Immunochemical studies, on the other hand, suggest that the antigenic determinants on the surface of the leghaemoglobins vary considerably. Thus, firstly the alpha-helix content of the leghaemoglobins as a class is very similar (60-65%) and approaches that of the myoglobins, secondly, the sign, magnitude and shape of their circular dichroism spectra in the near ultraviolet, Soret and visible regions suggest close similarities in the environment and orientation of a structurally important tryptophan residue and of the haem moiety, and thirdly, there is comparatively weak haem-protein interaction. The extent of immuno cross-reactivity was found to be best deomonstrated using the Farr radioimmunoassay procedure. The results were (a) 5 leghaemoglobins from one plant (soybean) crossreacted completely but with varying affinities. (b) The extent of cross reactivity between leghaemoglobins from different plants was compared to that within a single plant; the reaction of antiserum to a soybean leghaemoglobin with a serradella leghaemoglobin was weak, with a snake bean leghaemoglobin still weaker (and incomplete) while lupin leghaemoglobins showed no cross reactivity at all. (c) The "rapid" attenuation of cross reactivity among different plant leghaemoglobins is explicable in terms of the extensive amino acid substitutions which have been demonstrated in the literature and in the present studies. (d) In view of this rapid divergence it is not surprising that sperm whale and horse heart myoglobins showed no cross reactivity with soybean leghaemoglobins. In summary, amino acid substitutions in the leghaemoglobin family are conformationally but not immunochemically conservative.
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219
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Nöll GG. Simultaneous measurements of optical and electrical properties of artificial membranes composed of mitochondrial lipids and their interaction with cytochrome c. J Membr Biol 1976; 27:335-46. [PMID: 184285 DOI: 10.1007/bf01869144] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A newly constructed cell, which allows simultaneous measurements of optical and electrical properties, was used to study bimolecular black membranes composed of beef heart mitochondrial lipids and their interaction with cytochrome c. The results show that these highly charged membranes are stable only in relatively limited ranges of boundary conditions. In 0.1 n KCl their maximum direct current (dc) resistance is 7 X 10(8) Ohm cm2 +/- 10%; the series capacity at 1 kHz is 0.43 muF/cm2 +/- 3%; the entire thickness, determined by optical reflectivity, is 5.8 +/- 0.2 nm. The interaction between oxidized cytochrome c and these lipid membranes is primarily of electrostatic nature, and dependent on the presence of highly charged phospholipids, such as diphosphatidyl glycerol (cardiolipin) and phosphatidyl ethanolamine. The attachment of cytochrome c maximally causes a 2.5-fold increase in reflectivity, without any noticeable change in the capacity. This leads to a subsequent instability of the membrane (i.e., rupture) preceded by a rapid increase of the dc conductivity. This behavior is far less pronounced with reduced cytochrome c.
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220
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Jortner J. Temperature dependent activation energy for electron transfer between biological molecules. J Chem Phys 1976. [DOI: 10.1063/1.432142] [Citation(s) in RCA: 1181] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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221
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222
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Kihara H, Saigo S, Nakatani H, Hiromi K, Ikeda-Saito M, Iizuka T. Kinetic study of isomerization of ferricytochrome c at alkaline pH. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 430:225-43. [PMID: 6059 DOI: 10.1016/0005-2728(76)90081-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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223
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Patel DJ, Canuel LL. Nuclear magnetic resonance studies of slowly exchanging peptide protons in cytochrome c in aqueous solution. Proc Natl Acad Sci U S A 1976; 73:1398-402. [PMID: 5721 PMCID: PMC430301 DOI: 10.1073/pnas.73.5.1398] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The slowly exchanging protons in oxidized and reduced horse heart cytochrome c (D20, uncorrected pH meter reading 6.5 room temperature) have been monitored by recording the 270 and 360 MHz proton nuclear magnetic resonance spectra of the reduced protein between 5 and 11 parts per million downfield from 2,2-dimethyl-2-silapentane-5-sulfonate.
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224
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Scher B, Dubnau. Purification and properties of a manganese-stimulated endonuclease from Bacillus subtilis. J Bacteriol 1976; 126:429-38. [PMID: 816779 PMCID: PMC233299 DOI: 10.1128/jb.126.1.429-438.1976] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
An endonuclease stimulated by manganese or calcium ions was isolated from Bacillus subtilis. This enzyme attacked double- or single-stranded deoxyribonucleic acid from a variety of sources, including B. subtilis, and was purified from the material released into the medium during protoplast formation. The enzyme appeared as a single peak after glycerol gradient centrifugation and comprised approximately 30 to 35% of the protein in the most purified preparations, as estimated by gel electrophoresis. It had a molecular weight of about 46,000. The mode of action of the enzyme was endonucleolytic, and circular deoxyribonucleic acid was readily cleaved. The enzyme introduced a limited number of both double- and single-strand breaks into native deoxyribonucleic acid, generally yielding products of 1 X 10(6) daltons or more in size. The reasons for this limitation of cleavage were not clear. The activity of the enzyme was inhibited by low levels of Cu2+, Co2+, Hg2+, and Zn2+. It was also inhibited by high concentrations of NaCl. A role for this enzyme in bacterial transormation is suggested.
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225
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Timkovich R, Dickerson RE, Margoliash E. Amino acid sequence of Paracoccus denitrificans cytochrome c550. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33573-1] [Citation(s) in RCA: 26] [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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226
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Abstract
Cytochrome c has been chemically modified by methylene blue mediated photooxidation. It is established that the methionine residues of the protein have been specifically converted to methionine sulfoxide residues. No oxidation of any other amino acid residues or the cysteine thioether bridges of the molecule occurs during the photooxidation reaction. The absorbance spectrum of methionine sulfoxide ferricytochrome c at neutrality is similar to that of the unmodified protein except for an increase in the extinction coefficient of the Soret absorbance band and for the complete loss of the ligand sensitive 695 nm absorbance band in the spectrum of the derivative. The protein remains in the low spin configuration which implies the retention of two strong field ligands. Spin state sensitive spectral titrations and model studies of heme peptides indicate that the sixth ligand is definitely not provided by a lysine residue but may be methionine-80 sulfoxide coordinated via its sulfur atom. Circular dichroism spectra indicate that the heme crevice of methionine sulfoxide ferri- and ferrocytochrome c is weakened relative to native cytochrome c. The redox potential of methionine sulfoxide cytochrome c is 184 mV which is markedly diminished from the 260 mV redox potential of native cytochrome c. The modified protein is equivalent to native cytochrome c as a substrate for cytochrome oxidase and is not autoxidizable at neutral pH but is virtually inactive with succinate-cytochrome c reductase. These results indicate that the major role of the methionine-80 in cytochrome c is to preserve a closed hydrophobic heme crevice which is essential for the maintainance of the necessary redox potential.
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227
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Pettigrew GW, Aviram I, Schejter A. The role of the lysines in the alkaline heme-linked ionization of ferric cytochrome c. Biochem Biophys Res Commun 1976; 68:807-13. [PMID: 4069 DOI: 10.1016/0006-291x(76)91217-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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228
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Ferguson-Miller S, Brautigan DL, Margoliash E. Correlation of the kinetics of electron transfer activity of various eukaryotic cytochromes c with binding to mitochondrial cytochrome c oxidase. J Biol Chem 1976. [DOI: 10.1016/s0021-9258(17)33807-3] [Citation(s) in RCA: 238] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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229
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230
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Moore G, Williams R. The substance of this review was given at the Harden Conference, England, 1974. Coord Chem Rev 1976. [DOI: 10.1016/s0010-8545(00)82055-x] [Citation(s) in RCA: 102] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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231
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Shafferman A, Stein G. Study of biochemical redox processes by the technique of pulse radiolysis. BIOCHIMICA ET BIOPHYSICA ACTA 1975; 416:287-317. [PMID: 172158 DOI: 10.1016/0304-4173(75)90002-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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232
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Watts GD, Burns A. The thermochemical characterization of sodium dithionite, flavin mononucleotide, flavin-adenine dinucleotide and methyl and benzyl viologens as low-potential reductants for biological systems. Biochem J 1975; 152:33-7. [PMID: 1212225 PMCID: PMC1172436 DOI: 10.1042/bj1520033] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The heat of reaction (deltaH) of Fe(CN)63-, Methyl Viologen, FMN and FAD with S2O42- in aqueous buffer solutions was measured calorimetrically. In addition deltaH values for reduction of Fe(CN)63-, FMN and FAD by reduced Methyl Viologen were determined. The resulting calorimetric data and corresponding E0 values were combined to yield thermodynamic data for these simple reducing agents in a form useful for applications to biological reactions. Thermodynamic data for the reduction of spinach ferredoxin are also presented.
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233
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Pal PK, Verma B, Myer YP. Conformational and functional studies of chemically modified cytochrome c: nitrated and iodinated cytochromes c. Biochemistry 1975; 14:4325-34. [PMID: 170959 DOI: 10.1021/bi00690a029] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The purification of iodinated (E. B. McGowan and E. Stellwagen (1970), Biochemistry 9, 3074) and of nitrated (M. Sokolovsky et al. (1970), Biochemistry 9, 5113) cytochromes c resulted in the recovery from the former preparation of diiododityrosyl-cytochrome c (DIDT-) with modification of Tyr-67 and Tyr-74, and, from the latter, a mononitromonotyrosyl-cytochrome c (MNMT-), with modification of Tyr-67, and mononitrodityrosyl-cytochrome c (MNDT-), with the added modification of Tyr-48. The three purified preparations were conformationally characterized using pH-spectroscopy, circular dichroism, thermal denaturation, reducibility with ascorbate, autoxidation with molecular oxygen, and binding with CO. These results are related to the two aspects of biological function, reducibility, measured by NADH-cytochrome c reductase, and oxidizability, with cytochrome c oxidase, as well as to structure-function relationships in the protein. MNMT-cytochrome c was found to be, structurally and conformationally, a single isomer, reducible with ascorbate, with a small, but definite affinity for both oxidation with molecular oxygen and binding of CO. Conformationally, in both valence states of the metal atom, it represents a molecular form with native-like conformation with small but definite perturbations in the immediate vicinity of the heme group, reflected by the destabilization of the Met-80-S-Fe linkage. MNMT-ferricytochrome c exhibits a pK of 6.2 for the transformation of the low-spin, native-like spectral form II containing the 695-nm band to form lacking lacking the 695-nm band. The isomerization at pK = 6.2, when analyzed in terms of the isomerization of the native protein with a pK of 9.2 and the nature of the group involved, indicates that Tyr-67 is not involved in the isomerization of the modified preparation, and possibly not in the native protein as well. In terms of biological function, the partial derangement of redecibility (24%) and the unaltered oxidizability point to the functional significance of Tyr-67, and provide another example of selectivity between the two aspects of physiological functional function, in agreement with the two-function, two-path operational model of the protein. The MNDT- and DIDT-ferricytochromes c exhibited physicochemical properties indicative of gross derangement of both the conformation of the protein as well as of the coordination configuration of the metal atom. The complete inability to accept an electron from NADH-cytochrome c reductase in both cases, and the retention of 50% of the oxidizability property of DIDT-cytochrome c, were interpreted to be the result of conformational derangement, rather than the added modification of Tyr-48 or of Tyr-74.
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234
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Power SD, Choucair A, Palmer G. Is lysine 79 a ligand for iron hexacyanides bound to cytochrome c? Biochem Biophys Res Commun 1975; 66:103-7. [PMID: 240356 DOI: 10.1016/s0006-291x(75)80300-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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235
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Warme PK, Scheraga HA. Conformational energy refinement of horse-heart ferricytochrome c. Biochemistry 1975; 14:3509-17. [PMID: 169878 DOI: 10.1021/bi00687a001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The reported X-ray structure of horse-heart ferricytochrome c has been refined by conformational energy calculations, using a three-stage computational procedure. In stage I, the atomic positions are adjusted to conform to idealized bond lengths and bond angles characteristic of small amino acid derivatives, while yet remaining as close as possible to the X-ray coordinates. In stage II, atomic overlaps are eliminated by adjusting the backbone and side-chain dihedral angles to minimize the nonbonded energy, hydrogen-bonded energy, and rotational energy contributions. In the final stage of refinement, the electrostatic energy and a more accurate hydrogen-bonded energy treatment are considered, in addition to the energy contributions of stage II. A "fitting potential" of gradually decreasing strength is imposed in both stages II and III, in order to keep the computed structure as similar to the x-ray structure as is consistent with a low-energy conformation. The final computed structure of cytochrome c exhibits a very low conformational energy (-504 kcal/mol) and also closely resembles the X-ray structure (RMS deviation = 0.77 A for all atoms). However, a special treatment was required in order to alter the location of the phenyl ring of phenylalanine-82. In contrast to the originally published X-ray structure, which shows the phenyl ring pointing away from the heme, the phenyl ring in the computed structure is tucked into the heme crevice, in a position similar to that observed in the reduced form of tuna cytochrome c, in the oxidized form of Rhodospirillum rubrum cytochrome c2, and also in the recently determined structure of oxidized tuna cytochrome c.
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236
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Warme PK. The influence of amino acid substitutions on the conformational energy of cytochrome c. Biochemistry 1975; 14:3518-26. [PMID: 169879 DOI: 10.1021/bi00687a002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Conformational energies have been evaluated for each of the staggered side-chain conformations associated with the 261 amino acid substitutions known to occur among 60 eucaryotic species. At least 86% of these substitutions can be sterically accommodated (one at a time) within the structure of horse-heart cytochrome c resulting from conformational energy refinement. Simultaneous incorporation of all pertinent amino acid substitutions found in eight representative species into the refined horse-heart structure is also shown to be sterically possible, with few exceptions. In two cases (Pekin duck cytochrome with 10 substitutions and Samia cynthia cytochrome with 24 substitutions), all substitutions could be readily incorporated, and the total energies associated with their computed structures differed by less than 10 kcal/mol from that of horse-heart cytochrome c. In the cytochromes from rattlesnake (22 substitutions), tuna (18 substitutions), and Neurospora crassa (36 substitutions), tyrosine could not be substituted for phenylalanine at position 46, within the constraints of the calculations. However, when all of the remaining substitutions were incorporated into these three cytochromes, their computed conformational energies differed by less than 30 kcal/mol from that of horse-heart cytochrome c. Between two and four amino acid substitutions cause high energies in the cytochromes from human, baker's yeast, and cotton seed, but all of the remaining substitutions are consistent with a low energy conformation. These results suggest that the structures of homologous proteins may be even more similar than has previously been recognized. Substitutions of all possible amino acid types at the invariant positions (where all eucaryotic cytochromes c bear the same amino acid) have revealed some cases where different amino acids can be accommodated, thus demonstrating that the biological constraints on amino acid substitutions are often different from the purely steric constraints investigated in this work.
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237
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Schejter A, Aviram I, Margalit R, Goldkorn T. Ligand-binding reactions and oxidation-reduction equilibria of cytochrome c. Ann N Y Acad Sci 1975; 244:51-9. [PMID: 166594 DOI: 10.1111/j.1749-6632.1975.tb41521.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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238
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Tsong TY. An acid induced conformational transition of denatured cytochrome c in urea and guanidine hydrochloride solutions. Biochemistry 1975; 14:1542-7. [PMID: 235957 DOI: 10.1021/bi00678a031] [Citation(s) in RCA: 90] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Previous work has shown that at neutral pH ferricytochrome c (horse heart) retains certain residual structures in concentrated solutions of urea or guanidine hydrochloride (Tsong, T. Y. (1974), J. Biol. Chem. 249, 1988). Present studies reveal that cooperative unfolding of these residual structures can be achieved by acidification of the protein to pH 4 in 9 M urea but can only be partially achieved in a 6 M guanidine hydrochloride solution. The evidence that the residual structures unfold in 9 M urea upon acidification is twofold. (1) Further uncoupling of the Trp-59-heme interaction occurs; this is reflected in the intensification of the tryptophan fluorescence from 55 to 90 percent relative to that of free tryptophan in the same solvent. (2) The intrinsic viscosity of the protein solution increases from 15.0 to 21 ml/g. The acidification also induces a spin-state transformation of the heme group at pH 5 both in urea and in guanidine hydrochloride. Acidic titration of the protein in urea and guanidine hydrochloride indicates that the unfolding involves the absorption of a single proton. However, the kinetics of the spin-state transformation are triphasic. These results suggest that the displacement of the ligand His-18 by a solvent molecule and the subsequent disintegration of the residual structures are complex processes and involve at least three kinetic steps. The ineffectiveness of guanidine hydrochloride as a denaturant for ferricytochrome c is shown to be due to the presence of the high concentration of Cl minus which can stabilize certain elements of the protein structure.
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239
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Subramanian AR, Nehls E. Acetylase of ribosomal protein L12: constant level of activity during the growth cycle. FEBS Lett 1975; 52:103-6. [PMID: 1091514 DOI: 10.1016/0014-5793(75)80648-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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240
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Dobson CM, Moore GR, Williams RJ. Assignment of aromatic amino acid PMR resonances of horse ferricytochrome c. FEBS Lett 1975; 51:60-5. [PMID: 235463 DOI: 10.1016/0014-5793(75)80854-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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241
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Yu L, Chiang YL, Yu CA, King TE. A trypsin-resistant heme peptide from cardiac cytochrome c1. BIOCHIMICA ET BIOPHYSICA ACTA 1975; 379:33-42. [PMID: 235990 DOI: 10.1016/0005-2795(75)90006-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A tryptic resistant heme peptide has been prepared and purified from cardiac cytochrome c1. This purified peptide is not further hydrolyzed by reactions of other proteolytic enzymes, such as pronase. The peptide contains 2 residues each of serine, cysteine and valine, and 1 residue each of alanine, methionine, tyrosine, histidine, arginine, proline, glutamic acid (glutamine) and aspartic acid. The intensity of the absorption spectrum of the peptide has been found to be dependent upon, but the positions of the absorption maxima do not vary with, concentration. The heme peptide does not show multiple splitting of absorption peaks at liquid N2 temperatures as does the intact cytochrome C1. However, cyanide rapidly reacts with the peptide and causes significant spectral changes. CD spectra of the peptide exhibit a typical profile of a non-structured heme peptide with positive CD bands in the Soret region and around 250 nm, and a broad negative extreme of 320-360 nm. The similarities and differences between the tryptic resistant heme peptides from cytochromes c1 and c have been compared.
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242
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243
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Kirschenbaum DM. A compilation of amino acid analyses of proteins VI residues per molecule. IV. Anal Biochem 1974; 61:567-609. [PMID: 4608596 DOI: 10.1016/0003-2697(74)90425-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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244
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Lichtin NN, Shafferman A, Stein G. Reduction of ferricytochrome c by hydrogen atoms: evidence for intramolecular transfer of reducing equivalent. BIOCHIMICA ET BIOPHYSICA ACTA 1974; 357:386-98. [PMID: 4370322 DOI: 10.1016/0005-2728(74)90029-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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245
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Mims WB, Peisach J. Linear electric field effect measurements of variant low-spin forms of ferric cytochrome c. Biochemistry 1974; 13:3346-9. [PMID: 4366473 DOI: 10.1021/bi00713a026] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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246
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Dupré S, Brunori M, Wilson MT, Greenwood C. Kinetics of carbon monoxide binding and electron transfer by cytochrome c polymers. Biochem J 1974; 141:299-304. [PMID: 4375972 PMCID: PMC1168077 DOI: 10.1042/bj1410299] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Studies on horse heart cytochrome c polymers were carried out by stopped-flow and photolysis techniques, to investigate the properties of the CO complex and the kinetics of electron transfer, mainly of the dimeric and tetrameric forms. CO binding, which does not occur with native monomers, proceeds at both pH7.0 and pH9.6, and appears to follow complex kinetics: an initial phase is observed, which is CO-concentration-dependent, followed by a very slow monomolecular phase (k~2x10(-3)s(-1) at pH7) before establishment of equilibrium. Photodissociation of the CO complex has a very low quantum yield, probably less than 0.1. Static titration data of the dimer gave an ;n' value of 0.4. These data strongly suggest heterogeneity of the population of binding sites, and have been interpreted in terms of the existence of different structures, probably owing to the non-unique type of binding of monomers during polymerization. Polymers of cytochrome c carboxymethylated on the methionine residue normally ligated to iron show simple CO recombination kinetics after photolytic removal (k(on)=1.5x10(6)m(-1).s(-1) at pH6). We therefore suggest that, for native cytochrome c, polymerization has an effect on the lability of the haem crevice, rendering the iron available for binding ligands, without, however, forming the structure of a truly open crevice. Electron transfer is, on the other hand, a simple process, and no gross differences are observed between monomer and polymers. A simple model, taking into account all these data, is suggested.
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247
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Vinogradov SN, Bitar KG, Lowenkron S. Haem ligands of the ferricytochrome c of Ustilago sphaerogena. Biochem J 1974; 139:547-53. [PMID: 4368759 PMCID: PMC1166319 DOI: 10.1042/bj1390547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The mammalian-type cytochrome c of the basidiomycete Ustilago sphaerogena contains in a single polypeptide chain of 107 residues, two histidine residues located at positions 18 and 33, and one methionine residue situated at position 80 (Bitar et al., 1972). The reaction of Ustilago ferricytochrome c with bromoacetate at neutral pH resulted in the modification of histidine-33, but not of histidine-18 or of the invariant methionine residue. The activities of Ustilago cytochrome c with mitochondrial cytochrome c oxidase and with NADH-cytochrome c reductase were unaltered by the modification. The equilibrium constants for the formation of low-spin complexes of the ferrihaem octapeptide of horse cytochrome c (residues 14-21, including the haem bound covalently to cysteines 14 and 17) with imidazole, N(2)-acetylhistidine and monocarboxymethyl derivatives of N(2)-acetylhistidine were determined spectrophotometrically. Alkylation of the imidazole side-chain group of N(2)-acetylhistidine resulted in a marked decrease in its ability to form low-spin ferrihaem complexes. These results indicate that in Ustilago ferricytochrome c in solution histidine-33 is not involved in the central co-ordination complex. Since side-chain groups of residues other than histidine and methionine do not appear to be involved in the central complexes of other mammalian-type cytochromes c (Hettinger & Harbury, 1964, 1965; Myer & Harbury, 1965) it is likely that in Ustilago ferricytochrome c in solution at neutral pH, the side-chain groups of histidine-18 and methionine-80 are involved in the central co-ordination complex. The latter is stable over the pH range 2.6-8.4.
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248
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Grimes CJ, Piszkiewicz D, Fleischer EB. Electron transfer reactions in biological systems: the reduction of ferricytochrome c by chromous ions. Proc Natl Acad Sci U S A 1974; 71:1408-12. [PMID: 4364536 PMCID: PMC388238 DOI: 10.1073/pnas.71.4.1408] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Chromous ion reacts with ferricytochrome c to yield a one-to-one Cr(III)-ferrocytochrome c complex. This material, when hydrolyzed by trypsin and subjected to chromatographic procedures, yielded two fragments containing chromium. The amino-acid compositions and chemical characteristics of each of these fragments indicated that the chromium had crosslinked two segments of polypeptide chain; these were residues 40-53-Cr(III)-residues 61-72 and residues 40-53-Cr(III)-residues 61-73. Examination of a model of the ferricytochrome c molecule indicated that only two residues of the crosslinked peptides were sufficiently close to allow crosslinking to take place. These residues were tyrosine 67 and asparagine 52. Enzymatic hydrolysis of one of those fragments by aminopeptidase M supported this identification. The position of the chromic ion implies what is the path of electron transfer from the chromous ion to the ferric ion in this chemical reduction of cytochrome c, and suggests a possible path of electron transfer in biological oxidation-reduction reactions.
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