1
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Deng Y, Carnevale V, Ditchfield R, Pletneva EV. Applications of the Newly Developed Force-Field Parameters Uncover a Dynamic Nature of Ω-Loop C in the Lys-Ligated Alkaline Form of Cytochrome c. J Phys Chem B 2024; 128:5935-5949. [PMID: 38864552 DOI: 10.1021/acs.jpcb.4c00625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Lys-ligated cytochromes make up an emerging family of heme proteins. Density functional theory calculations on the amine/imidazole-ligated c-type ferric heme were employed to develop force-field parameters for molecular dynamics (MD) simulations of structural and dynamic features of these proteins. The new force-field parameters were applied to the alkaline form of yeast iso-1 cytochrome c to rationalize discrepancies resulting from distinct experimental conditions in prior structural studies and to provide insights into the mechanisms of the alkaline transition. Our simulations have revealed the dynamic nature of Ω-loop C in the Lys-ligated protein and its unfolding in the Lys-ligated conformer having this loop in the same position as in the native Met-ligated protein. The proximity of Tyr67 or Tyr74 to the Lys ligand of ferric heme iron suggests a possible mechanism of the backward alkaline transition where a proton donor Tyr assists in Lys dissociation. The developed force-field parameters will be useful in structural and dynamic characterization of other native or engineered Lys-ligated heme proteins.
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Affiliation(s)
- Yunling Deng
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Vincenzo Carnevale
- Institute for Genomics and Evolutionary Medicine, Institute for Computational Molecular Science, and Department of Biology, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Robert Ditchfield
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Ekaterina V Pletneva
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
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2
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Comparison of the structural dynamic and mitochondrial electron-transfer properties of the proapoptotic human cytochrome c variants, G41S, Y48H and A51V. J Inorg Biochem 2020; 203:110924. [DOI: 10.1016/j.jinorgbio.2019.110924] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 01/02/2023]
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3
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Deacon OM, Svistunenko DA, Moore GR, Wilson MT, Worrall JA. Naturally Occurring Disease-Related Mutations in the 40–57 Ω-Loop of Human Cytochrome c Control Triggering of the Alkaline Isomerization. Biochemistry 2018; 57:4276-4288. [DOI: 10.1021/acs.biochem.8b00520] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Oliver M. Deacon
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Dimitri A. Svistunenko
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Geoffrey R. Moore
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Michael T. Wilson
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
| | - Jonathan A.R. Worrall
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, U.K
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4
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Lei H, Bowler BE. Humanlike substitutions to Ω-loop D of yeast iso-1-cytochrome c only modestly affect dynamics and peroxidase activity. J Inorg Biochem 2018. [PMID: 29530594 DOI: 10.1016/j.jinorgbio.2018.02.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Structural studies of yeast iso-1-cytochrome c (L.J. McClelland, T.-C. Mou, M.E. Jeakins-Cooley, S.R. Sprang, B.E. Bowler, Proc. Natl. Acad. Sci. U.S.A. 111 (2014) 6648-6653) show that modest movement of Ω-loop D (residues 70-85, average RMSD versus the native structure: 0.81 Å) permits loss of Met80-heme ligation creating an available coordination site to catalyze the peroxidase activity mediated by cytochrome c early in apoptosis. However, Ala81 and Gly83 move significantly (RMSDs of 2.18 and 1.26 Å, respectively). Ala81 and Gly83 evolve to Ile and Val, respectively, in human cytochrome c and peroxidase activity decreases 25-fold relative to the yeast protein at pH 7. To test the hypothesis that these residues evolved to restrict the peroxidase activity of cytochrome c, A81I and G83V variants of yeast iso-1-cytochrome c were prepared. For both variants, the apparent pKa of the alkaline transition increases by 0.2 to 0.3 relative to the wild type (WT) protein and the rate of opening the heme crevice is slowed. The cooperativity of acid unfolding is decreased for the G83V variant. At pH 7 and 8, the catalytic rate constant, kcat, for the peroxidase activity of both variants decreases relative to WT, consistent with the effects on alkaline isomerization. Below pH 7, the loss in the cooperativity of acid unfolding causes kcat for peroxidase activity to increase for the G83V variant relative to WT. Neither variant decreases kcat to the level of the human protein, indicating that other residues also contribute to the low peroxidase activity of human cytochrome c.
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Affiliation(s)
- Haotian Lei
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, United States.
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5
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Alvarez-Paggi D, Hannibal L, Castro MA, Oviedo-Rouco S, Demicheli V, Tórtora V, Tomasina F, Radi R, Murgida DH. Multifunctional Cytochrome c: Learning New Tricks from an Old Dog. Chem Rev 2017; 117:13382-13460. [DOI: 10.1021/acs.chemrev.7b00257] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Damián Alvarez-Paggi
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Luciana Hannibal
- Department
of Pediatrics, Universitätsklinikum Freiburg, Mathildenstrasse 1, Freiburg 79106, Germany
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - María A. Castro
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Santiago Oviedo-Rouco
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
| | - Veronica Demicheli
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Veronica Tórtora
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Florencia Tomasina
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Rafael Radi
- Departamento
de Bioquímica and Center for Free Radical and Biomedical Research,
Facultad de Medicina, Universidad de la República, Av.
Gral. Flores 2125, Montevideo 11800, Uruguay
| | - Daniel H. Murgida
- Departamento
de Química Inorgánica, Analítica y Química
Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas
y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires C1428EHA, Argentina
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6
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Nold SM, Lei H, Mou TC, Bowler BE. Effect of a K72A Mutation on the Structure, Stability, Dynamics, and Peroxidase Activity of Human Cytochrome c. Biochemistry 2017; 56:3358-3368. [PMID: 28598148 PMCID: PMC5564420 DOI: 10.1021/acs.biochem.7b00342] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We test the hypothesis that Lys72 suppresses the intrinsic peroxidase activity of human cytochrome c, as observed previously for yeast iso-1-cytochrome c [McClelland, L. J., et al. (2014) Proc. Natl. Acad. Sci. U. S. A. 111, 6648-6653]. A 1.25 Å X-ray structure of K72A human cytochrome c shows that the mutation minimally affects structure. Guanidine hydrochloride denaturation demonstrates that the K72A mutation increases global stability by 0.5 kcal/mol. The K72A mutation also increases the apparent pKa of the alkaline transition, a measure of the stability of the heme crevice, by 0.5 unit. Consistent with the increase in the apparent pKa, the rate of formation of the dominant alkaline conformer decreases, and this conformer is no longer stabilized by proline isomerization. Peroxidase activity measurements show that the K72A mutation increases kcat by 1.6-4-fold at pH 7-10, an effect larger than that seen for the yeast protein. X-ray structures of wild type and K72A human cytochrome c indicate that direct interactions of Lys72 with the far side of Ω-loop D, which are seen in X-ray structures of horse and yeast cytochrome c and could suppress peroxidase activity, are lacking. Instead, we propose that the stronger effect of the K72A mutation on the peroxidase activity of human versus yeast cytochrome c results from relief of steric interactions between the side chains at positions 72 and 81 (Ile in human vs Ala in yeast), which suppress the dynamics of Ω-loop D necessary for the intrinsic peroxidase activity of cytochrome c.
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Affiliation(s)
- Shiloh M. Nold
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812
- Center for Bimolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
| | - Haotian Lei
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812
- Center for Bimolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
| | - Tung-Chung Mou
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
- Center for Bimolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
| | - Bruce E. Bowler
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812
- Center for Bimolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
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7
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Bandi S, Bowler BE. Effect of an Ala81His mutation on the Met80 loop dynamics of iso-1-cytochrome c. Biochemistry 2015; 54:1729-42. [PMID: 25671560 PMCID: PMC5065065 DOI: 10.1021/bi501252z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An A81H variant of yeast iso-1-cytochrome c is prepared to test the hypothesis that the steric size of the amino acid at sequence position 81 of cytochrome c, which has evolved from Ala in yeast to Ile in mammals, slows the dynamics of the opening of the heme crevice. The A81H mutation is used both to increase steric size and to provide a probe of the dynamics of the heme crevice through measurement of the thermodynamics and kinetics of the His81-mediated alkaline conformational transition of A81H iso-1-cytochrome c. Thermodynamic measurements show that the native conformer is more stable than the His81-heme alkaline conformer for A81H iso-1-cytochrome c. ΔGu°(H2O) is approximately 1.9 kcal/mol for formation of the His81-heme alkaline conformer. By contrast, for K79H iso-1-cytochrome c, the native conformer is less stable than the His79-heme alkaline conformer. ΔGu°(H2O) is approximately -0.34 kcal/mol for formation of the His79-heme alkaline conformer. pH jump and gated electron transfer kinetics demonstrate that this stabilization of the native conformer in A81H iso-1-cytochrome c arises primarily from a decrease in the rate constant for formation of the His81-heme alkaline conformer, kf,His81, relative to kf,His79 for formation of the His79-heme alkaline conformer, which forms by a mechanism similar to that observed for the His81-heme alkaline conformer. The result is discussed in terms of the effect of global protein stability on protein dynamics and in terms of optimization of the sequence of cytochrome c for its role as a peroxidase in the early stages of apoptosis in higher eukaryotes.
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Affiliation(s)
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812
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8
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Weinkam P, Zimmermann J, Sagle LB, Matsuda S, Dawson PE, Wolynes PG, Romesberg FE. Characterization of alkaline transitions in ferricytochrome c using carbon-deuterium infrared probes. Biochemistry 2009; 47:13470-80. [PMID: 19035653 DOI: 10.1021/bi801223n] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The alkaline-induced structural transitions of ferricytochrome c have been studied intensively as a model for how changes in metal ligation contribute to protein function and folding. Previous studies have demonstrated that multiple non-native species accumulate with increasing pH. Here, we used a combination of experiments and simulations to provide a high-resolution view of the changes associated with increasing alkaline conditions. Alkaline-induced transitions were characterized under equilibrium conditions by following changes in the IR absorptions of carbon-deuterium chromophores incorporated at Leu68, Lys72, Lys73, Lys79, and Met80. The data suggest that at least four intermediates are formed as the pH is increased prior to complete unfolding of the protein. The first alkaline transition observed appears to be driven by a single deprotonation and occurs with a midpoint of pH 8.8, but surprisingly, the intermediate formed does not appear to be one of the well-characterized lysine misligates. At higher pH, second and third deprotonations, with a combined apparent midpoint pH of 10.2, induce transitions to Lys73- or Lys79-misligated species. Interestingly, the lysine misligates appear to undergo iron reduction by the coordinated amine. A transition from the lysine misligates to another intermediate, likely a hydroxide-misligated species, is associated with a fourth deprotonation and a midpoint of pH 10.7. Finally, the protein loses tertiary structure with a fifth deprotonation that occurs with a midpoint of pH 12.7. Native topology-based models with enforced misligation are employed to help understand the structures of the observed intermediates.
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Affiliation(s)
- Patrick Weinkam
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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9
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Abstract
In this paper, we have described a stopped-flow apparatus that is capable of measuring infrared kinetics in the amide I' region of a protein's vibrational spectrum. The dead time of this setup, determined by the reducing reaction of 2,6-Dichlorophenolindophenol by L-ascorbic acid, is between 6 to 15 ms, depending on the flow rate. Therefore, this stopped-flow IR method provides a means of measuring infrared kinetics in a time window that is not easily accessible to other mixing-based IR techniques. Using this apparatus, we have studied the alkaline transition of cytrochrome c and have found that this conformational event proceeds in a biphasic manner. The characteristic time constants of these two phases were determined to be 68 +/- 20 ms and 624 +/- 37 ms, respectively.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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10
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Martinez RE, Bowler BE. Proton-mediated dynamics of the alkaline conformational transition of yeast iso-1-cytochrome c. J Am Chem Soc 2004; 126:6751-8. [PMID: 15161303 DOI: 10.1021/ja0494454] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The kinetics of the alkaline conformational transition of a Lys 73-->His variant of iso-1-cytochrome c have been investigated using pH jump stopped-flow methods to probe the nature of the ionizable "trigger" group for this conformational change. This mutation moves the pK(a) of the ligand replacing Met 80 from about 10.5 to approximately 6.6 and has unmasked two other ionizable groups, besides the ligand replacing Met 80, that modulate the kinetics of this process. The results are discussed in terms of the impact of ionization equilibria on protein folding mechanisms.
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Affiliation(s)
- Robert E Martinez
- Department of Chemistry and Biochemistry, University of Denver, 2190 East Iliff Avenue, Denver, Colorado 80208-2436, USA
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11
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Hoang L, Maity H, Krishna MMG, Lin Y, Englander SW. Folding units govern the cytochrome c alkaline transition. J Mol Biol 2003; 331:37-43. [PMID: 12875834 DOI: 10.1016/s0022-2836(03)00698-3] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The alkaline transition of cytochrome c is a model for protein structural switching in which the normal heme ligand is replaced by another group. Stopped flow data following a jump to high pH detect two slow kinetic phases, suggesting two rate-limiting structure changes. Results described here indicate that these events are controlled by the same structural unfolding reactions that account for the first two steps in the reversible unfolding pathway of cytochrome c. These and other results show that the cooperative folding-unfolding behavior of protein foldons can account for a variety of functional activities in addition to determining folding pathways.
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Affiliation(s)
- Linh Hoang
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6059, USA.
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12
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Rosell FI, Harris TR, Hildebrand DP, Döpner S, Hildebrandt P, Mauk AG. Characterization of an alkaline transition intermediate stabilized in the Phe82Trp variant of yeast iso-1-cytochrome c. Biochemistry 2000; 39:9047-54. [PMID: 10913318 DOI: 10.1021/bi001095k] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In general, mutation of the phylogenetically conserved residue Phe82 in yeast iso-1-cytochrome c destabilizes the native conformation of the protein by facilitating the ligand exchange reactions that are associated with the alkaline conformational transitions of the ferricytochrome. Of the Phe82 variants surveyed thus far, Phe82Trp is unique in that it adopts a thermodynamically stable, high-spin conformation at mildly alkaline pH. This species exhibits spectroscopic features that can only be detected transiently in other ferricytochromes c within the first 100 ms immediately after a pH-jump from neutrality to pH >10. Spectroscopic characterization of this high-spin reaction intermediate suggests that in addition to an obligatory pentacoordinate heme iron, a group within the heme pocket coordinates the heme iron but is then replaced either by Met80, to revert to the native conformation, or by Lys73 or Lys79, to yield one of the conventional alkaline conformers. Evidence is presented to suggest that this group is either a hydroxide ion or Tyr67 rather than a loosely bound Met80.
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Affiliation(s)
- F I Rosell
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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13
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Niu J, Guo Y, Dong S. The direct electrochemistry of cryo-hydrogel immobilized myoglobin at a glassy carbon electrode. J Electroanal Chem (Lausanne) 1995. [DOI: 10.1016/0022-0728(95)04083-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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14
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Bloemendal M, Johnson WC. Structural information on proteins from circular dichroism spectroscopy possibilities and limitations. PHARMACEUTICAL BIOTECHNOLOGY 1995; 7:65-100. [PMID: 8564023 DOI: 10.1007/978-1-4899-1079-0_2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- M Bloemendal
- Department of Protein and Molecular Biology, Royal Free Hospital School of Medicine, London, England
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15
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Blanchard L, Marion D, Pollock B, Voordouw G, Wall J, Bruschi M, Guerlesquin F. Overexpression of Desulfovibrio vulgaris Hildenborough cytochrome c553 in Desulfovibrio desulfuricans G200. Evidence of conformational heterogeneity in the oxidized protein by NMR. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 218:293-301. [PMID: 8269917 DOI: 10.1111/j.1432-1033.1993.tb18377.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Plasmid pRC41, containing the cyf gene encoding cytochrome c533 from Desulfovibrio vulgaris Hildenborough, was transferred by conjugation from Escherichia coli to Desulfovibrio desulfuricans G200. The structural properties of the purified protein were studied by one-dimensional and two-dimensional NMR. A heterogeneity in the folding of the cytochrome isolated from D. vulgaris Hildenborough and from D. desulfuricans G200 was observed for the oxidized from. Temperature, pH and salt-dependence studies indicated that the heterogeneity does not result from an intermediate in the protein unfolding process, but derives from two conformations which are not in dynamic equilibrium.
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Affiliation(s)
- L Blanchard
- Laboratoire de Chimie Bactérienne, CNRS, Marseille, France
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16
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Hasumi H, Ohmori D. Studies on the molecular structure of spinach ferredoxin. II. Effects of urea and sodium chloride. ACTA ACUST UNITED AC 1989. [DOI: 10.1016/0167-4838(89)90244-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Abstract
The pH-induced isomerization of horse heart cytochrome c has been studied by 1H NMR. We find that the transition occurring in D2O with a pKa measured as 9.5 +/- 0.1 is from the native species to a mixture of two basic forms which have very similar NMR spectra. The heme methyl peaks of these two forms have been assigned by 2D exchange NMR. The forward rate constant (native to alkaline cytochrome c) has a value of 4.0 +/- 0.6 s-1 at 27 degrees C and is independent of pH; the reverse rate constant is pH-dependent. The activation parameters are delta H not equal to = 12.8 +/- 0.8 kcal.mol1, delta S not equal to = -12.9 +/- 2.0 e.u. for the forward reaction and delta H not equal to = 6.0 +/- 0.3 kcal.mol-1, delta S not equal to = -35.1 +/- 1.3 e.u. for the reverse reaction (pH* = 9.28). delta H degree and delta S degree for the isomerization are 6.7 +/- 0.6 kcal.mol-1 and 21.9 +/- 1.0 e.u., respectively.
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Affiliation(s)
- X L Hong
- Department of Chemistry and Laboratory, Georgia State University, Atlanta 30303
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18
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19
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Takeda K, Takahashi K, Batra PP. Kinetic aspects of the interaction of horse heart cytochrome c with sodium dodecyl sulfate. Arch Biochem Biophys 1985; 236:411-7. [PMID: 2981509 DOI: 10.1016/0003-9861(85)90641-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The sodium dodecyl sulfate (SDS) concentration dependence of spectral changes in circular dichroism (CD) and in absorbance of cytochrome c were examined in the far-ultraviolet region, aromatic region, and the Soret band. The Soret peak obtained in 0.60 mM SDS was nine times greater than that of the native state. (The critical micelle concentration, CMC, of SDS was 2.2 mM in the phosphate buffer used.) The results indicated that the drastic change at the Soret band did not accompany the corresponding large-scale change in secondary structure of the protein. In the stopped-flow measurements, two and three processes were followed at 406 nm below and above the CMC, respectively. At 289 nm only one process was observed, and this corresponded to the second process at 406 nm. Therefore, the second process at 406 nm was considered to be a change in tertiary structure around the heme group. The first process and the third process seemed to reflect a change in the heme environment; the former appeared to be due to a solvent effect and the latter due to a binding effect of a large number of dodecyl sulfate ions.
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20
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Postnikova GB, Gorbunova NP, Volkenstein MV. A spin label study of conformational changes in cytochrome c. Biophys Chem 1983; 17:193-202. [PMID: 6305439 DOI: 10.1016/0301-4622(83)87004-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Spin-labeled pig heart cytochromes c singly modified at Met-65, Tyr-74 and at one of the lysine residues, Lys-72 or Lys-73, were investigated by the ESR method under conditions of different ligand and redox states of the heme and at various pH values. Replacement of Met-80 by the external ligand, cyanide, was shown to produce a sharp increase in the mobility of all the three bound labels while reduction of the spin-labeled ferricytochromes c did not cause any marked changes in their ESR spectra. In the pH range 6-13, two conformational transitions in ferricytochrome c were observed which preceded its alkaline denaturation: the first with pK 9.3 registered by the spin label at the Met-65 position, and the second with pK 11.1 registered by the labels bound to Tyr-74 and Lys-72(73). The conformational changes in the 'left-hand part' of ferricytochrome c are most probably induced in both cases by the exchange of internal protein ligands at the sixth coordination site of the heme.
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21
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22
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23
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Dyson HJ, Beattie JK. Spin state and unfolding equilibria of ferricytochrome c in acidic solutions. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34916-0] [Citation(s) in RCA: 85] [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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24
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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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