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Marantz Y, Nachliel E. Gauging of CytochromecStructural Fluctuation by Time-Resolved Proton Pulse. Isr J Chem 2013. [DOI: 10.1002/ijch.199900049] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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2
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Tang WX, Concar D, Moore GR, Williams RJP. NMR double resonance study of azide binding to cytochrome c. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.19920100108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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3
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Ma D, Lu J, Tang W. 1H NMR studies of azide binding to cytochrome c. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1384:32-42. [PMID: 9602041 DOI: 10.1016/s0167-4838(97)00210-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The binding of azide ion to the heme iron of ferricytochrome c in D2O is studied using 1H NMR methods at pH 7.0 and 300 K or 315 K. Some hyperfine shifted resonances arising from heme peripheral protons and resonances of side-chain protons of some amino acid residues in N3-cyt c have been assigned using 2D EXSY and DQF-COSY methods. The majority of the heme pocket side-chain proton signals have been identified. The 1D nuclear overhauser effect (NOE) difference spectra and 2D NOESY spectrum are presented and changes in NOE patterns between the heme and certain residues, and several residues around the axial ligand are interpreted in terms of changes in the pocket structure. Interpretation of NOE data indicates that conformation changes are obvious on the Met80 side of the heme cavity in the environment of the axial ligand in N3-cyt c. In addition, kinetics analysis of azide binding to cyt c is studied using 2D EXSY method.
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Affiliation(s)
- D Ma
- State Key Laboratory of Coordination Chemistry, Coordination Chemistry Institute, Nanjing University, China
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4
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Sukits SF, Satterlee JD. Assignment of 1H and 13C hyperfine-shifted resonances for tuna ferricytochrome c. Biophys J 1996; 71:2848-56. [PMID: 8913622 PMCID: PMC1233771 DOI: 10.1016/s0006-3495(96)79481-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Tuna ferricytochrome c has been used to demonstrate the potential for completely assigning 1H and 13C strongly hyperfine-shifted resonances in metalloprotein paramagnetic centers. This was done by implementation of standard two-dimensional NMR experiments adapted to take advantage of the enhanced relaxation rates of strongly hyperfine-shifted nuclei. The results show that complete proton assignments of the heme and axial ligands can be achieved, and that assignments of several strongly shifted protons from amino acids located close to the heme can also be made. Virtually all proton-bearing heme 13C resonances have been located, and additional 13C resonances from heme vicinity amino acids are also identified. These results represent an improvement over previous proton resonance assignment efforts that were predicated on the knowledge of specific assignments in the diamagnetic protein and relied on magnetization transfer experiments in heterogeneous solutions composed of mixtures of diamagnetic ferrocytochrome c and paramagnetic ferricytochrome c. Even with that more complicated procedure, complete heme proton assignments for ferricytochrome c have never been demonstrated by a single laboratory. The results presented here were achieved using a more generally applicable strategy with a solution of the uniformly oxidized protein, thereby eliminating the requirement of fast electron self-exchange, which is a condition that is frequently not met.
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Affiliation(s)
- S F Sukits
- Department of Chemistry, Washington State University, Pullman 99164-4630, USA
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5
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Morelle N, Simorre JP, Caffrey M, Meyer T, Cusanovich M, Marion D. 1H and 13C NMR assignment and secondary structure of Chlorobium limicola f. thiosulfatophilum ferrocytochrome c555. FEBS Lett 1995; 365:172-8. [PMID: 7781774 DOI: 10.1016/0014-5793(95)00450-n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The 1H resonances of the ferrocytochrome c555 from the anaerobic green sulfur bacterium Chlorobium limicola f thio-sulfatophilum (strain Tassajara) have been assigned. Identification of spin systems and sequential assignment of 1H was accomplished by automated assignment computer programs followed by manual verification. In addition, 13C resonances have been extensively assigned by HSQC experiments at natural abundance. As determined by short-range NOE connectivities, 13C alpha chemical shifts, and HN exchange experiments, the secondary structure consists of 3 helices ranging from residues 3-13, 43-53 and 70-86. Interestingly, the second helix is significantly longer than observed by X-ray crystallography [1977, Proc. Natl. Acad. Sci. USA 74, 5244-5247]. A topological model of the cytochrome c555 is presented based on a small number of long-range NOE contacts. The helices are shown to pack onto the heme according to the pattern common to all class I cytochromes c.
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Affiliation(s)
- N Morelle
- Laboratoire de Résonance Magnétique Nucléaire, Institut de Biologie Structurale Jean-Pierre Ebel (CEA-CNRS), Grenoble, France
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6
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Shao W, Liu G, Tang W. Binding of 1-methylimidazole to cytochrome c: kinetic analysis and resonance assignments by two-dimensional NMR. BIOCHIMICA ET BIOPHYSICA ACTA 1995; 1248:177-85. [PMID: 7748900 DOI: 10.1016/0167-4838(95)00015-m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The binding of 1-methylimidazole to the heme iron by displacing Met-80 of cytochrome c has been studied by two-dimensional (2D) exchange spectroscopy. Two components of cytochrome c ligated by 1-methylimidazole (1-MeIm-cyt c) are first identified, which are related to the sterically hindered orientation of 1-methylimidazole by the heme pocket. Based on a matrix formalism, the kinetic parameters are calculated from the 2D peak amplitudes. With the known resonance assignments of cytochrome c, some hyperfine shifted resonances arising from heme peripheral protons and two axial ligands, and some side-chain resonances of the aliphatic and aromatic protons of 1-MeIm-cyt c have been straightforwardly assigned, which provide a clue to ligand-induced electronic and molecular structural changes of the protein.
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Affiliation(s)
- W Shao
- State Key Laboratory of Coordination Chemistry, Nanjing University, People's Republic of China
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7
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8
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A comparative study of the retention behaviour and stability of cytochrome c in reversed-phase high-performance liquid chromatography. J Chromatogr A 1994. [DOI: 10.1016/0021-9673(94)00092-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Banci L, Bertini I, Cambria MT, Capozzi F, Dikiy A. 1H one-dimensional and two-dimensional NMR studies of the ferricytochrome c 551 from Rhodocyclus gelatinosus. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 219:663-9. [PMID: 8307031 DOI: 10.1111/j.1432-1033.1994.tb19982.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
1H two-dimensional NMR spectroscopy has been applied to the oxidized form of cytochrome c 551 from Rhodocyclus gelatinosus, which is paramagnetic with S = 1/2. The investigation has allowed a complete and unambiguous assignment of the heme protons and some residues around the heme. We have learned that: the conformation of the axial methionine is equal to that of horse heart cytochrome c and different from two isoenzymes of the same cytochrome c 551 from a different strain; pKa of 6.6 +/- 0.3 has been detected through the shift variations of seventh propionate protons. The detailed differences with other cytochromes c in the hyperfine shifts are discussed.
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Affiliation(s)
- L Banci
- Department of Chemistry, University of Florence, Italy
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10
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Abstract
Cytochromes c are small soluble proteins, which have been extensively studied by nuclear magnetic resonance spectroscopy. The specific NMR features of paramagnetic proteins are discussed for the oxidized form (paramagnetic shift and line broadening). Early NMR studies have focused on the electronic structure of the heme and its direct environment. The conformations of cytochromes c are now investigated by two-dimensional 1H NMR spectroscopy combined with restrained molecular dynamics. 15N and 13C NMR, which greatly benefit from isotopic enrichment, may help in obtaining reliable 1H assignments and thus high quality solution structure. Finally, hydrogen exchange rates provide insight in the rigidity (and stability) of cytochromes c in both redox states at the atomic level.
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Affiliation(s)
- D Marion
- Institut de Biologie Structurale Jean-Pierre Ebel, CNRS-CEA, Grenoble, France
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11
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Moratal JM, Donaire A, Salgado J, Jiménez HR, Castells J, Piccioli M. Two-dimensional 1H NMR spectra of ferricytochrome c551 from Pseudomonas aeruginosa. FEBS Lett 1993; 324:305-8. [PMID: 8405371 DOI: 10.1016/0014-5793(93)80140-p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The full assignment of 1H NMR signals of heme proton resonances of ferricytochrome c551 from Pseudomonas aeruginosa has been performed by means of 2D NMR experiments. This technique allows the complete and unequivocal assignment of all heme resonances, including methylene resonances of the propionic groups, directly implicated in the pH dependence of the redox properties of cytochrome c551.
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Affiliation(s)
- J M Moratal
- Department of Inorganic Chemistry, University of Valencia, Italy
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12
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Turner DL, Williams RJ. 1H- and 13C-NMR investigation of redox-state-dependent and temperature-dependent conformation changes in horse cytochrome c. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 211:555-62. [PMID: 8382154 DOI: 10.1111/j.1432-1033.1993.tb17582.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The redox-state dependent changes in chemical shift, which have been measured for almost 100 CHn groups in the 13C-NMR spectra of horse cytochrome c [Santos, H., and Turner, D. L. (1992) Eur. J. Biochem. 206, 721-728], have been used to investigate the nature of the redox-related change in conformation. Apart from the haem and its axial ligands, the shifts are found to be dominated by the electron-nuclear dipolar coupling in the oxidised form, as was the case in 1H-NMR studies. These pseudocontact shifts are well described by using an empirically determined magnetic susceptibility tensor in conjunction with atomic coordinates for the horse cytochrome c. The groups which fit least well are located in the vicinity of Trp59. Comparison between 1H and 13C shifts and their temperature dependence shows that the differences from expectation based on a single structure for both oxidation states are caused largely by changes in the diamagnetic contribution to the chemical shifts. Since these are different for 1H and 13C resonances they indicate, independently from crystal structure data, some redox-related movement of the protein under the haem. The significance of these results for understanding electron transfer pathways is discussed. Finally, the temperature dependence of the pseudocontact shifts in the range 30-50 degrees C is shown to be anomalous. Approximately half of the anomalous effect may be attributed to Zeeman mixing of the electronic wavefunctions with a spin-orbit coupling constant lambda = 241 cm-1, while the other half is attributed to thermal expansion of the protein.
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Affiliation(s)
- D L Turner
- Department of Chemistry, University of Southampton, England
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13
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Xavier AV, Turner DL, Santos H. Two-dimensional nuclear magnetic resonance of paramagnetic metalloproteins. Methods Enzymol 1993; 227:1-16. [PMID: 8255222 DOI: 10.1016/0076-6879(93)27003-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- A V Xavier
- Instituto de Tecnologia Qúimica e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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14
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Chapter 6 Protein-lipid interactions with peripheral membrane proteins. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/s0167-7306(08)60235-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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15
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Santos H, Turner DL. 13C and proton NMR studies of horse cytochrome c. Systematic assignment of methyl and methine resonances in both oxidation states. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 206:721-8. [PMID: 1318834 DOI: 10.1111/j.1432-1033.1992.tb16978.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The CHn groups in the aliphatic side chains of horse cytochrome c have been characterized according to the chemical shifts of both 13C-NMR and 1H-NMR signals, their temperature dependence and the number of attached protons, n. The primary assignments of resonances from the 55 side-chain methyl and the 27 methine groups were obtained directly for the oxidised and the reduced forms. Specific assignments of the 13C resonances were obtained through shift-correlation experiments and comparison with earlier 1H-NMR studies, by further measurements of proton-proton interactions, or by elimination. Comparison of the paramagnetic shifts of carbon and protons indicates a small redox-related change of conformation in the vicinity of Trp59 and a significant expansion of the protein over 30-50 degrees C.
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Affiliation(s)
- H Santos
- Centro de Tecnologia Química e Biológica, Oeiras, Portugal
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16
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McLendon GL, Bagby S, Charman JA, Driscoll PC, McIntire WS, Mathews FS, Hill HA. Subunit interactions change the heme active-site geometry in p-cresol methylhydroxylase. Proc Natl Acad Sci U S A 1991; 88:9463-7. [PMID: 1946360 PMCID: PMC52738 DOI: 10.1073/pnas.88.21.9463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The enzyme p-cresol methylhydroxylase [4-cresol: (acceptor) oxidoreductase (methyl-hydroxylating), EC 1.17.99.1] contains two subunits: a cytochrome c (electron transfer) subunit (cytochrome cpc) and a flavin (catalytic) subunit. When these subunits are separated by isoelectric focusing, a stable cytochrome subunit is obtained. Significant differences are observed between the one-dimensional NMR spectra of oxidized cytochrome cpc and of oxidized p-cresol methylhydroxylase. Analysis of the two-dimensional nuclear Overhauser enhancement and exchange spectroscopy (NOESY) spectrum of reduced cytochrome cpc suggests that the axial ligand, Met-50, of the stable subunit reorients by a rotation about the C gamma-S delta bond when cytochrome cpc binds to the flavin subunit. This reorientation must result in a change in bonding at the heme, which is reflected both in the para-magnetically shifted resonances and in the redox potential. p-Cresol methylhydroxylase thereby provides an interesting example of the coupling of subunit interactions to active-site structure and reactivity.
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Affiliation(s)
- G L McLendon
- Department of Chemistry, University of Rochester, NY 14627
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17
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Whitford D, Gao Y, Pielak GJ, Williams RJ, McLendon GL, Sherman F. The role of the internal hydrogen bond network in first-order protein electron transfer between Saccharomyces cerevisiae iso-1-cytochrome c and bovine microsomal cytochrome b5. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 200:359-67. [PMID: 1653702 DOI: 10.1111/j.1432-1033.1991.tb16193.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An internal water molecule (designated WAT166) is found in iso-1-cytochrome c which is part of a redox-state-dependent hydrogen bond network. The position of this water molecule with respect to the polypeptide fold can be altered or even displaced by site-directed mutagenesis leading to structural perturbations and associated changes in redox potential. Using saturation transfer 1H-NMR methods, this study measures changes in the electron transfer reactivity for three variants of yeast iso-1-cytochromes c in which the position of this water molecule is altered. In particular, the reverse electron transfer rate is measured within a complex formed between either wild-type or variant yeast iso-1-cytochromes c and the tryptic fragment of bovine liver microsomal cytochrome b5. For three variants of yeast iso-1-cytochrome c the rate constants measured by saturation transfer are wild-type (Asn52, E0 = 270 mV, kex = 0.3 s-1), Asn52----Ala (E0 = 240 mV, kex = 0.6 s-1), Asn52----Ile (E0 = 220 mV, kex = 1.0 s-1). The first-order rates are compared with that of a fourth variant Phe82----Gly which has been measured previously (E0 = 220 mV, kex = 0.7 s-1). An analysis of the variation in the observed cross exchange rate using Marcus theory shows that these changes can be predicted quantitatively by the shift in redox potential that accompanies mutagenesis. So, although the perturbation of the internal water molecule by mutagenesis alters both the structure and redox potential of cytochrome c, surprisingly it does not significantly influence the intrinsic electron transfer reactivity of the protein. Studies of the activation parameters suggests that a variation of temperature changes both delta G* and also the prefactor. These data are discussed in terms of models involving dynamic molecular recognition between proteins.
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Affiliation(s)
- D Whitford
- Department of Biochemistry, University of Oxford, England
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18
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Concar DW, Whitford D, Williams RJ. The location of the polyphosphate-binding sites on cytochrome c measured by NMR paramagnetic difference spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 199:569-74. [PMID: 1651238 DOI: 10.1111/j.1432-1033.1991.tb16156.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Analyses of unimolecular electron self-exchange reactions provide a comparatively simple and direct approach to understanding biological electron transfer. Such studies are currently limited by a lack of well characterised aggregating systems. In the presence of sodium hexametaphosphate, cytochrome c forms stable protein aggregates as a result of binding hexametaphosphate at a single site on its surface (preceding paper in this issue of the journal). Here we report the location of the principal polyphosphate binding site on the surface of cytochrome c for both hexametaphosphate and a second polyphosphate, tripolyphosphate determined using 1H-NMR spectroscopy in conjunction with the relaxation probe potassium hexacyanochromium(III). Addition of either hexametaphosphate or tripolyphosphate to ferricytochrome c in the presence of the relaxation probe causes a decrease in intensity of several resonances in the paramagnetic difference spectrum, including Phe82 ortho/meta, Ile85 delta methyl and Ile9 gamma methyl. Together these effects put the site of polyphosphate binding close to lysines 13, 86, and 87. Additionally the effect of sodium tripolyphosphate and sodium trimetaphosphate on cytochrome c aggregation is described. The potential role of this site in anion-induced cytochrome c aggregation is discussed.
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Affiliation(s)
- D W Concar
- Inorganic Chemistry Laboratory, University of Oxford, England
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19
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Gao Y, Boyd J, Pielak GJ, Williams RJ. Proton nuclear magnetic resonance as a probe of differences in structure between the C102T and F82S,C102T variants of iso-1-cytochrome c from the yeast Saccharomyces cerevisiae. Biochemistry 1991; 30:7033-40. [PMID: 1648968 DOI: 10.1021/bi00242a032] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Differences in chemical shifts and in nuclear Overhauser effects between the C102T and F82S,C102T variants of Saccharomyces cerevisiae iso-1-cytochrome c in both the reduced and oxidized forms are reported and analyzed. There is evidence for small conformational differences in both oxidation states of the double variant near position 82. Differences in structure are more evident in the oxidized forms of the variants. These differences extend to distant parts of the protein. It is concluded that the oxidized double variant has undergone a small rearrangement of several regions of the protein that are linked by a hydrogen-bond network. It is shown that the rearrangement involves hydrogen bonds associated with the two heme propionates and associated water molecules. The deductions from nuclear magnetic resonance data are compared with the differences in the crystal structures of the reduced forms of wild-type protein and the F82S variant [Louie, G. V., Pielak, G. J., Smith, M., & Brayer, G. D. (1988) Biochemistry 27, 7870-7876].
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Affiliation(s)
- Y Gao
- Inorganic Chemistry Laboratory, University of Oxford, U.K
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20
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Yamamoto Y, Iwafune K, Nanai N, Osawa A, Chûjô R, Suzuki T. NMR study of Galeorhinus japonicus myoglobin. 1H-NMR study of molecular structure of the heme cavity. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 198:299-306. [PMID: 2040296 DOI: 10.1111/j.1432-1033.1991.tb16016.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The molecular structure of the active site of myoglobin from the shark, Galeorhinus japonicus, has been studied by 1H-NMR. Some hyperfine-shifted amino acid proton resonances in the met-cyano form of G. japonicus myoglobin have been unambiguously assigned by the combined use of various two-dimensional NMR techniques; they were compared with the corresponding resonances in Physter catodon myoglobin. The orientations of ThrE10 and IleFG5 residues relative to the heme in G. japonicus met-cyano myoglobin were semiquantitatively estimated from the analysis of their shifts using the magnetic susceptibility tensor determined by a method called MATDUHM (magnetic anisotropy tensor determination utilizing heme methyls) [Yamamoto, Y., Nanai, N. & Chûjô, R. (1990) J. Chem. Soc., Chem. Commun., 1556-1557] and the results were compared with the crystal structure of P. catodon carbonmonoxy myoglobin [Hanson, J. C. & Schoenborn, B. P. (1981) J. Mol. Biol. 153, 117-124]. In spite of a substantial difference in shift between the corresponding amino acid proton resonances for the two proteins, the orientations of these amino acid residues relative to the heme in the active site of both myoglobins were found to be highly alike.
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Affiliation(s)
- Y Yamamoto
- Department of Biomolecular Engineering, Tokyo Institute of Technology, Japan
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21
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Feng YQ, Wand AJ, Roder H, Englander SW. Chemical exchange in two dimensions in the 1H NMR assignment of cytochrome c. Biophys J 1991; 59:323-8. [PMID: 1849027 PMCID: PMC1281149 DOI: 10.1016/s0006-3495(91)82226-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The important role played by chemical exchange in solving the proton assignment problem for oxidized and reduced horse cytochrome c is described. Some novel approaches for establishing oxidation-reduction exchange correlations in combinations of several two-dimensional spectra were used. Unambiguous chemical exchange correlations were established for 55 NH-C alpha H resonances and all the aromatic and side chain methyl resonances. Consistent although not fully unambiguous main chain proton correlations were observed for 47 of the remaining 49 residues. The many exchange correlations found serve to multiply cross-connect the two extensive, individually self-consistent networks of assignments found for the oxidized and reduced forms, and thus help to confirm both sets of assignments.
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Affiliation(s)
- Y Q Feng
- Department of Biochemistry and Biophysics, University of Pennsylvania
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22
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Jandu SK, Ray S, Brooks L, Leatherbarrow RJ. Role of arginine 67 in the stabilization of chymotrypsin inhibitor 2: examination of amide proton exchange rates and denaturation thermodynamics of an engineered protein. Biochemistry 1990; 29:6264-9. [PMID: 2207072 DOI: 10.1021/bi00478a022] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have examined the contribution to protein stability of an interaction involving a charged hydrogen bond from an arginyl side chain (Arg67) in the serine proteinase inhibitor chymotrypsin inhibitor 2 (CI-2), by replacing this side chain with an alanyl residue by protein engineering. Using nuclear magnetic resonance spectroscopy (NMR), we have examined the effect of this mutation on the hydrogen-deuterium exchange rates of several backbone amide protons in the native and engineered proteins at 50 degrees C. These exchange rates provide a localized probe at multiple discrete sites throughout the protein and from comparison of native and mutant exchange rates allow calculation of the difference in free energy of exchange (delta delta Gex) resulting from the mutation. The results show that for the majority of amides observed this mutation results in delta delta Gex of ca. 1.7 kcal mol-1 over the whole CI-2 molecule. However, for two relatively exposed amide protons the exchange rates are found to be far less perturbed, implying that local unfolding mechanisms predominate for these protons. Direct measurement of the stability of both proteins to denaturation by guanidinum hydrochloride shows that the interaction contributes 1.4 kcal mol-1 to the stability of the molecule. This value is comparable to those obtained from the NMR exchange measurements and indicates that the exchange processes reflect the differences in stability between the native and mutant proteins.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- S K Jandu
- Department of Chemistry, Imperial College of Science, Technology and Medicine, South Kensington, London, U.K
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23
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Feng Y, Roder H, Englander SW. Redox-dependent structure change and hyperfine nuclear magnetic resonance shifts in cytochrome c. Biochemistry 1990; 29:3494-504. [PMID: 2162193 DOI: 10.1021/bi00466a011] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Proton nuclear magnetic resonance assignments for reduced and oxidized equine cytochrome c show that many individual protons exhibit different chemical shifts in the two protein forms, reflecting diamagnetic shift effects due to structure change, and in addition contact and pseudocontact shifts that occur only in the paramagnetic oxidized form. To evaluate the chemical shift differences (delta delta) for structure change, we removed the pseudocontact shift contribution by a calculation based on knowledge of the electron spin g tensor. The g-tensor parameters were determined from the delta delta values of a large set (64) of C alpha H protons at well-defined spatial positions in the oxidized horse protein. The g-tensor calculation, when repeated using only 12 available C alpha H proton resonances for cytochrome c from tuna, proved to be remarkably stable. The largest principal value of the g tensor (gz) falls precisely along the ligand bond between the heme iron and methionine-80 sulfur, while gx and gy closely match the natural heme axes defined by the pyrrole nitrogens. The derived g tensor was then used together with spatial coordinates for the oxidized form to calculate the pseudocontact shift contribution (delta pc) to proton resonances at 400 identifiable sites throughout the protein, so that the redox-dependent chemical shift discrepancy, delta delta-delta pc, could be evaluated. Large residual changes in chemical shift define the Fermi contact shifts, which are found as expected to be limited to the immediate covalent structure of the heme and its ligands and to be asymmetrically distributed over the heme. Smaller chemical shift discrepancies point to a concerted change, involving residues 39-43 and 50-60 (bottom of the protein), and to other changes in the immediate vicinity of the heme ligands. Also, the three internal water molecules are implicated in redox sensitivity. The residues found to change are in good but not perfect agreement with prior X-ray diffraction observations of subangstrom redox-related displacements in the tuna protein. The chemical shift discrepancies observed appear in the main to reflect structure-dependent diamagnetic shifts rather than hyperfine effects due to displacements in the pseudocontact shift field. Although 51 protons in 29 different residues exhibit significant chemical shift changes, the general impression is one of small structural adjustments to redox-dependent strain rather than sizeable structural displacements or rearrangements.
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Affiliation(s)
- Y Feng
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia 19104-6059
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24
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Yu LP, Smith GM. Assignments of 15N and 1H NMR resonances and a neutral pH ionization in Rhodospirillum rubrum cytochrome c2. Biochemistry 1990; 29:2914-9. [PMID: 2159778 DOI: 10.1021/bi00464a004] [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: 12/30/2022]
Abstract
The phi NH proton and 15N resonances of the ligand histidine of Rhodospirillum rubrum fericytochrome c2 are found at 14.7 and 184 ppm, respectively, contradicting the proposal that this proton is absent in the R. rubrum ferricytochrome. Substitution of the deuterium atom for this proton causes small upfield shifts of the phi nitrogen in both oxidation states, indicating that the phi NH-peptide carboxyl hydrogen bond is not substantially weakened by the substitution. The proton and 15N resonances of the indolic NH group of the invariant tryptophan-62 and numerous proton resonances of the heme and extraheme ligands in the spectrum of the ferricytochrome are also assigned. An ionization in the ferrocytochrome occurring at neutral pH is assigned to the single nonligand histidine. This attribution is supported by the direct measurement of the ionization by NOE difference spectroscopy and by comparative structural arguments involving closely related cytochromes and chemically modified cytochromes.
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Affiliation(s)
- L P Yu
- Department of Food Science and Technology, University of California, Davis 95616
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25
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Yu LP, Smith GM. Characterization of pH-dependent conformational heterogeneity in Rhodospirillum rubrum cytochrome c2 using 15N and 1H NMR. Biochemistry 1990; 29:2920-5. [PMID: 2159779 DOI: 10.1021/bi00464a005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The 15N-enriched ferricytochrome c2 from Rhodospirillum rubrum has been studied by 15N and 1H NMR spectroscopy as a function of pH. The 15N resonances of the heme and ligand tau nitrogen are broadened beyond detection because of paramagnetic relaxation. The 15N resonance of the ligand histidine phi nitrogen was unambiguously identified at 184 ppm (pH 5.6). The 15N resonances of the single nonligand histidine are observed only at low pH, as in the ferrocytochrome because of the severe broadening caused by tautomerization. The dependence of the 15N and 1H spectra of the ferricytochrome on pH indicated that the ligand histidine tau NH does not dissociate in the neutral pH range and is involved in a hydrogen bond, similar to that in the reduced state. Because neither deprotonated nor non-hydrogen-bonded forms of the ligand histidine are observed in the spectra of either oxidation state, the participation of such forms in producing heterogeneous populations having different electronic g tensors is ruled out. Transitions having pKa's of 6.2, 8.6, and 9.2 are observed in the ferricytochrome. The localized conformational change around the omega loops is observed in the neutral pH range, as in the ferrocytochrome. Structural heterogeneity leads to multiple resonances of the heme ring methyl at position 8. The exchange rate between the conformations is temperature dependent. The transition with a pKa of 6.2 is assigned to the His-42 imidazole group. The displacement of the ligand methionine, which occurs with a pKa of 9.2, causes gross conformational change near the heme center.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- L P Yu
- Department of Food Science and Technology, University of California, Davis 95616
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26
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Emerson SD, La Mar G. Solution structural characteristics of cyanometmyoglobin: resonance assignment of heme cavity residues by two-dimensional NMR. Biochemistry 1990; 29:1545-56. [PMID: 2334713 DOI: 10.1021/bi00458a028] [Citation(s) in RCA: 126] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Steady-state nuclear Overhauser effects (NOE), two-dimensional (2D) nuclear Overhauser effect spectroscopy (NOESY), and 2D spin correlation spectroscopy (COSY) have been applied to the fully paramagnetic low-spin, cyanide-ligated complex of sperm whale ferric myoglobin to assign the majority of the heme pocket side-chain proton signals and the remainder of the heme signals. It is shown that the 2D NOESY map reveals essentially all dipolar connectivities observed in ordinary 1D NOE experiments and expected on the basis of crystal coordinates, albeit often more weakly than in a diamagnetic analogue. For extremely broad (approximately 600-Hz) and rapidly relaxing (Tf1 approximately 3 ms) signals which show no NEOSY peaks, we demonstrate that conventional steady-state NOEs obtained under very rapid pulsing conditions still allow detection of the critical dipoar connectivities that allow unambiguous assignments. The COSY map was found to be generally less useful for the hyperfine-shifted residues, with cross peaks detected only for protons greater than 6 A from the iron. Nevertheless, numerous critical COSY cross peaks between strongly hyperfine-shifted peaks were resolved and assigned. In all, 95% (53 of 56 signals) of the total proton sets within approximately 7.5 A of the iron, the region experiencing the strongest hyperfine shifts and paramagnetic relaxation, are now unambiguously assigned. Hence it is clear that the 2D methods can be profitably applied to paramagnetic proteins. The scope and limitations of such application are discussed. The resulting hyperfine shift pattern for the heme confirmed expectations based on model compounds. In contrast, while exhibiting fortuitous 1H NMR spectral similarities, a major discrepancy was uncovered between the hyperfine shift pattern of the axially bound (F8 histidyl) imidazole in the protein and that of the imidazole in a relevant model compound [Chacko, V.P., & La Mar, G. N. (1982) J. Am. Chem. Soc. 104, 7002-7007], providing direct evidence for a protein-based deformation of axial bonding in the protein.
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Affiliation(s)
- S D Emerson
- Department of Chemistry, University of California, Davis 95616
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27
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Zehfus MH, Reily MD, Ulrich EL, Westler WM, Markley JL. 1H, 13C, and 15N resonance assignments for a ferrocytochrome c553 heme by multinuclear NMR spectroscopy. Arch Biochem Biophys 1990; 276:369-73. [PMID: 2154947 DOI: 10.1016/0003-9861(90)90734-g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A novel strategy has been used to assign the 1H, 13C, and 15N resonances of the heme in Anabaena 7120 ferrocytochrome c553. 13C[13C] double-quantum coherence spectroscopy was used to delineate the heme carbons, 1H[13C] single-bond correlation spectroscopy was used to define the attached protons, and 1H[15N] multiple-bond correlation spectroscopy was used to assign the nitrogens. 1H[13C] multiple-bond correlation spectroscopy confirmed many of the assignments. Proteins were labeled uniformly with 13C or 15N to obtain the required spectral sensitivity.
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Affiliation(s)
- M H Zehfus
- Biochemistry Department, College of Agricultural and Life Sciences, University of Wisconsin, Madison 53706
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28
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Feng YQ, Roder H, Englander SW. Assignment of paramagnetically shifted resonances in the 1H NMR spectrum of horse ferricytochrome c. Biophys J 1990; 57:15-22. [PMID: 2153419 PMCID: PMC1280638 DOI: 10.1016/s0006-3495(90)82502-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The proton resonances of the heme, the axial ligands, and other hyperfine-shifted resonances in the 1H nuclear magnetic resonance spectrum of horse ferricytochrome c have been investigated by means of one- and two-dimensional nuclear Overhauser and magnetization transfer methods. Conditions for saturation transfer experiments in mixtures of ferro- and ferricytochrome c were optimized for the cross assignment of corresponding resonances in the two oxidation states. New resonance assignments were obtained for the methine protons of both thioether bridges, the beta and gamma meso protons, the propionate six heme substituent, the N pi H of His-18, and the Tyr-67 OH. In addition, several recently reported assignments were confirmed. All of the resolved hyperfine-shifted resonances in the spectrum of ferricytochrome c are now identified. The Fermi contact shifts experienced by the heme and ligand protons are discussed.
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Affiliation(s)
- Y Q Feng
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia 19104-6059
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29
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Kuroda Y, Goto M, Sakai T. Analysis of Isotropic1H and13C NMR Shifts of Low-Spin FeIIIComplexes: Tetracyano(1,2-ethanediamine)ferrate(III) and Tetracyano(N,N′-dimethyl-1,2-ethanediamine)ferrate(III). BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1989. [DOI: 10.1246/bcsj.62.3614] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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30
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Abstract
NMR studies of dynamics within structure have revealed that a quite new approach to protein structure and its relation to function is necessary. This approach requires the consideration in detail of the following: 1. Local movements of groups and small segments to allow fast recognition and fitting. The motion concerns on/off rates as well as binding. The observations affect surface/surface recognition, e.g. of antigen/antibody as well as of substrate and protein. 2. Somewhat larger interdomain or N- and C-terminal segments which allow rearrangement. Cases in point are the movement of segments in blood-clotting proteins or in histones. 3. Relative motion of helices in hinges. These actions are likely in such enzymes as kinases and P-450 cytochromes. 4. Relative motion of helices within domains (relative to other helices or sheets) in mechanical devices (triggers) e.g. in calmodulin. 5. General motion in random proteins. Examples extend from rubber-like proteins (entropy sensors), some glycoproteins, to proteins carrying peptide hormones to be generated only after hydrolysis. 6. Order----disorder transitions locally as in osteocalcin and metallothionine. 7. Swinging arm motions associated with special sequences such as (Ala-Pro)n. 8. Of great interest is the power of NMR to look at proteins which are relatively large, up to 50 kDa proteins, and to isolate certain zones of interest. This needs careful temperature dependent studies and analysis of separated domains [72] as well as the use of a great variety of pulse sequences [15] and of nuclei other than protons. 9. In this article I have illustrated the different possibilities using work in my own group. This is done to lessen the burden of extensive review. I fully realise that the range of examples is now large. I would stress though that the production of the necessary technology was the endeavour of several of us within the Oxford Enzyme Group from 1970 to 1985, i.e. from 270-600 MHz Fourier-transform NMR spectroscopy. 10. While all of these features have been demonstrated by NMR methods there are parallel developments both using X-ray diffraction methods and theoretical approaches. All these procedures are changing the view of protein structure to one which incorporates dynamics all the way from conventional vibronic/rotational coupling to the disordered motions characteristic of random polymers. It is the understanding of dynamics that leads to an appreciation of function.
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Affiliation(s)
- R J Williams
- Inorganic Chemistry Laboratory, University of Oxford
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31
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Gao Y, Lee AD, Williams RJ, Williams G. The effects of multiple amino acid substitutions on the polypeptide backbone of tuna and horse cytochromes c. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 182:57-65. [PMID: 2543575 DOI: 10.1111/j.1432-1033.1989.tb14800.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The cytochromes c provide a wide range of natural and mutant homologous proteins which may be used to study structure/function relationships in biological electron-transfer reactions. A description of the cytochrome c structure has been provided by high-resolution X-ray crystallography for the cytochromes from tuna, bonito, rice and yeast (Saccharomyces iso-1). Correlation of these structures with NMR parameters is necessary to confirm the structure of the protein in solution and to permit the routine characterisation of cytochromes c with novel sequences. We have previously reported a method based on the analysis of pseudocontact shifts which allowed us to compare the conformations of some amino acid side chains of tuna cytochrome c in solution and in the crystalline state. Here we report a comparison of the conformations of the polypeptide backbone of cytochromes c in proteins from tuna and horse, using the chemical shifts of the amide NH and C alpha H protons. It is found that the backbone conformation and hydrogen-bond network is closely conserved between these proteins, despite 19 amino acid substitutions. Appreciable differences occur in two regions, around Asn 31 and at the beginning of the 60s helix. Evidence for some rotational or translational motion of the C-terminal helix is also presented.
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Affiliation(s)
- Y Gao
- Inorganic Chemistry Laboratory, University of Oxford, England
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32
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Moench SJ, Satterlee JD. Proton NMR comparison of the Saccharomyces cerevisiae ferricytochrome c isozyme-1 monomer and covalent disulfide dimer. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)81748-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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33
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Pielak GJ, Boyd J, Moore GR, Williams RJ. Proton-NMR studies show that the Thr-102 mutant of yeast iso-1-cytochrome c is a typical member of the eukaryotic cytochrome c family. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 177:167-77. [PMID: 2846294 DOI: 10.1111/j.1432-1033.1988.tb14359.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Thr-102 mutant of yeast iso-1-cytochrome c is a useful system for the study of structure-function relationships in this important class of electron transfer proteins, but little is known about its structure. Furthermore, few assignments of individual amino acid residues in yeast iso-1-cytochrome c have been made by proton NMR. Here we report assignments for nearly half of the amino acids in the reduced Thr-102 mutant of yeast iso-1-cytochrome c. We also report assignments for the oxidized Thr-102 mutant. While the crystal structure of the reduced iso-1-cytochrome c (N. B. not the Thr-102 mutant) has been reported, there is currently little structural information concerning its solution structure and none concerning the oxidized protein. There is also no information concerning the structure of either oxidation state of the Thr-102 mutant. Comparison of the chemical shift and NOE data for the reduced Thr-102 mutant and comparison of paramagnetic shifts for analogous residues between this mutant and horse-heart and tuna cytochromes c reveal that both the basic fold of Thr-102 yeast iso-1-cytochrome c and the region around the site of the mutation are the same as those found in the latter two proteins. It is concluded that the results from structure function studies using the Thr-102 mutant will be applicable to eukaryotic cytochrome c in general. This knowledge allows us to proceed to a description of some mutants of yeast iso-1-cytochrome c in the next paper.
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Affiliation(s)
- G J Pielak
- Inorganic Chemistry Laboratory, University of Oxford, England
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34
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Arean CO, Moore GR, Williams G, Williams RJ. Ion binding to cytochrome c. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 173:607-15. [PMID: 2836194 DOI: 10.1111/j.1432-1033.1988.tb14042.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This paper is a further study of ion binding to protein surfaces and builds on the studies of the binding of [Cr(CN)6]3- and [Fe(edta)(H2O)]- previously reported [Williams et al. (1982) FEBS Lett. 15, 293-299; Eley et al. (1982) Eur. J. Biochem. 124, 295-303]. In the present paper the binding of polyaminocarboxylate complexes of gadolinium have been studied. Eight ion-binding sites have been identified on the surface of cytochrome c. These exhibit different binding specificities which, in some cases, are not full understood. However it is clear that simple outer-sphere interactions are not the sole determining factor for the association of metal ion complexes with proteins. The NMR paramagnetic difference spectrum method has been shown to be good at locating binding sites and revealing qualitative differences in their relative affinities for a range of complex types. However the use of relaxation probes is not a good method for the quantitative determination of binding constants; for this, isostructural shift probes must be sought.
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Affiliation(s)
- C O Arean
- Inorganic Chemistry Laboratory, University of Oxford, England
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35
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Yu LP, Smith GM. pH-induced changes in Rhodospirillum rubrum cytochrome c2 and subsequent renaturation: an 15N NMR study. Proc Natl Acad Sci U S A 1988; 85:2894-8. [PMID: 2834719 PMCID: PMC280109 DOI: 10.1073/pnas.85.9.2894] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The 15N-enriched ferrocytochrome c2 from Rhodospirillum rubrum was studied by 15N NMR at different solvent pH values. The mobility and chemical shift of the N-terminal glutamic acid (335.4 ppm at pH 5.1) were found to depend on pH. It was least mobile between pH 8 and 9.0, which is explained in terms of pH-dependent conformational changes and formation of salt linkages and/or hydrogen bonds. The resonances of the lysine side chains are centered around 341.7 ppm at low pH and move upfield with pH by about 8.4 ppm with pKa values of 10.8. The exchange rates of the epsilon NH protons are lowest near their pKa values. The protein is very stable in the pH range between 4.9 and 10.0 but unfolds abruptly at pH 10.5-11. Denaturation was verified by the measurement of several parameters by NMR. The renaturation of the protein demonstrates that the folding begins with reformation of heme coordination and establishment of a hydrophobic core, followed by positioning of side chains and peptide backbones linking the nucleation centers. The repositioning processes had time scales of minutes to hours in contrast to the reported values of seconds in some studies.
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Affiliation(s)
- L P Yu
- Department of Food Science and Technology, University of California, Davis 95616
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36
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Chapter 28. Applications of NMR Spectroscopy to Protein Structure Determination. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1988. [DOI: 10.1016/s0065-7743(08)60856-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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37
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Driscoll PC, Hill HA, Redfield C. 1H-NMR sequential assignments and cation-binding studies of spinach plastocyanin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1987; 170:279-92. [PMID: 3691523 DOI: 10.1111/j.1432-1033.1987.tb13697.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The essentially complete assignment of the 1H-NMR spectrum of the Cu(i) form of spinach plastocyanin has been achieved using two-dimensional NMR techniques and sequence-specific resonance assignment procedures. A variety of pH and temperature conditions was utilised to overcome the problems of resonance overlap in the spectrum, degeneracy of C alpha H and solvent H2O chemical shifts, and cross-saturation of labile NH resonances. A qualitative analysis of the long-range nuclear Overhauser effects observed indicates that the backbone fold of spinach plastocyanin is very similar to that of poplar plastocyanin, whose structure has been solved by X-ray crystallography and differs in 22 of its 99 amino acid residues. The assignments provide a basis for further investigations into the structural and ion- and protein-binding properties of plastocyanin in solution.
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Affiliation(s)
- P C Driscoll
- Inorganic Chemistry Laboratory, University of Oxford, England
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38
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Santos H, Turner DL. Proton NMR studies of horse ferricytochrome c. Completion of the assignment of the well resolved hyperfine shifted resonances. FEBS Lett 1987; 226:179-85. [PMID: 2826254 DOI: 10.1016/0014-5793(87)80575-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
1H NMR saturation transfer and nuclear Overhauser effect (NOE) measurements have been used together with two-dimensional spectra to complete the assignment of the well resolved hyperfine shifted resonances in the spectrum of horse ferricytochrome c and obtain their shifts in the reduced protein. New assignments include the beta-CH2 protons of Met-80, both ring protons of His-18, and the alpha-CH2 of Gly-29 and delta-CH2 of Pro-30, which resonate surprisingly far upfield despite the absence of any Fermi contact contribution to the shift.
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Affiliation(s)
- H Santos
- Centro de Quimica Estrutural, UNL, Lisboa, Portugal
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39
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Kuroda Y, Goto M, Sakai T. Orientation-Dependent1H and13C Isotropic Shifts of Low-Spin Tetracyano(1,2-diamine)ferrates(III). BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1987. [DOI: 10.1246/bcsj.60.3917] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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40
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Satterlee JD, Moench S. Proton hyperfine resonance assignments using the nuclear Overhauser effect for ferric forms of horse and tuna cytochrome c. Biophys J 1987; 52:101-7. [PMID: 3038205 PMCID: PMC1329988 DOI: 10.1016/s0006-3495(87)83193-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Proton hyperfine resonance assignments for cytochromes c from several species are currently being successfully pursued by several laboratories. These efforts focus mostly on the ferrous forms. In contrast to that work, we have pursued assignments of the proton hyperfine shifted resonances for horse and tuna ferricytochromes c. Our results indicate that assignments are nearly identical in those two proteins. Using the pre-steady state nuclear Overhauser effect, several additional assignments have been made for the tuna protein, whereas for the horse protein, the following protons have been assigned: heme 7, alpha CH2; heme 7, beta CH2; histidine 18, beta CH2 and alpha CH; and the methionine 80, beta CH2.
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41
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Williams RJP. The functions of structure and dynamics in proteins, peptides and metal ion complexes and their relationships to biological recognition and the handling of information. ACTA ACUST UNITED AC 1987. [DOI: 10.1007/bf02910424] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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42
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Abstract
1H Nuclear magnetic resonance assignments are given for the NH and C alpha H protons of two alpha-helical segments of tuna ferricytochrome c. The assignments were obtained using two-dimensional nuclear magnetic resonance sequential assignment procedures and illustrate the applicability of these methods to medium-sized proteins. By comparing nuclear Overhauser intensities between the NH and C alpha H protons the precise structures of the two helical segments are compared and their deviations from ideality are discussed.
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43
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Santos H, Turner DL. 13C and proton NMR studies of horse cytochrome c. Assignment and temperature dependence of methyl resonances. FEBS Lett 1986; 194:73-7. [PMID: 3000825 DOI: 10.1016/0014-5793(86)80054-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The 13C and proton chemical shifts of the 55 methyl groups of horse cytochrome c have been determined over a range of temperatures both in the diamagnetic ferrocytochrome and in the paramagnetic ferricytochrome. Specific assignments of many proton resonances have been published previously and all of the remaining methyl proton resonances are now specifically assigned. The corresponding 13C assignments follow directly, including those of contact shifted 13C resonances which are reported for the first time.
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44
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Solution structure of mitochondrial cytochrome c. II. 1H nuclear magnetic resonance of ferrocytochrome c. J Mol Biol 1985; 183:429-46. [PMID: 2991532 DOI: 10.1016/0022-2836(85)90012-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The 1H nuclear magnetic resonance spectrum of tuna ferrocytochrome c has been studied and the resonances of all 49 amino acid methyl groups have been assigned to specific absorption lines. In comparison with resonance assignments in the ferricytochrome c spectrum, the secondary shifts of resonances of ferrocytochrome c are smaller and the identification of characteristic spin-systems from comparison of spectra from homologous proteins more difficult. For this reason, two-dimensional nuclear magnetic resonance exchange correlated spectroscopy has been used to correlate the assigned resonances of tuna ferricytochrome c with previously unassigned resonances of tuna ferrocytochrome c.
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45
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Williams G, Clayden NJ, Moore GR, Williams RJ. Comparison of the solution and crystal structures of mitochondrial cytochrome c. Analysis of paramagnetic shifts in the nuclear magnetic resonance spectrum of ferricytochrome c. J Mol Biol 1985; 183:447-60. [PMID: 2991533 DOI: 10.1016/0022-2836(85)90013-0] [Citation(s) in RCA: 107] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The two accompanying papers describe the assignment of methyl-containing spin-systems in the 1H nuclear magnetic resonance spectra of tuna ferricytochrome c and tuna ferrocytochrome c. At present, 104 resonances from 208 C-H protons are assigned in both oxidation states. In this paper, the difference in chemical shift of a resonance between the two oxidation states is used together with a dipolar model of the unpaired electron spin of ferricytochrome c to compare the structure of cytochrome c in solution with three high-resolution structures of cytochrome c obtained by X-ray diffraction in single crystals. The overall protein fold and the positions of most of the haem-packing residues are shown to be invariant between the crystal and solution. However, three regions of the protein, at the C terminus, around the haem propionic acid groups and at the haem crevice near thioether-2, are found to undergo conformational changes on the removal of crystal packing constraints.
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