1
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Chen Y, Simmonds RS, Young JK, Timkovich R. Solution structure of the recombinant target recognition domain of zoocin A. Proteins 2013. [DOI: 10.1002/prot.24224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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2
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Chen Y, Liang Q, Arciero DM, Hooper AB, Timkovich R. Heme crevice disorder after sixth ligand displacement in the cytochrome c-551 family. Arch Biochem Biophys 2007; 457:95-104. [PMID: 17078921 DOI: 10.1016/j.abb.2006.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Accepted: 10/02/2006] [Indexed: 11/15/2022]
Abstract
1H NMR and visible absorption spectroscopy were used to monitor sixth ligand methionine displacement reactions in four members of the ferricytochrome c-551 family from Pseudomonas aeruginosa, Pseudomonas stutzeri, Pseudomonas stutzeri substrain ZoBell, and Nitrosomonas europae. Potassium cyanide displaces the methionine ligand with very modest changes in the visible spectra, but profound changes in the NMR spectra. The initial product formed kinetically, designated complex I, changes with time and/or heating to a more thermodynamically favored product termed complex II. Spectra indicate that both I and II are actually a family of closely related conformational isomers. Low temperature NMR spectra of complex II indicate that some of the isomers are in chemical exchange on the NMR time scale. High pH also displaces the methionine ligand in a manner similar to the well-known alkaline transition of mitochondrial cytochrome c. However, the reaction occurs at higher pH values and over a narrower pH range for the c-551 family, and the transition pH range is different for the different proteins studied. The final alkaline forms also show peak widths and a number of peaks indicative of multiple conformational isomers.
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Affiliation(s)
- Yinghua Chen
- Department of Chemistry, University of Alabama, Tuscaloosa, AL 35487-0336, USA
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3
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Jiménez HR, Pardal C, Moratal JM. 1H NMR studies of paramagnetic ferricytochrome c-551 from Pseudomonas aeruginosa at high pH: The role of histidine 16 in the spin transition. Polyhedron 2005. [DOI: 10.1016/j.poly.2005.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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4
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Zhong L, Wen X, Rabinowitz TM, Russell BS, Karan EF, Bren KL. Heme axial methionine fluxionality in Hydrogenobacter thermophilus cytochrome c552. Proc Natl Acad Sci U S A 2004; 101:8637-42. [PMID: 15161973 PMCID: PMC423247 DOI: 10.1073/pnas.0402033101] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The heme group in paramagnetic (S = 1/2) ferricytochromes c typically displays a markedly asymmetric distribution of unpaired electron spin density among the heme pyrrole beta substituents. This asymmetry is determined by the orientations of the heme axial ligands, histidine and methionine. One exception to this is ferricytochrome c(552) from Hydrogenobacter thermophilus, which has similar amounts of unpaired electron spin density at the beta substituents on all four heme pyrroles. Here, determination of the orientation of the magnetic axes and analysis of NMR line shapes for H. thermophilus ferricytochrome c(552) is performed. These data reveal that the unusual electronic structure for this protein is a result of fluxionality of the heme axial methionine. It is proposed that the ligand undergoes inversion at the pyramidal sulfur, and the rapid interconversion between two diastereomeric forms results in the unusual heme electronic structure. Thus a fluxional process for a metal-bound amino acid side chain has now been identified.
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Affiliation(s)
- Linghao Zhong
- Department of Chemistry, University of Rochester, Rochester, NY 14627-0216, USA
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5
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Miller GT, Mackay DQ, Standley MS, Fields SL, Clary WM, Timkovich R. Expression of Pseudomonas stutzeri Zobell cytochrome c-551 and its H47A variant in Escherichia coli. Protein Expr Purif 2003; 29:244-51. [PMID: 12767816 DOI: 10.1016/s1046-5928(03)00065-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nirM gene encoding cytochrome c-551 from Pseudomonas stutzeri Zobell (PZ) has been expressed in Escherichia coli at levels higher than those previously reported but only under strict anaerobic growth conditions. Expression yields for wild-type cytochrome in this study typically reached 0.6 micromol per liter of saturated E. coli culture (5.5mg/L). Culture conditions investigated are compared to obtained c-551 expression levels; the results may lead to a greater understanding of the challenges encountered when expressing c-type hemoproteins in E. coli. The nirM gene was mutated to produce a histidine-47-alanine mutation of c-551 that been heterologously expressed in E. coli using optimum culture conditions and had its physiochemical properties compared to those of the wild-type protein. In PZ, the histidine-47 residue is part of a conserved hydrogen-bonding network located at the bottom of the heme crevice that also involves tryptophan-56 and a heme propionate. Ionization events within this network are experimentally demonstrated to modulate c-551 oxidation-reduction potential and its observed dependence on pH around neutrality. The redox potential of the mutant cytochrome still displays pH-dependence; however, the midpoint potential is approximately 25mV lower with respect to wild-type c-551 at neutral pH while the pK at which the heme propionate (HP-17) ionizes is lowered by 1.3 pH units. Temperature and chemical denaturant studies also show that loss of the hydrogen-bond-donating imidazole leads to a large decrease in c-551 tertiary stability.
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Affiliation(s)
- Gregory T Miller
- Department of Chemistry, Southern Oregon University, Ashland, OR 97520, USA.
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6
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Sivakolundu SG, Mabrouk PA. Structure-function relationship of reduced cytochrome c probed by complete solution structure determination in 30% acetonitrile/water solution. J Biol Inorg Chem 2003; 8:527-539. [PMID: 12764601 DOI: 10.1007/s00775-002-0437-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2002] [Accepted: 12/03/2002] [Indexed: 12/01/2022]
Abstract
The complete solution structure of ferrocytochrome c in 30% acetonitrile/70% water has been determined using high-field 1D and 2D (1)H NMR methods and deposited in the Protein Data Bank with codes 1LC1 and 1LC2. This is the first time a complete solution protein structure has been determined for a protein in nonaqueous media. Ferrocyt c retains a native protein secondary structure (five alpha-helices and two omega loops) in 30% acetonitrile. H18 and M80 residues are the axial heme ligands, as in aqueous solution. Residues believed to be axial heme ligands in the alkaline-like conformers of ferricyt c, specifically H33 and K72, are positioned close to the heme iron. The orientations of both heme propionates are markedly different in 30% acetonitrile/70% water. Comparative structural analysis of reduced cyt c in 30% acetonitrile/70% water solution with cyt c in different environments has given new insight into the cyt c folding mechanism, the electron transfer pathway, and cell apoptosis.
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Affiliation(s)
| | - Patricia Ann Mabrouk
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
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7
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Miller GT, Hardman JK, Timkovich R. Solution Conformation of the Met 61 to His 61 Mutant of Pseudomonas stutzeri ZoBell Ferrocytochrome c-551. Biophys J 2001; 80:2928-34. [PMID: 11371465 PMCID: PMC1301476 DOI: 10.1016/s0006-3495(01)76258-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The gene encoding for bacterial cytochrome c-551 from Pseudomonas stutzeri substrain ZoBell has been mutated to convert the invariant sixth ligand methionine residue into histidine, creating the site-specific mutant M61H. Proton NMR resonance assignments were made for all main-chain and most-side chain protons in the diamagnetic, reduced form at pH 9.2 and 333 K by two-dimensional NMR techniques. Distance constraints (1074) were determined from nuclear Overhauser enhancements and main-chain torsion-angle constraints (72) from scalar coupling estimates. Solution conformations for the protein were computed by the simulated annealing approach. For 28 computed structures, the root mean squared displacement from the average structure excluding the terminal residues 1, 2, 81, and 82 was 0.52 A (sigma = 0.096) for backbone atoms and 0.90 A (sigma = 0.122) for all heavy atoms. The global folding of the mutant protein is the same as for wild type. The biggest changes are localized in a peptide span over residues 60-65. The most striking behavior of the mutant protein is that at room temperature and neutral pH it exists in a state similar to the molten globular state that has been described for several proteins under mild denaturing conditions, but the mutant converts to a more ordered state at high pH and temperature.
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Affiliation(s)
- G T Miller
- Department of Chemistry, University of Alabama, Tuscaloosa, Alabama 35487, USA
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8
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Bersch B, Brutscher B, Meyer TE, Marion D. 1H and 13C NMR assignments and structural aspects of a ferrocytochrome c-551 from the purple phototrophic bacterium Ectothiorhodospira halophila. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 227:249-60. [PMID: 7851392 DOI: 10.1111/j.1432-1033.1995.tb20382.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two-dimensional nuclear magnetic resonance was used to assign the 1H and 13C resonances of ferrocytochrome c-551 from Ectothiorhodospira halophila, a halophilic phototrophic purple bacterium. This 78-residue protein belongs to a small subgroup of class I cytochromes c together with the analogous cytochromes c-551 from E. halochloris and E. abdelmalekii. A nearly complete assignment of 13C resonances was obtained at natural abundance using a gradient-enhanced 1H-detected heteronuclear single quantum coherence experiment (HSQC). This was found to be extremely useful for the unambigous assignment of side chain protons. The secondary structure of the protein was determined from analyses of short- and medium-range nuclear Overhauser enhancements (NOE), amide proton exchange and 13C alpha chemical shifts. Three helices could be identified which are well conserved among the class I cytochromes c. There is some evidence for two other regions of less well defined helical structure. From a preliminary analysis of long-range NOE it is shown that in the E. halophila cytochrome c-551 the general cytochrome c fold is well conserved, including the three conserved helices (residues 2-8, 41-50, 63-76), the regions around the heme ligands (Cys14-Ser15-Ser16-Cys17-His18, Met55) and the omega loop (residues 18-28). In addition, three variable segments of the protein are discussed in detail, one of those including a cis-proline, a feature so far unique in the cytochrome c family. Structural alignments of the E. halophila cytochrome c-551 with two other Pseudomonas cytochrome c5 homologs (Azotobacter vinelandii cytochrome c5 and Chlorobium limicola cytochrome c-555) are provided which are based on sequence similarities and secondary structure alignments.
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Affiliation(s)
- B Bersch
- Institut de Biologie Structurale-Jean-Pierre Ebel, CNRS-CEA, Grenoble, France
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9
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Timkovich R, Cai M, Zhang B, Arciero DM, Hooper AB. Characteristics of the paramagnetic 1H-NMR spectra of the ferricytochrome c-551 family. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 226:159-68. [PMID: 7957244 DOI: 10.1111/j.1432-1033.1994.tb20037.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Heme proton resonances have been assigned for ferricytochromes c-551 isolated from four distinct species of bacteria. While the available structure information indicates that the four cytochromes have very similar conformations in solution, including the chirality of the methionine ligand sulfur bond, the chemical shifts of the paramagnetically shifted resonances are surprisingly different, more so than has been previously reported for a homologous series of ferricytochromes. The resonances are contrasted in terms of chemical shift and the temperature dependence of the shift, which gives rise to a very strong anti-Curie effect for some specific protons. Non-methyl heme resonances do display an approximately conserved set of chemical shifts, but the heme methyl groups demonstrate a wide range of values. The 12(1) heme methyl group is always the highest frequency heme methyl, but the relative positions of the other methyl groups may change. The 7(1) heme methyl group always displayed strong anti-Curie behavior, while the 12(1) methyl group displayed normal Curie behavior. The behavior of the other methyl groups was variable. Possible reasons for the range of observations will be discussed. In spite of their NMR differences, all the ferricytochromes c-551 demonstrated comparable electron-transfer rates to a membrane-bound cytochrome reductase system.
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Affiliation(s)
- R Timkovich
- Department of Chemistry, University of Alabama, Tuscaloosa 35487-0336
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10
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Caffrey MS, Cusanovich MA. Site-specific mutagenesis studies of cytochromes c. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1187:277-88. [PMID: 7918530 DOI: 10.1016/0005-2728(94)90001-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- M S Caffrey
- Department of Biochemistry, University of Arizona, Tucson 85721
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11
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Cai M, Timkovich R. Solution conformation of cytochrome c-551 from Pseudomonas stutzeri ZoBell determined by NMR. Biophys J 1994; 67:1207-15. [PMID: 7811935 PMCID: PMC1225477 DOI: 10.1016/s0006-3495(94)80590-9] [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: 01/27/2023] Open
Abstract
1H NMR spectroscopy and solution structure computations have been used to examine ferrocytochrome c-551 from Pseudomonas stutzeri ZoBell (ATCC 14405). Resonance assignments are proposed for all main-chain and most side-chain protons. Stereospecific assignments were also made for some of the beta-methylene protons and valine methyl protons. Distance constraints were determined based upon nuclear Overhauser enhancements between pairs of protons. Dihedral angle constraints were determined from estimates of scalar coupling constants and intra-residue NOEs. Twenty structures were calculated by distance geometry and refined by energy minimization and simulated annealing on the basis of 1012 interproton distance and 74 torsion angle constraints. Both the main-chain and side-chain atoms are well defined except for two terminal residues, and some side-chain atoms located on the molecular surface. The average root mean squared deviation in the position for equivalent atoms between the 20 individual structures and the mean structure obtained by averaging their coordinates is 0.56 +/- 0.10 A for the main-chain atoms, and 0.95 +/- 0.09 A for all nonhydrogen atoms of residue 3 to 80 plus the heme group. The average structure was compared with an analogous protein, cytochrome c-551 from pseudomonas stutzeri. The main-chain folding patterns are very consistent, but there are some differences, some of which can be attributed to the loss of normally conserved aromatic residues in the ZoBell c-551.
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Affiliation(s)
- M Cai
- Department of Chemistry, University of Alabama, Tuscaloosa 35487-0336
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12
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Caffrey M, Brutscher B, Simorre JP, Fitch J, Cusanovich M, Marion D. Assignment of the 13C and 13CO resonances for Rhodobacter capsulatus ferrocytochrome c2 using double-resonance and triple-resonance NMR spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 221:63-75. [PMID: 8168550 DOI: 10.1111/j.1432-1033.1994.tb18715.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Rhodobacter capsulatus cytochrome c2 uniformly labelled with 13C/15N has been prepared. The 13C resonances of the reduced state, including those of the carbonyl and heme 13C, have been assigned using a combination of various two- and three-dimensional correlated NMR experiments. Assignment of the sidechain 13C resonances facilitated correction of a small number of previously misassigned sidechain 1H and led to the additional assignment of 32 1H. It was found that 13C alpha and 13CO secondary shifts were better indicators of secondary structure than 1H alpha and 13C beta secondary shifts. Moreover, it was demonstrated that, despite the significant ring current effects present in heme proteins, 13C alpha and 13CO secondary shifts can be employed to accurately identify secondary structure in heme proteins, independently of NOE experiments.
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Affiliation(s)
- M Caffrey
- Institut de Biologie Structurale, Grenoble, France
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13
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Arciero DM, Hooper AB, Cai M, Timkovich R. Evidence for the structure of the active site heme P460 in hydroxylamine oxidoreductase of Nitrosomonas. Biochemistry 1993; 32:9370-8. [PMID: 8369308 DOI: 10.1021/bi00087a016] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Hydroxylamine oxidoreductase (HAO) is responsible for the oxidation of hydroxylamine to nitrite in nitrification by Nitrosomonas europaea. It has an alpha n subunit structure and eight covalently bound hemes per subunit. Seven of these have visible spectra indistinguishable from heme c. The eighth, designated as P460, has unusual visible spectroscopic features in the enzyme and in a heme-containing proteolytic fragment. Its structure has not been previously determined. Enzymatic digestions of HAO were performed, and various proteolytic fragments were purified. Mass spectrometry confirmed the presence of authentic heme c in some fragments, that is, iron protoporphyrin IX cross-linked by two thioether bonds to cysteine residues. It was possible to detect the presence of the P460 pigment in some fragments, based upon the sensitivity of this pigment to treatment of the holoenzyme with hydrogen peroxide. A proteolytic fragment produced by sequential digestion with trypsin and pronase was shown to contain heme c and a hydrogen peroxide-sensitive heme with an unusual visible spectrum. This fragment contained two covalently cross-linked peptides. Mass spectrometry and NMR indicated that the P460 heme was iron protoporphyrin IX covalently bonded by two thioether bridges to peptide, but in addition there was a new, third covalent bond between a meso heme carbon and an aromatic ring carbon on a tyrosyl residue. The new covalent bond has been tentatively assigned to the C2 carbon of the tyrosyl ring and the 5-meso heme carbon (IUPAC-IUB tetrapyrrole nomenclature), although this location requires further proof.
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Affiliation(s)
- D M Arciero
- Department of Genetics and Cell Biology, University of Minnesota, St. Paul 55108
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14
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Greene RM, Betz SF, Hilgen-Willis S, Auld DS, Fencl JB, Pielak GJ. Changes in global stability and local structure of cytochrome c upon substituting phenylalanine-82 with tyrosine. J Inorg Biochem 1993; 51:663-76. [PMID: 8409983 DOI: 10.1016/0162-0134(93)85038-a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We have examined the F82Y;C102T variant of Saccharomyces cerevisiae iso-1-cytochrome c using high-resolution proton nuclear magnetic resonance spectroscopy, chemical denaturation, and differential scanning calorimetry. Comparison of proton chemical shifts, paramagnetic shifts, and nuclear Overhauser effects indicates structural changes are localized to the vicinity of position 82. One alteration involves the rearrangement of the side chain of leucine-85. Using many more proton assignments than were available in the initial report [G. J. Pielak, R. A. Atkinson, J. Boyd, and R. J. P. Williams, Eur. J. Biochem. 177, 179-185 (1988)], a second alteration involving an interaction between arginine-13 and tyrosine-82 is observed. The interaction appears to involve a hydrogen bond with the eta-protons of arginine's guanido group acting as donor and tyrosine's phenolic eta-oxygen as acceptor. In spite of this potentially-stabilizing interaction, the free energy of denaturation decreases by approximately 2.4 kcal mol-1. Results are discussed with respect to alterations in the native and denatured states.
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Affiliation(s)
- R M Greene
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290
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15
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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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16
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Abstract
The heme propionate substituents in Pseudomonas cytochrome c-551 are partially buried by folds of polypeptide in the structure of the protein, and are involved in several hydrogen bonds. The ionization behavior of these groups has been of interest because the oxidation potential of the heme changes with pH in a manner that may parallel ionization of a propionate. The ionization pKa's of these groups have been determined by following the NMR chemical shifts of nearby protons acting as probes of the ionization state of the propionates. In Pseudomonas aeruginosa c-551 the 13-propionate (IUB-IUPAC porphyrin nomenclature) has been assigned a pKa of 3.1, and the 17-propionate a pKa of 7.2. In the homologous Pseudomonas stutzeri c-551, the respective propionates both have pKa values of 3.0.
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Affiliation(s)
- M Cai
- Department of Chemistry, University of Alabama, Tuscaloosa 35487-0336
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17
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Timkovich R, Walker LA, Cai M. Hydrogen exchange in Pseudomonas cytochrome c-551. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1121:8-15. [PMID: 1318080 DOI: 10.1016/0167-4838(92)90330-g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Hydrogen exchange rates were measured or estimated for 75 amide protons in in ferrocytochrome c-551 from Pseudomonas aeruginosa (82 residues total) at neutral pH and 300 K. Rate constants span at least eight orders of magnitude. Rate constants or limiting estimates were determined by a combination of methods relying upon 1H-NMR spectroscopy, including the direct observation in one- or two-dimensional spectra of the decrease in proton intensity for samples dissolved in deuterium oxide, or, in a few favorable cases, saturation transfer from the solvent protic water. The heme ligand residues and the thioether bridge residues were slowly exchanging backbone amides, but the slowest exchanging backbone amides were found in two clusters. One was composed of Ile-48 and Lys-49 in the last turn of what is termed the 40's helix in the protein. The second was composed of Leu-74, Ala-75, Lys-76 and Val-78 in the C-terminal alpha helix.
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Affiliation(s)
- R Timkovich
- Department of Chemistry, University of Alabama, Tuscaloosa 35487-0336
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18
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Wishart DS, Sykes BD, Richards FM. Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J Mol Biol 1991; 222:311-33. [PMID: 1960729 DOI: 10.1016/0022-2836(91)90214-q] [Citation(s) in RCA: 1499] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An analysis of the 1H nuclear magnetic resonance chemical shift assignments and secondary structure designations for over 70 proteins has revealed some very strong and unexpected relationships. Similar studies, performed on smaller databases, for 13C and 15N chemical shifts reveal equally strong correlations to protein secondary structure. Among the more interesting results to emerge from this work is the finding that all 20 naturally occurring amino acids experience a mean alpha-1H upfield shift of 0.39 parts per million (from the random coil value) when placed in a helical configuration. In a like manner, the alpha-1H chemical shift is found to move downfield by an average of 0.37 parts per million when the residue is placed in a beta-strand or extended configuration. Similar changes are also found for amide 1H, carbonyl 13C, alpha-13C and amide 15N chemical shifts. Other relationships between chemical shift and protein conformation are also uncovered; in particular, a correlation between helix dipole effects and amide proton chemical shifts as well as a relationship between alpha-proton chemical shifts and main-chain flexibility. Additionally, useful relationships between alpha-proton chemical shifts and backbone dihedral angles as well as correlations between amide proton chemical shifts and hydrogen bond effects are demonstrated.
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Affiliation(s)
- D S Wishart
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
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19
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Wishart DS, Sykes BD, Richards FM. Simple techniques for the quantification of protein secondary structure by 1H NMR spectroscopy. FEBS Lett 1991; 293:72-80. [PMID: 1959674 DOI: 10.1016/0014-5793(91)81155-2] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Previous work by Wishart et al. (in press) and others [(1989) J. Magn. Reson. 83, 441-449; (1990) J. Magn. Reson. 90, 165-176] has shown a strong tendency for protein secondary structure to be manifested in 1H NMR chemical shifts. Based on these earlier results, two techniques have been developed for the quantification of secondary structure in proteins. Both methods allow for the rapid and accurate determination of the percent content of helix, coil, and beta-strand based on the integration (or peak enumeration) of selected portions of either 1-D or 2-D 1H NMR spectra. These new and very simple procedures have been found to compare quite favorably to other well established techniques for secondary structure determination such as CD, Raman and IR spectroscopy.
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Affiliation(s)
- D S Wishart
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
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20
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Detlefsen DJ, Thanabal V, Pecoraro VL, Wagner G. Solution structure of Fe(II) cytochrome c551 from Pseudomonas aeruginosa as determined by two-dimensional 1H NMR. Biochemistry 1991; 30:9040-6. [PMID: 1654086 DOI: 10.1021/bi00101a019] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The solution structure of Fe(II) cytochrome c551 from Pseudomonas aeruginosa based on 2D 1H NMR data is reported. Two sets of structure calculations were completed with a combination of simulated annealing and distance geometry calculations: one set of 20 structures included the heme-peptide covalent linkages, and one set of 10 structures excluded them. The main-chain atoms were well constrained within the two structural ensembles (1.30 and 1.35 A average RMSD, respectively) except for two regions spanning residues 30-40 and 60-70. The results were essentially the same when global fold comparisons were made between the ensembles with an average RMSD of 1.33 A. In total, 556 constraints were used, including 479 NOEs, 53 volume constraints, and 24 other distances. This report represents the first solution structure determination of a heme protein by 2D 1H NMR and should provide a basis for the application of these techniques to other proteins containing large prosthetic groups or cofactors.
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Affiliation(s)
- D J Detlefsen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
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21
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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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22
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Cai ML, Timkovich R. Proton resonance assignments for Pseudomonas aeruginosa ferrocytochrome c-551. Biochem Biophys Res Commun 1991; 178:309-14. [PMID: 1648911 DOI: 10.1016/0006-291x(91)91815-t] [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: 12/28/2022]
Abstract
A comparison between two sets of resonance assignments for ferrocytochrome c-551 from Pseudomonas aeruginosa reveals that major differences can be explained by pH effects. In turn, these reveal side chain protonation events in c-551 that markedly influence spectra. The behavior of resonances in a homologous protein from Pseudomonas stutzeri help to clarify ambiguities in the P. aeruginosa case. A corrected and completed set of proline assignments is presented. Labile side chain protons in residue 47, which hydrogen bonds to the inner heme propionate, appear to be in fast exchange with the solvent.
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Affiliation(s)
- M L Cai
- Department of Chemistry, University of Alabama, Tuscaloosa 35487
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23
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Gooley PR, Caffrey MS, Cusanovich MA, Mackenzie NE. A spectroscopic analysis of the Pro35----Ala mutant of Rhodobacter capsulatus cytochrome c2. The strictly conserved Pro35 is not structurally essential. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 196:653-61. [PMID: 1849479 DOI: 10.1111/j.1432-1033.1991.tb15862.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Visible, near-ultraviolet circular dichroic, near-infrared and nuclear magnetic resonance spectroscopies show that the secondary and tertiary structures of the mutant Pro35----Ala Rhodobacter capsulatus ferrocytochrome c2 are similar to the wild-type protein. The near-infrared spectrum shows that the methionine-S--Fe-heme bond is intact; however, a small red shift in the heme M transition of the near-ultraviolet circular dichroic spectrum of the mutant indicates that the heme environment may differ slightly between the two proteins. This difference may be a consequence of changes in the ligand and hydrogen bonds of His17 [Gooley, P. R. & MacKenzie, N. E. (1990) FEBS Lett. 260, 225-228]. 1H and 15N chemical shift differences suggest that the microenvironment of pyrrole rings III and IV of the heme prosthetic group differs between the two proteins. As the rings of the Phe51 and Tyr53 flip faster in the mutant protein than the wild type, these chemical shift differences may reflect changes in the time-average ring-current effects and not structural alterations.
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Affiliation(s)
- P R Gooley
- Department of Pharmaceutical Sciences, University of Arizona, Tucson 85721
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24
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Gao YA, Boyd J, Pielak GJ, Williams RJ. Comparison of reduced and oxidized yeast iso-1-cytochrome c using proton paramagnetic shifts. Biochemistry 1991; 30:1928-34. [PMID: 1847077 DOI: 10.1021/bi00221a028] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dipolar paramagnetic shifts for protons of yeast iso-1-cytochrome c have been calculated by using an optimized g-tensor and the X-ray crystallographic coordinates of the reduced form of yeast iso-1-cytochrome c [Louie, G. V., & Brayer, G. D. (1990) J. Mol. Biol. 214, 527-555]. The calculated values are compared with the observed paramagnetic shift determined from over 450 nonequivalent protons that have been assigned in both oxidation states [Gao, Y., Boyd, J., Williams, R. J. P., & Pielak, G. J. (1990) Biochemistry 29, 6994-7003]. There is good agreement between the calculated and the experimental data with a few exceptions. This indicates that, overall, the solution structures must be very similar in both the reduced and oxidized states in solution as is the case in crystals. The differences between observed and calculated shift values for the molecule in solution are most readily explained by slight movement of the heme and certain changes in diamagnetic shift due to small rearrangements of a few residues and some considerable changes in a few hydrogen bonds. It is also known that small differences exist between the structures of the two oxidation states in crystals but the hydrogen-bond changes are not so easily observed there. Structural changes from nuclear magnetic resonance data are in reasonable agreement with those deduced from crystallography, but additional information is clearly available concerning changes in hydrogen bonding.
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Affiliation(s)
- Y A Gao
- Inorganic Chemistry Laboratory, University of Oxford, U.K
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25
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Detlefsen DJ, Thanabal V, Pecoraro VL, Wagner G. Sequential 1H NMR assignments of iron(II) cytochrome c551 from Pseudomonas aeruginosa. Biochemistry 1990; 29:9377-86. [PMID: 2174259 DOI: 10.1021/bi00492a011] [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
Sequence-specific 1H NMR resonance assignments for all but the C-terminal Lys 82 are reported for iron(II) cytochrome c551 from Pseudomonas aeruginosa at 25 degrees C and pH = 6.8. Spin systems were identified by using TOCSY and DQF-COSY spectra in 2H2O and 1H2O. Sequential assignments were made by using NOESY connectivities between adjacent amide, alpha, and beta protons. Resonances from several amino acids including His 16, Gly 24, Ile 48, and Met 61 experience strong ring-current shifts due to their placement near the heme. All heme protons, including the previously unassigned propionates, have been identified. Preliminary analysis of sequential and medium-range NOEs provides evidence for substantial amounts of helix in the solution structure. Long-range NOEs indicate that the folds in solution and crystal structures are similar. For one aromatic side chain (Tyr 27) that is close to the heme group we found a transition from hindered ring rotation at low temperature to rapid rotation at high temperature.
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Affiliation(s)
- D J Detlefsen
- Department of Chemistry, University of Michigan, Willard H. Dow Laboratory, Ann Arbor 48109
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