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Determination of the magnetic properties and orientation of the heme axial ligands of PpcA from Geobacter metallireducens by paramagnetic NMR. J Inorg Biochem 2019; 198:110718. [PMID: 31153111 DOI: 10.1016/j.jinorgbio.2019.110718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 11/22/2022]
Abstract
The rising interest in the use of Geobacter bacteria for biotechnological applications demands a deep understanding of how these bacteria are able to thrive in a variety of environments and perform extracellular electron transfer. The Geobacter metallireducens bacterium can couple the oxidation of a wide range of compounds to the reduction of several extracellular acceptors, including heavy metals, toxic organic compounds or electrode surfaces. The periplasmic c-type cytochrome PpcA from this bacterium is a member of a family composed of five periplasmic triheme cytochromes, which are important to bridge the electron transfer between the cytoplasm and the extracellular environment. To better understand the functional mechanism of PpcA it is essential to obtain structural data for this cytochrome. In this work, the geometry of the heme axial ligands, as well as the magnetic properties of the hemes were determined for the oxidized form of the cytochrome, using the 13C NMR chemical shifts of the heme α-substituents. The results were further compared with those previously obtained for the homologous cytochrome from Geobacter sulfurreducens. The orientations of the axial histidine planes and the magnetic properties of the hemes are conserved in both proteins. Overall, the results obtained allowed the definition of the orientation of the magnetic axes of PpcA from G. metallireducens, which will be used as constraints to assist the solution structure determination of the cytochrome in the oxidized form.
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2
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Balakrishnan S, Sarma SP. Engineering Aromatic–Aromatic Interactions To Nucleate Folding in Intrinsically Disordered Regions of Proteins. Biochemistry 2017; 56:4346-4359. [DOI: 10.1021/acs.biochem.7b00437] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Swati Balakrishnan
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Siddhartha P. Sarma
- Molecular
Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
- NMR
Research Center, Indian Institute of Science, Bangalore, Karnataka 560012, India
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3
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Redox- and pH-linked conformational changes in triheme cytochrome PpcA from Geobacter sulfurreducens. Biochem J 2016; 474:231-246. [PMID: 28062839 DOI: 10.1042/bcj20160932] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/10/2016] [Accepted: 11/14/2016] [Indexed: 11/17/2022]
Abstract
The periplasmic triheme cytochrome PpcA from Geobacter sulfurreducens is highly abundant; it is the likely reservoir of electrons to the outer surface to assist the reduction of extracellular terminal acceptors; these include insoluble metal oxides in natural habitats and electrode surfaces from which electricity can be harvested. A detailed thermodynamic characterization of PpcA showed that it has an important redox-Bohr effect that might implicate the protein in e-/H+ coupling mechanisms to sustain cellular growth. This functional mechanism requires control of both the redox state and the protonation state. In the present study, isotope-labeled PpcA was produced and the three-dimensional structure of PpcA in the oxidized form was determined by NMR. This is the first solution structure of a G. sulfurreducens cytochrome in the oxidized state. The comparison of oxidized and reduced structures revealed that the heme I axial ligand geometry changed and there were other significant changes in the segments near heme I. The pH-linked conformational rearrangements observed in the vicinity of the redox-Bohr center, both in the oxidized and reduced structures, constitute the structural basis for the differences observed in the pKa values of the redox-Bohr center, providing insights into the e-/H+ coupling molecular mechanisms driven by PpcA in G. sulfurreducens.
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4
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Solution structure of a mutant of the triheme cytochrome PpcA from Geobacter sulfurreducens sheds light on the role of the conserved aromatic residue F15. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:484-92. [DOI: 10.1016/j.bbabio.2012.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 12/11/2012] [Accepted: 12/14/2012] [Indexed: 11/22/2022]
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5
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Direct electrochemical analyses of human cytochromes b5 with a mutated heme pocket showed a good correlation between their midpoint and half wave potentials. J Biomed Sci 2010; 17:90. [PMID: 21129218 PMCID: PMC3014896 DOI: 10.1186/1423-0127-17-90] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 12/04/2010] [Indexed: 11/10/2022] Open
Abstract
Background Cytochrome b5 performs central roles in various biological electron transfer reactions, where difference in the redox potential of two reactant proteins provides the driving force. Redox potentials of cytochromes b5 span a very wide range of ~400 mV, in which surface charge and hydrophobicity around the heme moiety are proposed to have crucial roles based on previous site-directed mutagenesis analyses. Methods Effects of mutations at conserved hydrophobic amino acid residues consisting of the heme pocket of cytochrome b5 were analyzed by EPR and electrochemical methods. Cyclic voltammetry of the heme-binding domain of human cytochrome b5 (HLMWb5) and its site-directed mutants was conducted using a gold electrode pre-treated with β-mercarptopropionic acid by inclusion of positively-charged poly-L-lysine. On the other hand, static midpoint potentials were measured under a similar condition. Results Titration of HLMWb5 with poly-L-lysine indicated that half-wave potential up-shifted to -19.5 mV when the concentration reached to form a complex. On the other hand, midpoint potentials of -3.2 and +16.5 mV were obtained for HLMWb5 in the absence and presence of poly-L-lysine, respectively, by a spectroscopic electrochemical titration, suggesting that positive charges introduced by binding of poly-L-lysine around an exposed heme propionate resulted in a positive shift of the potential. Analyses on the five site-specific mutants showed a good correlation between the half-wave and the midpoint potentials, in which the former were 16~32 mV more negative than the latter, suggesting that both binding of poly-L-lysine and hydrophobicity around the heme moiety regulate the overall redox potentials. Conclusions Present study showed that simultaneous measurements of the midpoint and the half-wave potentials could be a good evaluating methodology for the analyses of static and dynamic redox properties of various hemoproteins including cytochrome b5. The potentials might be modulated by a gross conformational change in the tertiary structure, by a slight change in the local structure, or by a change in the hydrophobicity around the heme moiety as found for the interaction with poly-L-lysine. Therefore, the system consisting of cytochrome b5 and its partner proteins or peptides might be a good paradigm for studying the biological electron transfer reactions.
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Yu CT, Guo YL, Lü L, Wang YH, Yao P, Huang ZX. Study on the Gas Phase Stability of Heme-binding Pocket in Cytochrome Tb5 and Its Mutants by Electrospray Mass Spectrometry. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.20020201215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Paixão VB, Salgueiro CA, Brennan L, Reid GA, Chapman SK, Turner DL. The Solution Structure of a Tetraheme Cytochrome from Shewanella frigidimarina Reveals a Novel Family Structural Motif. Biochemistry 2008; 47:11973-80. [DOI: 10.1021/bi801326j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vitor B. Paixão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal, Requimte, CQFB, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal, UCD Conway Institute, UCD School of Agriculture, Food Science and Veterinary Medicine, UCD, Belfield, Dublin 4, Ireland, Institute of Structural and Molecular Biology, University of Edinburgh, Mayfield Road,
| | - Carlos A. Salgueiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal, Requimte, CQFB, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal, UCD Conway Institute, UCD School of Agriculture, Food Science and Veterinary Medicine, UCD, Belfield, Dublin 4, Ireland, Institute of Structural and Molecular Biology, University of Edinburgh, Mayfield Road,
| | - Lorraine Brennan
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal, Requimte, CQFB, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal, UCD Conway Institute, UCD School of Agriculture, Food Science and Veterinary Medicine, UCD, Belfield, Dublin 4, Ireland, Institute of Structural and Molecular Biology, University of Edinburgh, Mayfield Road,
| | - Graeme A. Reid
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal, Requimte, CQFB, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal, UCD Conway Institute, UCD School of Agriculture, Food Science and Veterinary Medicine, UCD, Belfield, Dublin 4, Ireland, Institute of Structural and Molecular Biology, University of Edinburgh, Mayfield Road,
| | - Stephen K. Chapman
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal, Requimte, CQFB, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal, UCD Conway Institute, UCD School of Agriculture, Food Science and Veterinary Medicine, UCD, Belfield, Dublin 4, Ireland, Institute of Structural and Molecular Biology, University of Edinburgh, Mayfield Road,
| | - David L. Turner
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal, Requimte, CQFB, Requimte, CQFB, Departamento de Química da Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal, UCD Conway Institute, UCD School of Agriculture, Food Science and Veterinary Medicine, UCD, Belfield, Dublin 4, Ireland, Institute of Structural and Molecular Biology, University of Edinburgh, Mayfield Road,
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Vu BC, Vuletich DA, Kuriakose SA, Falzone CJ, Lecomte JTJ. Characterization of the heme–histidine cross-link in cyanobacterial hemoglobins from Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002. J Biol Inorg Chem 2004; 9:183-94. [PMID: 14727166 DOI: 10.1007/s00775-003-0512-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2003] [Accepted: 11/28/2003] [Indexed: 12/16/2022]
Abstract
The recombinant product of the hemoglobin gene of the cyanobacterium Synechocystis sp. PCC 6803 forms spontaneously a covalent bond linking one of the heme vinyl groups to a histidine located in the C-terminal helix (His117, or H16). The present report describes the (1)H, (15)N, and (13)C NMR spectroscopy experiments demonstrating that the recombinant hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002, a protein sharing 59% identity with Synechocystis hemoglobin, undergoes the same facile heme adduct formation. The observation that the extraordinary linkage is not unique to Synechocystis hemoglobin suggests that it constitutes a noteworthy feature of hemoglobin in non-N(2)-fixing cyanobacteria, along with the previously documented bis-histidine coordination of the heme iron. A qualitative analysis of the hyperfine chemical shifts of the ferric proteins indicated that the cross-link had modest repercussions on axial histidine ligation and heme electronic structure. In Synechocystis hemoglobin, the unreacted His117 imidazole had a normal p K(a) whereas the protonation of the modified residue took place at lower pH. Optical experiments revealed that the cross-link stabilized the protein with respect to thermal and acid denaturation. Replacement of His117 with an alanine yielded a species inert to adduct formation, but inspection of the heme chemical shifts and ligand binding properties of the variant identified position 117 as important in seating the cofactor in its site and modifying the dynamic properties of the protein. A role for bis-histidine coordination and covalent adduct formation in heme retention is proposed.
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Affiliation(s)
- B Christie Vu
- Chemistry Department, The Pennsylvania State University, 152 Davey Laboratory, University Park, PA 16802, USA
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9
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Cao C, Zhang Q, Wang ZQ, Wang YF, Wang YH, Wu H, Huang ZX. 1H NMR studies of the effect of mutation at Valine45 on heme microenvironment of cytochrome b5. Biochimie 2003; 85:1007-16. [PMID: 14644556 DOI: 10.1016/j.biochi.2003.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
1D and 2D (1)H NMR were employed to probe the effects on the heme microenvironment of cytochrome b(5) caused by the mutation from Val45 to Tyr45, His45 and Glu45. Compared with wild type (WT) cytochrome b(5), in all mutants the heme ring are CCW rotated relative to the imidazole planes of axial ligands and the angles beta between two axial ligand imidazole planes are not changed, being in agreement with the temperature dependence of the shifts of the heme protons. The ratios of heme isomers (major to minor) are smaller than that in WT. The 4-vinyl group of the heme in V45Y assumes cis-orientation, being similar to that of WT, while in V45E and V45H, both cis and trans orientation are found. The relationships between the structure and biological function of the mutants are discussed in terms of the geometry of heme and axial ligands, the hydrophobicity of heme pocket and the electrostatic potential of the heme-exposed area.
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Affiliation(s)
- Chunyang Cao
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Feng Lin Lu (Road), Shanghai 200032, China
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Banci L, Bertini I, Branchini BR, Hajieva P, Spyroulias GA, Turano P. Dimethyl propionate ester heme-containing cytochrome b5: structure and stability. J Biol Inorg Chem 2001; 6:490-503. [PMID: 11472013 DOI: 10.1007/s007750100217] [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] [Indexed: 11/30/2022]
Abstract
A derivative of rat microsomal cytochrome b5, obtained by substitution of the native heme moiety with protoporphyrin IX dimethyl ester, has been characterized by 1H and 15N NMR spectroscopy. Besides the two usual A and B forms, which depend on the orientation of the heme in the prostethic group cavity, two other minor forms have been detected which presumably indicate different conformations of the vinyl side chains. The shifts of the heme methyls, as well as the directions of the rhombic axes of the magnetic susceptibility tensor, indicate a small difference in the orientation of the imidazole planes of the histidine axial ligands. The solution structure was determined by using 1,303 meaningful NOEs and 241 pseudocontact shifts, the latter being derived from the native reduced protein. A family of 40 energy-minimized conformers was obtained with average RMSD of 0.56+/-0.09 A and 1.04+/-0.12 A for backbone and heavy atoms, respectively, and distance and pseudocontact shift penalty functions of 0.50+/-0.07 A2 and 0.51+/-0.02 ppm2. The structure shows some changes around the cavity and in particular a movement of the 60-70 backbone segment owing to the absence of two hydrogen bonds between the Ser64 backbone NH and side-chain OH and the carboxylate oxygen of propionate-7, present in the native protein. The analysis of the NMR spectra in the presence of unfolding agents indicates that this protein is less stable than the native form. The decrease in stability may be the result of the loss of the two hydrogen bonds connecting propionate-7 to Ser64 in the native protein. The available data on the reduction potential and the electron transfer rates are discussed on the basis of the present structural data.
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Affiliation(s)
- L Banci
- Magnetic Resonance Center, University of Florence, Italy
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11
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Wang ZQ, Wang YH, Wang WH, Xue LL, Wu XZ, Xie Y, Huang ZX. The effect of mutation at valine-45 on the stability and redox potentials of trypsin-cleaved cytochrome b5. Biophys Chem 2000; 83:3-17. [PMID: 10631476 DOI: 10.1016/s0301-4622(99)00119-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In an attempt to elucidate the determinants of redox potential and protein stability in cytochrome b5, three mutants at a highly conserved residue Val45, which is a member of heme hydrophobic pocket residues have been characterized. The V45Y mutant was designed to introduce a bulkier residue and a hydroxyl group to the heme pocket. The mutants V45H and V45E were constructed to test the effect of positive and negative charge on the stability and redox potential of proteins. The influence of these mutants on the protein stability towards thermal, urea, acid, ethanol and on the redox potential were studied. It is concluded that the decrease of hydrophobic free energy and the larger volume of the tyrosine make the phenylhydroxyl group of tyrosine still sitting inside the hydrophobic pocket, while the side chain of the mutant V45E and V45H shift away from the heme pocket. The redox potentials of mutants V45Y, V45H, V45E and wild-type of cytochrome b5 are -35 mV, 8 mV, -26 mV and -3 mV, respectively. The bigger change of the V45Y on redox potential is due to the close contact between the hydroxyl group and the heme, while the changes of the V45E and V45H result from the alteration of charge density and distribution around the heme. Different relative stability of these mutants towards heat have been observed with the order: WT > V45Y-V45H > V45E being both in the oxidized and reduced state. The relative stability induced by addition of urea decreases in the order: WT > V45Y > V45H > V45E. These results suggest that the difference in the hydrophobic free energy is a major factor contributing to the stability of the Val45 mutants. Also the loose of the helix III in the mutant V45E makes it more unstable. These results indicate that residue Val45 plays an important role in the stability and redox potential of the protein.
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Affiliation(s)
- Z Q Wang
- Chemistry Department, Fudan University, Shanghai, PR China
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12
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Walker F. Magnetic spectroscopic (EPR, ESEEM, Mössbauer, MCD and NMR) studies of low-spin ferriheme centers and their corresponding heme proteins. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(99)00029-6] [Citation(s) in RCA: 234] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Dangi B, Blankman JI, Miller CJ, Volkman BF, Guiles RD. Contribution of Backbone Dynamics to Entropy Changes Occurring on Oxidation of Cytochrome b5. Can Redox Linked Changes in Hydrogen Bond Networks Modulate Reduction Potentials? J Phys Chem B 1998. [DOI: 10.1021/jp981050h] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bindi Dangi
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, Maryland 21201, The Medical Biotechnology Center, an institute of the Maryland Biotechnology Institutes, 725 W Lombard Street, Baltimore, Maryland 21201, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Nuclear Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, Wisconsin 53706
| | - Jeffrey I. Blankman
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, Maryland 21201, The Medical Biotechnology Center, an institute of the Maryland Biotechnology Institutes, 725 W Lombard Street, Baltimore, Maryland 21201, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Nuclear Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, Wisconsin 53706
| | - Cary J. Miller
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, Maryland 21201, The Medical Biotechnology Center, an institute of the Maryland Biotechnology Institutes, 725 W Lombard Street, Baltimore, Maryland 21201, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Nuclear Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, Wisconsin 53706
| | - Brian F. Volkman
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, Maryland 21201, The Medical Biotechnology Center, an institute of the Maryland Biotechnology Institutes, 725 W Lombard Street, Baltimore, Maryland 21201, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Nuclear Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, Wisconsin 53706
| | - R. D. Guiles
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 North Pine Street, Baltimore, Maryland 21201, The Medical Biotechnology Center, an institute of the Maryland Biotechnology Institutes, 725 W Lombard Street, Baltimore, Maryland 21201, Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, and Nuclear Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, Wisconsin 53706
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Shokhirev NV, Walker FA. Co- and Counterrotation of Magnetic Axes and Axial Ligands in Low-Spin Ferriheme Systems. J Am Chem Soc 1998. [DOI: 10.1021/ja972265s] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nikolai V. Shokhirev
- Contribution from the Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - F. Ann Walker
- Contribution from the Department of Chemistry, University of Arizona, Tucson, Arizona 85721
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Banci L, Bertini I, Ferroni F, Rosato A. Solution structure of reduced microsomal rat cytochrome b5. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 249:270-9. [PMID: 9363779 DOI: 10.1111/j.1432-1033.1997.t01-1-00270.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The solution structure of the major form of the reduced soluble fragment of rat microsomal cytochrome b5 has been solved through 1H-NMR spectroscopy. The protein contains 98 amino acids. Proton assignment was available for residues 1-94, except 90 [Guiles, R. D., Basus, V. J., Kuntz, I. D. & Waskell, L. (1992) Biochemistry 31, 11,365-11,375] and has been confirmed. From 1722 NOEs, of which 1203 were found to be meaningful, a family of 40 energy-minimized structures has been obtained with average backbone rmsd (for residues 5-89) of 0.078 +/- 0.018 nm and average target function of 0.0045 nm2, no distance violations being larger than 0.029 nm. The structure has been compared with the X-ray structure of the oxidized rat mitochondrial isoenzyme and with that of the highly similar bovine microsomal isoenzyme in the oxidized form. The analysis of the elements of secondary structure is instructive in terms of their stability and of their occurrence in related structures, and of the capability of NMR and X-ray spectroscopy to observe them. Some detailed structural variations are noticed among the solved structures of the various isoenzymes and between solid and solution. The structural features in solution of the residues proposed to be involved in protein-protein recognition are found to be largely conserved with respect to the solid state.
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Affiliation(s)
- L Banci
- Department of Chemistry, University of Florence, Italy
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