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Müntener T, Joss D, Häussinger D, Hiller S. Pseudocontact Shifts in Biomolecular NMR Spectroscopy. Chem Rev 2022; 122:9422-9467. [PMID: 35005884 DOI: 10.1021/acs.chemrev.1c00796] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.
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Affiliation(s)
- Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Daniel Joss
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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2
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Falke S, Feiler C, Chapman H, Sarrou I. Crystal structures of native cytochrome c 6 from Thermosynechococcus elongatus in two different space groups and implications for its oligomerization. Acta Crystallogr F Struct Biol Commun 2020; 76:444-452. [PMID: 32880593 PMCID: PMC7470040 DOI: 10.1107/s2053230x20010249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/23/2020] [Indexed: 11/10/2022] Open
Abstract
Native cytochrome c6 was purified from an extract of strain BP-1 of the thermophilic cyanobacterium Thermosynechococcus elongatus. The protein was crystallized, and with only slight modifications of the buffer and vapour-diffusion conditions two different space groups were observed, namely H3 and C2. Both crystal structures were solved; they contained three and six molecules per asymmetric unit and were refined to 1.7 and 2.25 Å resolution, respectively. To date, the structure of native cytochrome c6 from T. elongatus has only been reported as a monomer using NMR spectroscopy, i.e. without addressing putative oligomerization, and related structures have only previously been solved using X-ray crystallography after recombinant gene overexpression in Escherichia coli. The reported space groups of related cyanobacterial cytochrome c6 structures differ from those reported here. Interestingly, the protein-protein interfaces that were observed utilizing X-ray crystallography could also explain homo-oligomerization in solution; specifically, trimerization is indicated by infra-red dynamic light scattering and blue native gel electrophoresis in solution. Trimers were also detected by mass spectrometry. Furthermore, there is an indication of post-translational methylation in the crystal structure. Additionally, the possibility of modifying the crystal size and the redox activity in the context of photosynthesis is shaping the investigated cytochrome as a highly suitable model protein for advanced serial crystallography at highly brilliant X-ray free-electron laser sources.
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Affiliation(s)
- Sven Falke
- Institute for Biochemistry and Molecular Biology, University of Hamburg, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Christian Feiler
- Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Henry Chapman
- Center for Free-Electron Laser Science, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Iosifina Sarrou
- Center for Free-Electron Laser Science, c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
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3
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Teixeira LR, Cordas CM, Fonseca MP, Duke NEC, Pokkuluri PR, Salgueiro CA. Modulation of the Redox Potential and Electron/Proton Transfer Mechanisms in the Outer Membrane Cytochrome OmcF From Geobacter sulfurreducens. Front Microbiol 2020; 10:2941. [PMID: 32010071 PMCID: PMC6971198 DOI: 10.3389/fmicb.2019.02941] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/06/2019] [Indexed: 11/13/2022] Open
Abstract
The monoheme outer membrane cytochrome F (OmcF) from Geobacter sulfurreducens plays an important role in Fe(III) reduction and electric current production. The electrochemical characterization of this cytochrome has shown that its redox potential is modulated by the solution pH (redox-Bohr effect) endowing the protein with the necessary properties to couple electron and proton transfer in the physiological range. The analysis of the OmcF structures in the reduced and oxidized states showed that with the exception of the side chain of histidine 47 (His47), all other residues with protonatable side chains are distant from the heme iron and, therefore, are unlikely to affect the redox potential of the protein. The protonatable site at the imidazole ring of His47 is in the close proximity to the heme and, therefore, this residue was suggested as the redox-Bohr center. In the present work, we tested this hypothesis by replacing the His47 with non-protonatable residues (isoleucine – OmcFH47I and phenylalanine – OmcFH47F). The structure of the mutant OmcFH47I was determined by X-ray crystallography to 1.13 Å resolution and showed only minimal changes at the site of the mutation. Both mutants were 15N-labeled and their overall folding was confirmed to be the same as the wild-type by NMR spectroscopy. The pH dependence of the redox potential of the mutants was measured by cyclic voltammetry. Compared to the wild-type protein, the magnitude of the redox-Bohr effect in the mutants was smaller, but not fully abolished, confirming the role of His47 on the pH modulation of OmcF’s redox potential. However, the pH effect on the heme substituents’ NMR chemical shifts suggested that the heme propionate P13 also contributes to the overall redox-Bohr effect in OmcF. In physiological terms, the contribution of two independent acid–base centers to the observed redox-Bohr effect confers OmcF a higher versatility to environmental changes by coupling electron/proton transfer within a wider pH range.
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Affiliation(s)
- Liliana R Teixeira
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Cristina M Cordas
- LAQV, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Marta P Fonseca
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Norma E C Duke
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Phani Raj Pokkuluri
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Carlos A Salgueiro
- UCIBIO-Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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4
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The dynamic complex of cytochrome c6 and cytochrome f studied with paramagnetic NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1305-15. [DOI: 10.1016/j.bbabio.2014.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/13/2014] [Accepted: 03/16/2014] [Indexed: 11/23/2022]
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5
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 559] [Impact Index Per Article: 55.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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6
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Affiliation(s)
- LUCIA BANCI
- Dipartimento di Chimica and CERM, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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7
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García-Rubio I, Medina M, Cammack R, Alonso PJ, Martínez JI. CW-EPR and ENDOR study of cytochrome c6 from Anabaena PCC 7119. Biophys J 2006; 91:2250-63. [PMID: 16798796 PMCID: PMC1557542 DOI: 10.1529/biophysj.105.080358] [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] [Received: 12/23/2005] [Accepted: 06/05/2006] [Indexed: 11/18/2022] Open
Abstract
The detailed analysis of the continuous-wave electron paramagnetic resonance and electron nuclear double resonance measurements on cytochrome c(6) from Anabaena PCC7119 reveals several electronic and structural properties of this hemeprotein. The oxidized protein shows two forms that differ in the arrangement of the residues that act as heme axial ligands. Information about the orientation of these residues is obtained for one of the forms, which turns out to differ from that found in the reduced protein from x-ray experiments. The biological significance of these results is discussed.
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Affiliation(s)
- Inés García-Rubio
- Instituto de Ciencia de Materiales de Aragón, CSIC-Universidad de Zaragoza, C/Pedro Cerbuna 12, E-50009 Zaragoza, Spain
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8
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Arnesano F, Banci L, Bertini I, Capozzi F, Ciofi-Baffoni S, Ciurli S, Luchinat C, Mangani S, Rosato A, Turano P, Viezzoli MS. An Italian contribution to structural genomics: Understanding metalloproteins. Coord Chem Rev 2006. [DOI: 10.1016/j.ccr.2006.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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9
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Lange C, Luque I, Hervás M, Ruiz-Sanz J, Mateo PL, De la Rosa MA. Role of the surface charges D72 and K8 in the function and structural stability of the cytochrome c6 from Nostoc sp. PCC 7119. FEBS J 2005; 272:3317-27. [PMID: 15978038 DOI: 10.1111/j.1742-4658.2005.04747.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated the role of electrostatic charges at positions D72 and K8 in the function and structural stability of cytochrome c6 from Nostoc sp. PCC 7119 (cyt c6). A series of mutant forms was generated to span the possible combinations of charge neutralization (by mutation to alanine) and charge inversion (by mutation to lysine and aspartate, respectively) in these positions. All forms of cyt c6 were functionally characterized by laser flash absorption spectroscopy, and their stability was probed by urea-induced folding equilibrium relaxation experiments and differential scanning calorimetry. Neutralization or inversion of the positive charge at position K8 reduced the efficiency of electron transfer to photosystem I. This effect could not be reversed by compensating for the change in global charge that had been introduced by the mutation, indicating a specific role for K8 in the formation of the electron transfer complex between cyt c6 and photosystem I. Replacement of D72 by asparagine or lysine increased the efficiency of electron transfer to photosystem I, but destabilized the protein. D72 apparently participates in electrostatic interactions that stabilize the structure of cyt c6. The destabilizing effect was reduced when aspartate was replaced by the small amino acid alanine. Complementing the mutation D72A with a charge neutralization or inversion at position K8 led to mutant forms of cyt c6 that were more stable than the wild-type under all tested conditions.
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Affiliation(s)
- Christian Lange
- Instituto de Bioquímica Vegetal y Fotosíntesis, Centro de Investigaciones Científicas Isla de la Cartuja, Seville, Spain.
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10
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Crowley PB, Díaz-Quintana A, Molina-Heredia FP, Nieto P, Sutter M, Haehnel W, De La Rosa MA, Ubbink M. The interactions of cyanobacterial cytochrome c6 and cytochrome f, characterized by NMR. J Biol Chem 2002; 277:48685-9. [PMID: 12356767 DOI: 10.1074/jbc.m203983200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During oxygenic photosynthesis, cytochrome c(6) shuttles electrons between the membrane-bound complexes cytochrome bf and photosystem I. Complex formation between Phormidium laminosum cytochrome f and cytochrome c(6) from both Anabaena sp. PCC 7119 and Synechococcus elongatus has been investigated by nuclear magnetic resonance spectroscopy. Chemical-shift perturbation analysis reveals a binding site on Anabaena cytochrome c(6), which consists of a predominantly hydrophobic patch surrounding the heme substituent, methyl 5. This region of the protein was implicated previously in the formation of the reactive complex with photosytem I. In contrast to the results obtained for Anabaena cytochrome c(6), there is no evidence for specific complex formation with the acidic cytochrome c(6) from Synechococcus. This remarkable variability between analogous cytochromes c(6) supports the idea that different organisms utilize distinct mechanisms of photosynthetic intermolecular electron transfer.
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Affiliation(s)
- Peter B Crowley
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P. O. Box 9502, The Netherlands
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11
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Goodfellow BJ, Nunes SG, Rusnak F, Moura I, Ascenso C, Moura JJG, Volkman BF, Markley JL. Zinc-substituted Desulfovibrio gigas desulforedoxins: resolving subunit degeneracy with nonsymmetric pseudocontact shifts. Protein Sci 2002; 11:2464-70. [PMID: 12237467 PMCID: PMC2373705 DOI: 10.1110/ps.0208802] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2002] [Revised: 07/09/2002] [Accepted: 07/17/2002] [Indexed: 10/27/2022]
Abstract
Desulfovibrio gigas desulforedoxin (Dx) consists of two identical peptides, each containing one [Fe-4S] center per monomer. Variants with different iron and zinc metal compositions arise when desulforedoxin is produced recombinantly from Escherichia coli. The three forms of the protein, the two homodimers [Fe(III)/Fe(III)]Dx and [Zn(II)/Zn(II)]Dx, and the heterodimer [Fe(III)/Zn(II)]Dx, can be separated by ion exchange chromatography on the basis of their charge differences. Once separated, the desulforedoxins containing iron can be reduced with added dithionite. For NMR studies, different protein samples were prepared labeled with (15)N or (15)N + (13)C. Spectral assignments were determined for [Fe(II)/Fe(II)]Dx and [Fe(II)/Zn(II)]Dx from 3D (15)N TOCSY-HSQC and NOESY-HSQC data, and compared with those reported previously for [Zn(II)/Zn(II)]Dx. Assignments for the (13)C(alpha) shifts were obtained from an HNCA experiment. Comparison of (1)H-(15)N HSQC spectra of [Zn(II)/Zn(II)]Dx, [Fe(II)/Fe(II)]Dx and [Fe(II)/Zn(II)]Dx revealed that the pseudocontact shifts in [Fe(II)/Zn(II)]Dx can be decomposed into inter- and intramonomer components, which, when summed, accurately predict the observed pseudocontact shifts observed for [Fe(II)/Fe(II)]Dx. The degree of linearity observed in the pseudocontact shifts for residues >/=8.5 A from the metal center indicates that the replacement of Fe(II) by Zn(II) produces little or no change in the structure of Dx. The results suggest a general strategy for the analysis of NMR spectra of homo-oligomeric proteins in which a paramagnetic center introduced into a single subunit is used to break the magnetic symmetry and make it possible to obtain distance constraints (both pseudocontact and NOE) between subunits.
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12
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De la Rosa MA, Navarro JA, Díaz-Quintana A, De la Cerda B, Molina-Heredia FP, Balme A, Murdoch PDS, Díaz-Moreno I, Durán RV, Hervás M. An evolutionary analysis of the reaction mechanisms of photosystem I reduction by cytochrome c(6) and plastocyanin. Bioelectrochemistry 2002; 55:41-5. [PMID: 11786337 DOI: 10.1016/s1567-5394(01)00136-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Photosystem I reduction by the soluble metalloproteins cytochrome c(6) and plastocyanin, which are alternatively synthesized by some photosynthetic organisms depending on the relative availability of copper and iron, has been investigated in cyanobacteria, green algae and plants. The reaction mechanism is classified in three different types on the basis of the affinity of the membrane complex towards its electron donor protein. The role of electrostatic interactions in forming an intermediate transient complex, as well as the structural and functional similarities of cytochrome c(6) and plastocyanin are analysed from an evolutionary point of view. The proposal made is that the heme protein was first "discovered" by nature, when iron was much more abundant on the Earth's surface, and replaced by plastocyanin when copper became available because of the oxidizing conditions of the new atmosphere.
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Affiliation(s)
- Miguel A De la Rosa
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla y Consejo Superior de Investigaciones Científicas, Américo Vespucio s/n, E-41092 Seville, Spain.
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13
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Affiliation(s)
- I Bertini
- Magnetic Resonance Center (CERM), University of Florence, Florence 50019, Italy
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14
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Metzler DE, Metzler CM, Sauke DJ. Transition Metals in Catalysis and Electron Transport. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Pristovsek P, Lücke C, Reincke B, Ludwig B, Rüterjans H. Solution structure of the functional domain of Paracoccus denitrificans cytochrome c552 in the reduced state. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:4205-12. [PMID: 10866825 DOI: 10.1046/j.1432-1327.2000.01456.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In order to determine the solution structure of Paracoccus denitrificans cytochrome c552 by NMR, we cloned and isotopically labeled a 10.5-kDa soluble fragment (100 residues) containing the functional domain of the 18.2-kDa membrane-bound protein. Using uniformly 15N-enriched samples of cytochrome c552 in the reduced state, a variety of two-dimensional and three-dimensional heteronuclear double-resonance NMR experiments was employed to achieve complete 1H and 15N assignments. A total of 1893 distance restraints was derived from homonuclear 2D-NOESY and heteronuclear 3D-NOESY spectra; 1486 meaningful restraints were used in the structure calculations. After restrained energy minimization a family of 20 structures was obtained with rmsd values of 0.56 +/- 0. 10 A and 1.09 +/- 0.09 A for the backbone and heavy atoms, respectively. The overall topology is similar to that seen in previously reported models of this class of proteins. The global fold consists of two long helices at the N-terminus and C-terminus and three shorter helices surrounding the heme moiety; the helices are connected by well-defined loops. Comparison with the X-ray structure shows some minor differences in the positions of the Trp57 and Phe65 side-chain rings as well as the heme propionate groups.
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Affiliation(s)
- P Pristovsek
- Institute of Biophysical Chemistry, J.W. Goethe-University of Frankfurt, Germany
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16
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Bertini I, Luchinat C, Rosato A. The use of propionate α-proton contact shifts as structural constraints. Inorganica Chim Acta 2000. [DOI: 10.1016/s0020-1693(99)00311-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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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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18
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Abstract
The methodological accessibility to solution structure and dynamic investigation of paramagnetic metallobiomolecules has afforded the ability to tackle the redox pairs of electron transfer proteins of which at least one is paramagnetic, to study the orientation effects of high magnetic fields on paramagnetic biomolecules, and finally to study the role of metal-based cofactors in protein folding and stability.
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Affiliation(s)
- I Bertini
- Department of Chemistry, University of Florence, Via Gino Capponi 7, 50121 Florence, Italy.
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19
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Arnesano F, Banci L, Bertini I, Felli IC, Koulougliotis D. Solution structure of the B form of oxidized rat microsomal cytochrome b5 and backbone dynamics via 15N rotating-frame NMR-relaxation measurements. Biological implications. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 260:347-54. [PMID: 10095768 DOI: 10.1046/j.1432-1327.1999.00167.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cytochrome b5 in solution has two isomers (A and B) differing by a 180 degrees rotation of the protoporphyrin IX plane around the axis defined by the alpha and gamma meso protons. Homonuclear and heteronuclear NMR spectroscopy has been employed in order to solve the solution structure of the minor (B) form of the oxidized state of the protein and to probe its backbone dynamics in the microsecond--ms timescale in both oxidation states. A family of 40 conformers has been obtained using 1302 meaningful NOEs and 220 pseudocontact shifts and is characterized by high quality and good resolution (rmsd to the mean structure of 0.055 +/- 0.009 nm and 0.103 +/- 0.011 nm for backbone and heavy atoms, respectively). Extensive comparisons of the structural and dynamics changes associated with the A-to-B form interconversion for both oxidation states were subsequently performed. Propionate 6 experiences a redox-state-dependent reorientation as does propionate 7 in the A form. Significant insights are obtained into the role of the protein frame for efficient biological function and backbone mobility is proposed to be one of the factors that could control the reduction potential of the heme.
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Affiliation(s)
- F Arnesano
- Department of Chemistry, University of Florence, Italy
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20
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Case DA. The use of chemical shifts and their anisotropies in biomolecular structure determination. Curr Opin Struct Biol 1998; 8:624-30. [PMID: 9818268 DOI: 10.1016/s0959-440x(98)80155-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The existence of chemical shift dispersion is crucial for the application of NMR spectroscopy to biomolecules, but the direct interpretation of shift tensors in terms of structure and dynamics is often difficult. Proton shifts reflect environmental influences from nearby aromatic groups, metal sites or hydrogen-bonding partners. These effects can be reasonably modeled with empirical equations, but multiple contributions to shifts can be difficult to disentangle. Shifts for carbon and nitrogen generally reflect local bonding interactions, often in ways that allow the local structure to be inferred. The anisotropy of the shielding tensor is also of interest. It influences the resonance position in partially-ordered samples and has consequences for spin relaxation, even in isotropic systems. There has been recent progress in measuring and interpreting these anisotropies.
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Affiliation(s)
- D A Case
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
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