1
|
Paramagnetic NMR Spectroscopy Is a Tool to Address Reactivity, Structure, and Protein–Protein Interactions of Metalloproteins: The Case of Iron–Sulfur Proteins. MAGNETOCHEMISTRY 2020. [DOI: 10.3390/magnetochemistry6040046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The study of cellular machineries responsible for the iron–sulfur (Fe–S) cluster biogenesis has led to the identification of a large number of proteins, whose importance for life is documented by an increasing number of diseases linked to them. The labile nature of Fe–S clusters and the transient protein–protein interactions, occurring during the various steps of the maturation process, make their structural characterization in solution particularly difficult. Paramagnetic nuclear magnetic resonance (NMR) has been used for decades to characterize chemical composition, magnetic coupling, and the electronic structure of Fe–S clusters in proteins; it represents, therefore, a powerful tool to study the protein–protein interaction networks of proteins involving into iron–sulfur cluster biogenesis. The optimization of the various NMR experiments with respect to the hyperfine interaction will be summarized here in the form of a protocol; recently developed experiments for measuring longitudinal and transverse nuclear relaxation rates in highly paramagnetic systems will be also reviewed. Finally, we will address the use of extrinsic paramagnetic centers covalently bound to diamagnetic proteins, which contributed over the last twenty years to promote the applications of paramagnetic NMR well beyond the structural biology of metalloproteins.
Collapse
|
2
|
Sánchez-López C, Fernández CO, Quintanar L. Neuroprotective alpha-cleavage of the human prion protein significantly impacts Cu(ii) coordination at its His111 site. Dalton Trans 2018; 47:9274-9282. [DOI: 10.1039/c7dt03400h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Alpha-cleavage proteolytic processing of human prion protein significantly impacts its Cu(ii) coordination properties at the His111 site.
Collapse
Affiliation(s)
- Carolina Sánchez-López
- Departamento de Química
- Centro de Investigación y de Estudios Avanzados (Cinvestav)
- Mexico City
- Mexico
| | - Claudio O. Fernández
- Max Planck Laboratory for Structural Biology
- Chemistry and Molecular Biophysics of Rosario (MPLbioR
- UNR-MPIbpC) and Instituto de Investigaciones para el Descubrimiento de Fármacos de Rosario (IIDEFAR
- UNR-CONICET)
- Universidad Nacional de Rosario
| | - Liliana Quintanar
- Departamento de Química
- Centro de Investigación y de Estudios Avanzados (Cinvestav)
- Mexico City
- Mexico
| |
Collapse
|
3
|
Sánchez-López C, Cortés-Mejía R, Miotto MC, Binolfi A, Fernández CO, Del Campo JM, Quintanar L. Copper Coordination Features of Human Islet Amyloid Polypeptide: The Type 2 Diabetes Peptide. Inorg Chem 2016; 55:10727-10740. [PMID: 27704849 DOI: 10.1021/acs.inorgchem.6b01963] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Human islet amyloid polypeptide (hIAPP) is the major component of amyloid deposits found in pancreatic β-cells of patients with type 2 diabetes (T2D). Copper ions have an inhibitory effect on the amyloid aggregation of hIAPP, and they may play a role in the etiology of T2D. However, deeper knowledge of the structural details of the copper-hIAPP interaction is required to understand the molecular mechanisms involved. Here, we performed a spectroscopic study of Cu(II) binding to hIAPP and several variants, using electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electronic absorption, and circular dichroism (CD) in the UV-vis region in combination with Born-Oppenheimer molecular dynamics (BOMD) and density functional theory geometry optimizations. We find that Cu(II) binds to the imidazole N1 of His18, the deprotonated amides of Ser19 and Ser20, and an oxygen-based ligand provided by Ser20, either via its hydroxyl group or its backbone carbonyl, while Asn22 might also play a role as an axial ligand. Ser20 plays a crucial role in stabilizing Cu(II) coordination toward the C-terminal, providing a potential link between the S20G mutation associated with early onset of T2D, its impact in Cu binding properties, and hIAPP amyloid aggregation. Our study defines the nature of the coordination environment in the Cu(II)-hIAPP complex, revealing that the amino acid residues involved in metal ion binding are also key residues for the formation of β-sheet structures and amyloid fibrils. Cu(II) binding to hIAPP may lead to the coexistence of more than one coordination mode, which in turn could favor different sets of Cu-induced conformational ensembles. Cu-induced hIAPP conformers would display a higher energetic barrier to form amyloid fibrils, hence explaining the inhibitory effect of Cu ions in hIAPP aggregation. Overall, this study provides further structural insights into the bioinorganic chemistry of T2D.
Collapse
Affiliation(s)
- Carolina Sánchez-López
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav) , Mexico City, Mexico
| | - Rodrigo Cortés-Mejía
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México (UNAM) , Mexico City, Mexico
| | - Marco C Miotto
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and Instituto de Investigaciones para el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario , Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Andres Binolfi
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and Instituto de Investigaciones para el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario , Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Claudio O Fernández
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR, UNR-MPIbpC) and Instituto de Investigaciones para el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario , Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Jorge M Del Campo
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México (UNAM) , Mexico City, Mexico
| | - Liliana Quintanar
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav) , Mexico City, Mexico
| |
Collapse
|
4
|
Affiliation(s)
- LUCIA BANCI
- Dipartimento di Chimica and CERM, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| |
Collapse
|
5
|
Hansen DF, Westler WM, Kunze MBA, Markley JL, Weinhold F, Led JJ. Accurate structure and dynamics of the metal-site of paramagnetic metalloproteins from NMR parameters using natural bond orbitals. J Am Chem Soc 2012; 134:4670-82. [PMID: 22329704 PMCID: PMC3303200 DOI: 10.1021/ja209348p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A natural bond orbital (NBO) analysis of unpaired electron
spin
density in metalloproteins is presented, which allows a fast and robust
calculation of paramagnetic NMR parameters. Approximately 90% of the
unpaired electron spin density occupies metal–ligand NBOs,
allowing the majority of the density to be modeled by only a few NBOs
that reflect the chemical bonding environment. We show that the paramagnetic
relaxation rate of protons can be calculated accurately using only
the metal–ligand NBOs and that these rates are in good agreement
with corresponding rates measured experimentally. This holds, in particular,
for protons of ligand residues where the point-dipole approximation
breaks down. To describe the paramagnetic relaxation of heavy nuclei,
also the electron spin density in the local orbitals must be taken
into account. Geometric distance restraints for 15N can
be derived from the paramagnetic relaxation enhancement and the Fermi
contact shift when local NBOs are included in the analysis. Thus,
the NBO approach allows us to include experimental paramagnetic NMR
parameters of 15N nuclei as restraints in a structure optimization
protocol. We performed a molecular dynamics simulation and structure
determination of oxidized rubredoxin using the experimentally obtained
paramagnetic NMR parameters of 15N. The corresponding structures
obtained are in good agreement with the crystal structure of rubredoxin.
Thus, the NBO approach allows an accurate description of the geometric
structure and the dynamics of metalloproteins, when NMR parameters
are available of nuclei in the immediate vicinity of the metal-site.
Collapse
Affiliation(s)
- D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom.
| | | | | | | | | | | |
Collapse
|
6
|
Binolfi A, Rodriguez EE, Valensin D, D'Amelio N, Ippoliti E, Obal G, Duran R, Magistrato A, Pritsch O, Zweckstetter M, Valensin G, Carloni P, Quintanar L, Griesinger C, Fernández CO. Bioinorganic chemistry of Parkinson's disease: structural determinants for the copper-mediated amyloid formation of alpha-synuclein. Inorg Chem 2010; 49:10668-79. [PMID: 20964419 DOI: 10.1021/ic1016752] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aggregation of alpha-synuclein (AS) is a critical step in the etiology of Parkinson's disease (PD). A central, unresolved question in the pathophysiology of PD relates to the role of AS-metal interactions in amyloid fibril formation and neurodegeneration. Our previous works established a hierarchy in alpha-synuclein-metal ion interactions, where Cu(II) binds specifically to the protein and triggers its aggregation under conditions that might be relevant for the development of PD. Two independent, non-interacting copper-binding sites were identified at the N-terminal region of AS, with significant difference in their affinities for the metal ion. In this work we have solved unknown details related to the structural binding specificity and aggregation enhancement mediated by Cu(II). The high-resolution structural characterization of the highest affinity N-terminus AS-Cu(II) complex is reported here. Through the measurement of AS aggregation kinetics we proved conclusively that the copper-enhanced AS amyloid formation is a direct consequence of the formation of the AS-Cu(II) complex at the highest affinity binding site. The kinetic behavior was not influenced by the His residue at position 50, arguing against an active role for this residue in the structural and biological events involved in the mechanism of copper-mediated AS aggregation. These new findings are central to elucidate the mechanism through which the metal ion participates in the fibrillization of AS and represent relevant progress in the understanding of the bioinorganic chemistry of PD.
Collapse
Affiliation(s)
- Andrés Binolfi
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Valensin D, Szyrwiel Ł, Camponeschi F, Rowińska-Zyrek M, Molteni E, Jankowska E, Szymanska A, Gaggelli E, Valensin G, Kozłowski H. Heteronuclear and homonuclear Cu2+ and Zn2+ complexes with multihistidine peptides based on zebrafish prion-like protein. Inorg Chem 2009; 48:7330-40. [PMID: 19586023 DOI: 10.1021/ic9008202] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The homeostasis of metal ions, especially copper and zinc, is a major factor that may influence the prion diseases and the biological function of prion protein (PrP). The His-rich regions are basic sites for metal binding and antioxidant activity of the PrP structures. Animal prion-like proteins contain also His-rich domains, and their coordination chemistry may provide better insight into the chemistry and biology of PrP structures and related diseases. Herein, we report an equilibrium study on heteronuclear Zn(2+)-Cu(2+) complexes with zrel-PrP fragments from zebrafish. Potentiometric, spectroscopic, and mass spectrometric methods showed that the binding of copper is much more effective than the binding of zinc. At physiological pH, both metals bind to the histidine imidazole N donors of the studied peptides.
Collapse
Affiliation(s)
- Daniela Valensin
- Department of Chemistry, University of Siena, Via Aldo Moro, 53100 Siena, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Balenci D, Bonechi G, D'Amelio N, Gaggelli E, Gaggelli N, Molteni E, Valensin G, Szczepanik W, Dziuba M, Swiecicki G, Jezowska-Bojczuk M. Structural features and oxidative stress towards plasmid DNA of apramycin copper complex. Dalton Trans 2008:1123-30. [PMID: 19322482 DOI: 10.1039/b815046j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of apramycin with copper at different pH values was investigated by potentiometric titrations and EPR, UV-vis and CD spectroscopic techniques. The Cu(II)-apramycin complex prevailing at pH 6.5 was further characterized by NMR spectroscopy. Metal-proton distances derived from paramagnetic relaxation enhancements were used as restraints in a conformational search procedure in order to define the structure of the complex. Longitudinal relaxation rates were measured with the IR-COSY pulse sequence, thus solving the problems due to signal overlap. At pH 6.5 apramycin binds copper(II) with a 2 : 1 stoichiometry, through the vicinal hydroxyl and deprotonated amino groups of ring III. Plasmid DNA electrophoresis showed that the Cu(II)-apramycin complex is more active than free Cu(II) in generating strand breakages. Interestingly, this complex in the presence of ascorbic acid damages DNA with a higher yield than in the presence of H(2)O(2).
Collapse
Affiliation(s)
- D Balenci
- Department of Chemistry, University of Siena, Via Aldo Moro, 53100 Siena, Italy
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
The His–His sequence of the antimicrobial peptide demegen P-113 makes it very attractive ligand for Cu2+. J Inorg Biochem 2008; 102:960-72. [DOI: 10.1016/j.jinorgbio.2007.12.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2007] [Revised: 11/09/2007] [Accepted: 12/22/2007] [Indexed: 11/24/2022]
|
10
|
Kulon K, Valensin D, Kamysz W, Nadolny R, Gaggelli E, Valensin G, Kozłowski H. Binding of Ni2+ and Cu2+ ions to peptides with a Cys–His motif. Dalton Trans 2008:5323-30. [DOI: 10.1039/b806851h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
11
|
Berti F, Gaggelli E, Guerrini R, Janicka A, Kozlowski H, Legowska A, Miecznikowska H, Migliorini C, Pogni R, Remelli M, Rolka K, Valensin D, Valensin G. Structural and Dynamic Characterization of Copper(II) Binding of the Human Prion Protein Outside the Octarepeat Region. Chemistry 2007; 13:1991-2001. [PMID: 17152102 DOI: 10.1002/chem.200601225] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Human prion protein (hPrP) fragments encompassing the 91-120 region, namely hPrP92-100 (SP1), hPrP106-113 (SP2), hPrP91-120 (LP1), and hPrP91-114 (LP2), were considered for delineation of the Cu(II)-binding site(s). NMR and EPR spectroscopy results obtained from LP1 or LP2 were compared with those obtained from SP1 and SP2. The coexistence of two binding sites, one centered at His96 and the other at His111, was evidenced and ratified by ESI mass spectrometry at low and high metal:peptide ratios. While room-temperature NMR spectroscopy data were consistent with the binding site centered on His111 being approximately fourfold stronger than that centered on His96, low-temperature EPR spectroscopy results yielded evidence for the opposite trend. This disagreement, which has also occurred in the literature, was clarified by temperature-dependent molecular dynamics runs that demonstrated Met112 approaching the metal at room temperature, a process that is expected to stabilize the His111-centered binding site through hydrophobic shielding of the metal coordination sphere.
Collapse
Affiliation(s)
- Francesco Berti
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 15, 50383 Wroclaw, Poland
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Riley EA, Petros AK, Smith KA, Gibney BR, Tierney DL. Frequency-switching inversion-recovery for severely hyperfine-shifted NMR: evidence of asymmetric electron relaxation in high-spin Co(II). Inorg Chem 2007; 45:10016-8. [PMID: 17140197 DOI: 10.1021/ic061207h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new method for reliably measuring longitudinal relaxation rates for severely hyperfine-shifted NMR signals in aqueous solutions is presented. The method is illustrated for a well-defined cobalt tetracysteinate, with relevance to cobalt-substituted metalloproteins. The relaxation measurements are indicative of asymmetric electronic relaxation of the high-spin Co(II) ion.
Collapse
Affiliation(s)
- Erin A Riley
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | | | | | | | | |
Collapse
|
13
|
Bernardi F, Gaggelli E, Molteni E, Porciatti E, Valensin D, Valensin G. 1H and 13C-NMR and molecular dynamics studies of cyclosporin a interacting with magnesium(II) or cerium(III) in acetonitrile. Conformational changes and cis-trans conversion of peptide bonds. Biophys J 2006; 90:1350-61. [PMID: 16299069 PMCID: PMC1367286 DOI: 10.1529/biophysj.105.074245] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 11/17/2005] [Indexed: 11/18/2022] Open
Abstract
Cyclosporin A (CsA) is an important drug used to prevent graft rejection in organ transplantations. Its immunosuppressive activity is related to the inhibition of T-cell activation through binding with the proteins Cyclophilin (Cyp) and, subsequently, Calcineurin (CN). In the complex with its target (Cyp), CsA adopts a conformation with all trans peptide bonds and this feature is very important for its pharmacological action. Unfortunately, CsA can cause several side effects, and it can favor the excretion of calcium and magnesium. To evaluate the possible role of conformational effects induced by these two metal ions in the action mechanism of CsA, its complexes with Mg(II) and Ce(III) (the latter as a paramagnetic probe for calcium) have been examined by two-dimensional NMR and relaxation rate analysis. The conformations of the two complexes and of the free form have been determined by restrained molecular dynamics calculations based on the experimentally obtained metal-proton and interproton distances. The findings here ratify the formation of 1:1 complexes of CsA with both Mg(II) and Ce(III), with metal coordination taking place on carbonyl oxygens and substantially altering the peptide structure with respect to the free form, although the residues involved and the resulting conformational changes, including cis-trans conversion of peptide bonds, are different for the two metals.
Collapse
Affiliation(s)
- Francesca Bernardi
- Department of Chemistry and NMR Centre, University of Siena, Siena 53100, Italy
| | | | | | | | | | | |
Collapse
|
14
|
Gaggelli E, Bernardi F, Molteni E, Pogni R, Valensin D, Valensin G, Remelli M, Luczkowski M, Kozlowski H. Interaction of the human prion PrP(106-126) sequence with copper(II), manganese(II), and zinc(II): NMR and EPR studies. J Am Chem Soc 2005; 127:996-1006. [PMID: 15656638 DOI: 10.1021/ja045958z] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthetic peptide encompassing residues 106-126 (PrP106-126, KTNMKHMAGAAAAGAVVGGLG) of the human prion protein was considered for its binding properties toward copper(II), manganese(II) and zinc(II) at pH 5.7. 1H and 13C 1D spectra, 1H spin-lattice relaxation rates, and 1H-15N and 1H-13C HSQC 2D experiments were obtained in the absence and in the presence of metal ions. While Zn(II) was found to yield negligible effects upon any NMR parameter, metal-peptide association was demonstrated by the paramagnetic effects of Cu(II) and Mn(II) upon 1D and 2D spectra. Delineation of structures of metal complexes was sought by interpreting the paramagnetic effect on 1H spin-lattice relaxation rates. Exchange of peptide molecules from the metal coordination sphere was shown to provide sizable contribution to the observed relaxation rates. Such contribution was calculated in the case of Cu(II); whereas the faster paramagnetic rates of peptide molecules bound to Mn(II) were determining spin-lattice relaxation rates almost exclusively dominated by exchange. Proton-metal distances were therefore evaluated in the case of the Cu(II) complex only and used as restraints in molecular dynamics calculations where from the structure of the complex was obtained. The peptide was shown to bind copper through the imidazole nitrogen and the ionized amide nitrogen of His-111 and the amino-terminal group with the terminal carboxyl stabilizing the coordination sphere through ionic interactions. The data were interpreted as to demonstrate that the hydrophobic C-terminal region was not affecting the copper-binding properties of the peptide and that this hydrophobic tail is left free to interact with other target molecules. As for the complex with Mn(II), qualitative information was obtained on carbonyl oxygens of Gly-124 and Leu-125, beyond the terminal Gly-126 carboxyl, being at close distance from the metal ion, that also interacts, most likely, through a hydrogen bond of metal-bound water, with the imidazole ring of His-111.
Collapse
Affiliation(s)
- Elena Gaggelli
- Department of Chemistry, University of Siena, Via A. Moro, 53100, Siena, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Gaggelli E, Kozlowski H, Valensin D, Valensin G. NMR studies on Cu(ii)–peptide complexes: exchange kinetics and determination of structures in solution. MOLECULAR BIOSYSTEMS 2005; 1:79-84. [PMID: 16880967 DOI: 10.1039/b419413f] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of copper(II) with histidine containing peptides has recently acquired renewed interest following the established link between abnormal protein behaviour in neurodegenerative processes and unpaired copper homeostasis. Five peptide sequences taken from the amyloid precursor protein and the prion protein were considered. Addition of paramagnetic Cu(II) ions to solutions of such peptides was not found to severely affect the appearance of NMR spectra, thus limiting the usual approach for structural determination. Exchange kinetics was shown to play a major role in determining the observed paramagnetic spin-lattice relaxation rates. Two independent methods were suggested for evaluating the exchange rates of His-containing peptides from the copper-coordination sphere and to calculate copper-proton distances. In such a way NMR was demonstrated to have the potential of providing detailed structures of the Cu(II)-peptide complexes in solution.
Collapse
Affiliation(s)
- Elena Gaggelli
- Department of Chemistry, University of Siena, Via Aldo Moro, Siena 53100, Italy
| | | | | | | |
Collapse
|
16
|
Machonkin TE, Westler WM, Markley JL. Strategy for the study of paramagnetic proteins with slow electronic relaxation rates by nmr spectroscopy: application to oxidized human [2Fe-2S] ferredoxin. J Am Chem Soc 2004; 126:5413-26. [PMID: 15113213 DOI: 10.1021/ja037077i] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NMR studies of paramagnetic proteins are hampered by the rapid relaxation of nuclei near the paramagnetic center, which prevents the application of conventional methods to investigations of the most interesting regions of such molecules. This problem is particularly acute in systems with slow electronic relaxation rates. We present a strategy that can be used with a protein with slow electronic relaxation to identify and assign resonances from nuclei near the paramagnetic center. Oxidized human [2Fe-2S] ferredoxin (adrenodoxin) was used to test the approach. The strategy involves six steps: (1) NMR signals from (1)H, (13)C, and (15)N nuclei unaffected or minimally affected by paramagnetic effects are assigned by standard multinuclear two- and three-dimensional (2D and 3D) spectroscopic methods with protein samples labeled uniformly with (13)C and (15)N. (2) The very broad, hyperfine-shifted signals from carbons in the residues that ligate the metal center are classified by amino acid and atom type by selective (13)C labeling and one-dimensional (1D) (13)C NMR spectroscopy. (3) Spin systems involving carbons near the paramagnetic center that are broadened but not hyperfine-shifted are elucidated by (13)C[(13)C] constant time correlation spectroscopy (CT-COSY). (4) Signals from amide nitrogens affected by the paramagnetic center are assigned to amino acid type by selective (15)N labeling and 1D (15)N NMR spectroscopy. (5) Sequence-specific assignments of these carbon and nitrogen signals are determined by 1D (13)C[(15)N] difference decoupling experiments. (6) Signals from (1)H nuclei in these spin systems are assigned by paramagnetic-optimized 2D and 3D (1)H[(13)C] experiments. For oxidized human ferredoxin, this strategy led to assignments (to amino acid and atom type) for 88% of the carbons in the [2Fe-2S] cluster-binding loops (residues 43-58 and 89-94). These included complete carbon spin-system assignments for eight of the 22 residues and partial assignments for each of the others. Sequence-specific assignments were determined for the backbone (15)N signals from nine of the 22 residues and ambiguous assignments for five of the others.
Collapse
Affiliation(s)
- Timothy E Machonkin
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | | |
Collapse
|
17
|
Jensen MR, Led JJ. Determination of the electron relaxation rates in paramagnetic metal complexes: applicability of available NMR methods. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 167:169-177. [PMID: 15040973 DOI: 10.1016/j.jmr.2003.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2003] [Revised: 12/03/2003] [Indexed: 05/24/2023]
Abstract
Four different approaches for determining the electron relaxation rates in paramagnetic metallo-proteins are investigated, using a paramagnetic Ni2+ complex of a protein as an example. All four approaches rely on the determination of the longitudinal paramagnetic relaxation enhancements, R1p, of the 1H nuclei and the backbone 15N nuclei. Three of the methods utilize the field dependence of the R1p rates. It is found that the applicability of each of these methods depends on whether the fast-motion condition, omegaS2tau2<<1, applies to the electron relaxation, omegaS being the Larmor frequency of the electron spin S and tau the correlation time of the electron relaxation. If the fast-motion condition is fulfilled, the electron relaxation rate can be obtained from the ratio of the R1p rates of one or more protons at two magnetic field strengths (method A). On the other hand, if the fast-motion condition does not apply, more elaborate methods must be used that, in general, require a determination of the R1p rates over a larger range of magnetic field strengths (method C). However, in the case of paramagnetic metal ions with relatively slow electron relaxation rates only two magnetic field strengths suffice, if the R1p rates of a hetero nucleus are included in the analysis (method B). In the fourth method (method D), the electron relaxation is estimated as a parameter in a structure calculation, using distance constraints derived from proton R1p rates at only one magnetic field strength. In general, only methods B and C give unambiguous electron relaxation rates.
Collapse
Affiliation(s)
- Malene Ringkjøbing Jensen
- Department of Chemistry, University of Copenhagen, The HC Ørsted Institute, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | | |
Collapse
|
18
|
Hansen DF, Led JJ. Mapping the Electronic Structure of the Blue Copper Site in Plastocyanin by NMR Relaxation. J Am Chem Soc 2004; 126:1247-52. [PMID: 14746497 DOI: 10.1021/ja0379464] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The biological function of metalloproteins stems from the electronic and geometric structures of their active sites. Thus, in blue copper proteins such as plastocyanins, an unusual electronic structure of the metal site is believed to contribute to the rapid, long-range electron-transfer reactivity that characterizes these proteins. To clarify this structure-function relationship, numerous quantum chemical calculations of the electronic structure of the blue copper proteins have been made. However, the obtained structures depend strongly on the applied model. Experimental approaches based on ENDOR spectroscopy and X-ray absorption have also been used to elucidate the electronic structure of the blue copper site. Still, the determination of the electronic structure relies on a calibration with quantum chemical calculations, performed on small model complexes. Here we present an approach that allows a direct experimental mapping of the electron spin delocalization in paramagnetic metalloproteins using oxidized plastocyanin from Anabaena variabilis as an example. The approach utilizes the longitudinal paramagnetic relaxation of protons close to the metal site and relies on the dependence of these relaxations on the spatial distribution of the unpaired electron of the metal ion. Surprisingly it is found that the unpaired electron of the copper ion in plastocyanin is less delocalized than predicted by most of the quantum chemical calculations.
Collapse
Affiliation(s)
- D Flemming Hansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | | |
Collapse
|
19
|
Valensin D, Mancini FM, Łuczkowski M, Janicka A, Wisniewska K, Gaggelli E, Valensin G, Łankiewicz L, Kozlowski H. Identification of a novel high affinity copper binding site in the APP(145–155) fragment of amyloid precursor protein. Dalton Trans 2004:16-22. [PMID: 15356736 DOI: 10.1039/b312411h] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The copper(II) binding features of the APP(145-155) and APP(145-157) fragments of the amyloid precursor protein, Ac-Glu-Thr-His-Leu-His-Trp-His-Thr-Val-Ala-Lys-NH2 and Ac-Glu-Thr-His-Leu-His-Trp-His-Thr-Val-Ala-Lys-Glu-Thr-NH2 were studied by NMR spectroscopy and NMR findings were supported by UV-vis, CD and EPR spectra. Potentiometric measurements were performed only for the more soluble Ac-Glu-Thr-His-Leu-His-Trp-His-Thr-Val-Ala-Lys-Glu-Thr-NH2 peptide fragment. The following was shown: (i) the imidazole rings of all the three His residues are involved in metal coordination; (ii) metal binding induces ionisation of Leu-148 and His-149 amide nitrogens that complete the donor set to copper(II) in the species dominant at neutral pH; (iii) the unusual coordination scheme of the His-Xxx-His-Xxx-His consensus sequence justifies the high specificity for Cu(II) when compared to SOD-like or albumin-like peptides or even in amyloid Abeta fragments. The present findings may represent the key for interpreting the observed requirement of His residues conservation for the redox cycling between Cu(II) and Cu(I) by soluble APP.
Collapse
Affiliation(s)
- Daniela Valensin
- Department of Chemistry and the NMR Center, University of Siena, via Moro, 53100 Siena, Italy.
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
D'Amelio N, Gaggelli E, Gaggelli N, Molteni E, Baratto MC, Valensin G, Jezowska-Bojczuk M, Szczepanik W. NMR and EPR structural delineation of copper(ii) complexes formed by kanamycin A in water. Dalton Trans 2004:363-8. [PMID: 15252540 DOI: 10.1039/b313060f] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The complexes formed by kanamycin A at three different pH values (5.5, 7.4 and 12.0) were investigated by NMR and EPR spectroscopy. Paramagnetic relaxation contributions to proton relaxation rates were measured using a combination of the TOCSY sequence with the inversion recovery experiment in order to gain signal resolution in the bulk region. Measured contributions were converted into distances and used for structural determination by restrained simulated annealing where all possible chair and boat conformations of the rings were taken into account. The interaction of the Cu(II) ion with the nitrogen of the C ring is apparent at all pH values. At higher pH also the amino group of ring A starts to be involved in the metal coordination sphere. This is accompanied by a switch in conformation of ring C. Structures are consistent with the involvement in the coordination sphere either of the 2' or 4' hydroxyl oxygens at pH 5.5 and the 5 and the 6' hydroxyl oxygens (or the ring oxygen) at pH 12.0.
Collapse
Affiliation(s)
- Nicola D'Amelio
- Department of Chemistry and the NMR Center, University of Siena, Via A.Moro 2, Siena 53100, Italy
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Hansen DF, Hass MAS, Christensen HM, Ulstrup J, Led JJ. Detection of short-lived transient protein-protein interactions by intermolecular nuclear paramagnetic relaxation: plastocyanin from Anabaena variabilis. J Am Chem Soc 2003; 125:6858-9. [PMID: 12783525 DOI: 10.1021/ja034013z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An NMR approach is presented that provides detailed information about short-lived, transient interactions between protein molecules in solution. The approach is based on the longitudinal paramagnetic relaxation rates of the protein nuclei and requires that at least one of the interacting molecules is paramagnetic. The specific interactions are monitored by the intermolecular paramagnetic contribution to the relaxation of protons at or close to the interaction surface. By applying the approach to plastocyanin from Anabaena variabilis, specific regions of interaction that may be involved in the electron self-exchange process of this plastocyanin were identified. This is in accord with recent 15N NMR relaxation studies of the backbone dynamics of Anabaena variabilis plastocyanin, with site-directed mutagenesis studies of the functional importance of the corresponding regions in Phormidium laminosum plastocyanin and with the crystal packing surface of P. laminosum plastocyanin.
Collapse
Affiliation(s)
- D Flemming Hansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | | | | | | | | |
Collapse
|
22
|
Lieutaud C, Nitschke W, Verméglio A, Parot P, Schoepp-Cothenet B. HiPIP in Rubrivivax gelatinosus is firmly associated to the membrane in a conformation efficient for electron transfer towards the photosynthetic reaction centre. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1557:83-90. [PMID: 12615351 DOI: 10.1016/s0005-2728(02)00397-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
High potential iron-sulfur protein (HiPIP), a small soluble redox protein, has been shown to serve in vivo as electron donor to the photosynthetic reaction centre (RC) in Rubrivivax gelatinosus [Biochemistry 34 (1995) 11736]. The results of time-resolved optical spectroscopy on membrane-fragments from this organism indicates that the photooxidized RC is re-reduced by HiPIP even in the absence of the soluble fraction. This implies that a significant fraction of HiPIP can firmly bind to the membrane in a conformation able to interact with the RCs. Salt treatment of the membrane-fragments abolishes these re-reduction kinetics, demonstrating the presence of HiPIP on the membrane due to association with the RC rather than due to simple trapping in hypothetical chromatophores. The existence of such a functional complex in membranes is confirmed and its structure further examined by electron paramagnetic resonance (EPR) performed on membrane-fragments. Orientation-dependent EPR spectra of HiPIP were recorded on partially ordered membranes, oxidized either chemically or photochemically. Whereas hardly any preferential orientation of the HiPIP was seen in the chemically oxidised sample, a subpopulation of HiPIP showing specific orientations could be photooxidised. This fraction arises from the electron transfer complex between HiPIP and the RC.
Collapse
Affiliation(s)
- Clément Lieutaud
- Laboratoire de Biophysique des Transporteurs d'Electrons, Faculté des Sciences de Luminy, 136 Avenue de Luminy, 13288 Marseille Cedex 9, France
| | | | | | | | | |
Collapse
|
23
|
Bertini I, Luchinat C, Parigi G. Paramagnetic constraints: An aid for quick solution structure determination of paramagnetic metalloproteins. ACTA ACUST UNITED AC 2002. [DOI: 10.1002/cmr.10027] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
24
|
Daizadeh I, Medvedev DM, Stuchebrukhov AA. Electron transfer in ferredoxin: are tunneling pathways evolutionarily conserved? Mol Biol Evol 2002; 19:406-15. [PMID: 11919281 DOI: 10.1093/oxfordjournals.molbev.a004095] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A theoretical study of electron transfer (ET) pathways in a recently crystallized Clostridium acidurici ferredoxin is reported. The electronic structure of the protein complex is treated at the semiempirical extended Hückel level, and the tunneling pathways are calculated with the rigorous quantum mechanical method of tunneling currents. The model predicts two pathways between the two [4Fe-4S] cubanes: a strong one running directly from Cys(14) to Cys(43) and a weaker one from Cys(14) via Ile(23) to Cys(18), whereas other amino acids do not play a significant role in the electron tunneling. The cysteine ligands conduct almost all of the current when Ile(23) is mutated to valine in silico, so that there is no appreciable change in the ET rate. The calculated value of the transfer matrix element is consistent with the experimentally determined rate of transfer. Results of the sequence analysis performed on this ferredoxin reveal that Ile(23) is a highly variable amino acid compared with the cubane-ligating cysteine amino acids, even though Ile(23) lies directly between the donor and acceptor complexes. We further argue that the homologous proteins with a [3Fe-4S] cofactor, which does not have one of the four cysteine ligands, use the same tunneling pathways as those in this ferredoxin, on the basis of the high homology as well as the absolute conservation of Cys(14) and Cys(43) which serve as the main tunneling conduit. Our results explain why mutation of amino acids around and between the donor and acceptor cubane clusters, including that of Ile(23), does not appreciably affect the rate of transfer and add support to the proposal that there exist evolutionarily conserved electron tunneling pathways in biological ET reactions.
Collapse
Affiliation(s)
- Iraj Daizadeh
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | | | | |
Collapse
|
25
|
Affiliation(s)
- I Bertini
- Magnetic Resonance Center (CERM), University of Florence, Florence 50019, Italy
| | | | | |
Collapse
|
26
|
Affiliation(s)
- G N La Mar
- Department of Chemistry, University of California, Davis, California 95616, USA
| |
Collapse
|
27
|
Crozet M, Chaussade M, Bardet M, Emsley L, Lamotte B, Mouesca JM. Carbon-13 Solid-State NMR Studies on Synthetic Model Compounds of [4Fe−4S] Clusters in the 2+ State. J Phys Chem A 2000. [DOI: 10.1021/jp002005o] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marielle Crozet
- Service de Chimie Inorganique et Biologique, UMR 5046, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France, Laboratoire des Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France, and Laboratoire de Stéréochimie et des Interactions Moléculaires, UMR 5532 CNRS/ENS, Ecole Normale
| | - Marc Chaussade
- Service de Chimie Inorganique et Biologique, UMR 5046, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France, Laboratoire des Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France, and Laboratoire de Stéréochimie et des Interactions Moléculaires, UMR 5532 CNRS/ENS, Ecole Normale
| | - Michel Bardet
- Service de Chimie Inorganique et Biologique, UMR 5046, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France, Laboratoire des Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France, and Laboratoire de Stéréochimie et des Interactions Moléculaires, UMR 5532 CNRS/ENS, Ecole Normale
| | - Lyndon Emsley
- Service de Chimie Inorganique et Biologique, UMR 5046, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France, Laboratoire des Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France, and Laboratoire de Stéréochimie et des Interactions Moléculaires, UMR 5532 CNRS/ENS, Ecole Normale
| | - Bernard Lamotte
- Service de Chimie Inorganique et Biologique, UMR 5046, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France, Laboratoire des Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France, and Laboratoire de Stéréochimie et des Interactions Moléculaires, UMR 5532 CNRS/ENS, Ecole Normale
| | - Jean-Marie Mouesca
- Service de Chimie Inorganique et Biologique, UMR 5046, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France, Laboratoire des Lésions des Acides Nucléiques, Service de Chimie Inorganique et Biologique, Département de Recherche Fondamentale sur la Matière Condensée, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France, and Laboratoire de Stéréochimie et des Interactions Moléculaires, UMR 5532 CNRS/ENS, Ecole Normale
| |
Collapse
|
28
|
Ma L, Jørgensen AMM, Sørensen GO, Ulstrup J, Led JJ. Elucidation of the Paramagnetic R1 Relaxation of Heteronuclei and Protons in Cu(II) Plastocyanin from Anabaena variabilis. J Am Chem Soc 2000. [DOI: 10.1021/ja001368z] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lixin Ma
- Contribution from the Department of Chemistry, University of Copenhagen, The H. C. Ørsted Institute, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, and the Department of Chemistry, The Technical University of Denmark, Building 207, DK-2800 Lyngby, Denmark
| | - Anne-Marie M. Jørgensen
- Contribution from the Department of Chemistry, University of Copenhagen, The H. C. Ørsted Institute, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, and the Department of Chemistry, The Technical University of Denmark, Building 207, DK-2800 Lyngby, Denmark
| | - G. Ole Sørensen
- Contribution from the Department of Chemistry, University of Copenhagen, The H. C. Ørsted Institute, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, and the Department of Chemistry, The Technical University of Denmark, Building 207, DK-2800 Lyngby, Denmark
| | - Jens Ulstrup
- Contribution from the Department of Chemistry, University of Copenhagen, The H. C. Ørsted Institute, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, and the Department of Chemistry, The Technical University of Denmark, Building 207, DK-2800 Lyngby, Denmark
| | - Jens J. Led
- Contribution from the Department of Chemistry, University of Copenhagen, The H. C. Ørsted Institute, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, and the Department of Chemistry, The Technical University of Denmark, Building 207, DK-2800 Lyngby, Denmark
| |
Collapse
|
29
|
Antonkine ML, Bentrop D, Bertini I, Luchinat C, Shen G, Bryant DA, Stehlik D, Golbeck JH. Paramagnetic 1H NMR spectroscopy of the reduced, unbound photosystem I subunit PsaC: sequence-specific assignment of contact-shifted resonances and identification of mixed- and equal-valence Fe-Fe pairs in [4Fe-4S] centers FA- and FB-. J Biol Inorg Chem 2000; 5:381-92. [PMID: 10907749 DOI: 10.1007/pl00010667] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The PsaC subunit of Photosystem I (PS I) is a 9.3-kDa protein that binds two important cofactors in photosynthetic electron transfer: the [4Fe-4S] clusters FA and FB. The g-tensor orientation of FA- and FB- is believed to be correlated to the preferential localization of the mixed-valence and equal-valence (ferrous) iron pairs in each [4Fe-4S]+ cluster. The preferential position of the mixed-valence and equal-valence pairs, in turn. can be inferred from the study of the temperature dependence of contact-shifted resonances by 1H NMR spectroscopy. For this, a sequence-specific assignment of these signals is required. The 1H NMR spectrum of reduced, unbound PsaC from Synechococcus sp. PCC 7002 at 280.4 K in 99% D2O solution shows 18 hyperfine-shifted resonances. The non-solvent-exchangeable, hyperfine-shifted resonances of reduced PsaC are clearly identified as belonging to the cysteines coordinating the clusters FA- and FB- by their downfield chemical shifts, by their temperature dependencies, and by their short T1 relaxation times. The usual fast method of assigning the 1H NMR spectra of reduced [4Fe-4S] proteins through magnetization transfer from the oxidized to the reduced state was not feasible in the case of reduced PsaC. Therefore, a de novo self-consistent sequence-specific assignment of the hyperfine-shifted resonances was obtained based on dipolar connectivities from 1D NOE difference spectra and on longitudinal relaxation times using the X-ray structure of Clostridium acidi urici 2[4Fe-4S] cluster ferredoxin at 0.94 A resolution as a model. The results clearly show the same sequence-specific distribution of Curie and anti-Curie cysteines for unbound, reduced PsaC as established for other [4Fe-4S]-containing proteins; therefore, the mixed-valence and equal-valence (ferrous) Fe-Fe pairs in FA- and FB- have the same preferential positions relative to the protein. The analysis reveals that the magnetic properties of the two [4Fe-4S] clusters are essentially indistinguishable in unbound PsaC, in contrast to the PsaC that is bound as a component of the PS I complex.
Collapse
Affiliation(s)
- M L Antonkine
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park 16802, USA
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Kümmerle R, Kyritsis P, Gaillard J, Moulis JM. Electron transfer properties of iron-sulfur proteins. J Inorg Biochem 2000; 79:83-91. [PMID: 10830851 DOI: 10.1016/s0162-0134(99)00160-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The details of most electron transfer reactions involving iron-sulfur proteins have remained undisclosed because of the lack of experimental methods suitable to measure precisely the relevant rates. Nuclear magnetic resonance (NMR) provides a powerful means to overcome these problems, at least with selected proteins. A combination of NMR studies and site-directed mutagenesis experiments has been instrumental in defining both the site of interaction and the main trends of the intracomplex electron transfer in the case of rubredoxin electron self-exchange. Analysis of the NMR data obtained for mixtures of different redox levels of several 2[4Fe-4S] ferredoxins provided both first-order, for intramolecular, and second-order, for intermolecular, rate constants. Their dependence as a function of structural changes gave insight into the mechanism of electron transfer in this type of protein. Contrary to some expectations, the high-spin [4Fe-4Se]+ clusters assembled in isopotential ferredoxins do not change the intramolecular electron transfer rate as compared to low-spin [4Fe-4S]+ homologs. In combination with activity measurements, the kinetic data have been used to model the electron transfer competent complexes between Clostridium pasteurianum ferredoxin and the main enzymes acting as redox partners in vivo.
Collapse
Affiliation(s)
- R Kümmerle
- CEA, Département de Recherche Fondamentale sur la Matière Condensée, SCIB/SCPM, Grenoble, France
| | | | | | | |
Collapse
|
31
|
The 3Fe containing ferredoxin from Desulfovibrio gigas: an NMR characterization of the oxidised and intermediate states. Coord Chem Rev 1999. [DOI: 10.1016/s0010-8545(99)00126-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
32
|
Millet O, Chiarparin E, Pelupessy P, Pons M, Bodenhausen G. Measurement of relaxation rates of N(H) and H(alpha) backbone protons in proteins with tailored initial conditions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1999; 139:434-438. [PMID: 10423382 DOI: 10.1006/jmre.1999.1815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Several methods are presented for the selective determination of spin-lattice and spin-spin relaxation rates of backbone protons in labeled proteins. The relaxation rates of amide protons in (15)N labeled proteins can be measured by using two-way selective cross-polarization (SCP). The measurement of H(alpha) relaxation rates can be achieved by combining this method with homonuclear Hartmann-Hahn transfer using doubly selective irradiation. Various schemes for selective or nonselective inversion of the longitudinal proton magnetization lead to different initial recovery rates. The methods have been applied to lysine K6 in (15)N-labeled human ubiquitin and to leucine L5 in (15)N- and (13)C-labeled octapeptide YG*G*F*LRRI (GFL) in which the marked residues are (15)N- and (13)C-labeled.
Collapse
Affiliation(s)
- O Millet
- Departament de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1-11, Barcelona, 08028, Spain
| | | | | | | | | |
Collapse
|
33
|
Guigliarelli B, Bertrand P. Application of EPR Spectroscopy to the Structural and Functional Study of Iron-Sulfur Proteins. ADVANCES IN INORGANIC CHEMISTRY 1999. [DOI: 10.1016/s0898-8838(08)60084-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
34
|
Bertini I, Luchinat C, Rosato A. NMR Spectra of Iron-Sulfur Proteins. ADVANCES IN INORGANIC CHEMISTRY 1999. [DOI: 10.1016/s0898-8838(08)60080-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
35
|
Bondon A, Mouro C. PASE (PAramagnetic signals enhancement): a new method for NMR study of paramagnetic proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1998; 134:154-157. [PMID: 9740741 DOI: 10.1006/jmre.1998.1523] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A new method for NMR spectra acquisition of paramagnetic proteins is described, based on the simple use of homonuclear broadband decoupling of the diamagnetic region. Several advantages are associated with this method which was applied to one-dimensional spectra, to 1D NOE-difference spectroscopy, and to 2D NOESY. The main advantage is a very flat baseline obtained using the PASE (paramagnetic signals enhancement) method. Furthermore, the bulky region of the diamagnetic protons being suppressed, clean NOE-difference spectra can be acquired as well as improved 2D NOESY maps. Applications on 1D 1H spectrum of bovine liver catalase (MW 230,000), and 1D and 2D on the high-spin form of the myoglobin, used as a model protein, are presented.
Collapse
Affiliation(s)
- A Bondon
- LCOB, UMR CNRS 6509, Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France.
| | | |
Collapse
|
36
|
Davy SL, Osborne MJ, Moore GR. Determination of the structure of oxidised Desulfovibrio africanus ferredoxin I by 1H NMR spectroscopy and comparison of its solution structure with its crystal structure. J Mol Biol 1998; 277:683-706. [PMID: 9533888 DOI: 10.1006/jmbi.1998.1631] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The solution structure of the 64 amino acid Fe4S4 ferredoxin I from Desulfovibrio africanus has been determined using two-dimensional 1H NMR spectroscopy. Sequence-specific assignments were obtained for 59 amino acid residues and the structure determined with the program DIANA on the basis of 549 nuclear Overhauser enhancement (NOE) upper distance limits, and four dihedral angle and 52 distance constraints for the Fe4S4 cluster. The NMR structure was refined using the simulated annealing and energy minimisation protocols of the program X-PLOR to yield a final family of 19 structures selected on the basis of good covalent geometry and minimal restraint violations. The r.m.s.d. values to the average structure for this family are 0.49(+/-0.07) A and 0.94(+/-0.09) A for the backbone and heavy-atoms of residues 3 to 62, respectively. The NMR structure has been compared to the previously reported X-ray structures for the two molecules within the asymmetric unit of the crystal, which have a network of seven hydrogen bonds between them. This intermolecular interface, involving residues 38, 40 to 43 and 46, has the same conformation in the solution structures showing that the crystal packing does not perturb the structure. There are three regions in which the NMR and X-ray structures differ: around the cluster, a turn involving residues 8 to 10, and a loop involving residues 29 to 32. In the family of solution structures the backbone of the loop region incorporating residues 29 to 32 is well-defined whilst in both of the X-ray molecules it is ill-defined. The small differences between the X-ray and NMR structures for the cluster environment and the turn between residues 8 to 10 probably reflects a lack of NMR constraints. The observation of relatively rapid amide NH hydrogen exchange of NH groups close to the cluster, together with rapid flipping for Phe25, which is also close to the cluster, indicates that the cluster environment is more dynamic than the corresponding regions of related Fe/S proteins.
Collapse
Affiliation(s)
- S L Davy
- School of Chemical Sciences, University of East Anglia, Norwich, NR4 7TJ, U.K
| | | | | |
Collapse
|
37
|
Calzolai L, Gorst CM, Bren KL, Zhou ZH, Adams MWW, La Mar GN. Solution NMR Study of the Electronic Structure and Magnetic Properties of Cluster Ligation Mutants of the Four-Iron Ferredoxin from the Hyperthermophilic Archaeon Pyrococcus furiosus. J Am Chem Soc 1997. [DOI: 10.1021/ja9715455] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luigi Calzolai
- Contribution from the Department of Chemistry, University of California, Davis, California 95616, and Department of Biochemistry and Molecular Biology, Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602
| | - Carol M. Gorst
- Contribution from the Department of Chemistry, University of California, Davis, California 95616, and Department of Biochemistry and Molecular Biology, Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602
| | - Kara L. Bren
- Contribution from the Department of Chemistry, University of California, Davis, California 95616, and Department of Biochemistry and Molecular Biology, Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602
| | - Zhi-Hao Zhou
- Contribution from the Department of Chemistry, University of California, Davis, California 95616, and Department of Biochemistry and Molecular Biology, Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602
| | - Michael W. W. Adams
- Contribution from the Department of Chemistry, University of California, Davis, California 95616, and Department of Biochemistry and Molecular Biology, Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602
| | - Gerd N. La Mar
- Contribution from the Department of Chemistry, University of California, Davis, California 95616, and Department of Biochemistry and Molecular Biology, Center for Metalloenzyme Studies, University of Georgia, Athens, Georgia 30602
| |
Collapse
|
38
|
Bertini I, Donaire A, Felli IC, Luchinat C, Rosato A. 1H and (13)C NMR Studies of an Oxidized HiPIP. Inorg Chem 1997; 36:4798-4803. [PMID: 11670159 DOI: 10.1021/ic970057v] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
1H-(13)C HETCOR NMR spectra have been recorded for the oxidized HiPIP I from Ectothiorhodospira halophila for which an extended (1)H assignment was available. The hyperfine shifts of the alpha and beta carbons of the coordinated cysteines, as well as those of their attached protons, have been discussed in terms of the current magnetic coupling models and of the mechanisms of spin density delocalization. Through HSQC spectra preceded by a proton 180 degrees pulse, the nonselective T(1) values of the protons have been accurately obtained. It is shown how the nuclear T(1) values can be used as constraints, together with NOEs, for solution structure determination even when the present magnetic coupling scheme occurs. The oxidized cluster is shown to have an effective relaxation time much shorter than that in the reduced state.
Collapse
Affiliation(s)
- Ivano Bertini
- Departments of Chemistry and of Soil Science and Plant Nutrition, University of Florence, Florence, Italy
| | | | | | | | | |
Collapse
|
39
|
Bentrop D, Bertini I, Cremonini MA, Forsén S, Luchinat C, Malmendal A. Solution structure of the paramagnetic complex of the N-terminal domain of calmodulin with two Ce3+ ions by 1H NMR. Biochemistry 1997; 36:11605-18. [PMID: 9305950 DOI: 10.1021/bi971022+] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The solution structure of the dicerium(III) complex of the N-terminal domain of calmodulin (Ce2-TR1C hereafter) has been solved employing paramagnetic T1 relaxation enhancements and pseudocontact shifts introduced by the Ce3+ ions, together with conventional NOE constraints. The use of pseudocontact shift constraints constitutes the first attempt to locate metal ions within a protein structure by NMR. Like calcium(II), paramagnetic cerium(III) has been found to bind to the two metal binding sites of the TR1C fragment of calmodulin in a cooperative manner. Due to the presence of pseudocontact interactions between the Ce3+ ions and protons of the 76-residue protein, the 1H NMR spectra of the complex show resonances shifted between +22 and -9 ppm. Eighty percent of its proton resonances could be assigned through a standard approach using TOCSY/COSY and NOESY spectra and through 1D NOE difference spectra for the broad resonances of protons close to the paramagnetic ions. A family of structures was calculated by means of the torsion angle dynamics program DYANA [Güntert, P., Mumenthaler, C., & Wüthrich, K. (1996) XVIIthInternational Conference on Magnetic Resonance inBiological Systems (Abstract)] using 1012 NOEs. Longitudinal proton relaxation times helped to roughly define the position of the metal ions within the protein. A total of 381 pseudocontact shift constraints, whose evaluation and use are critically discussed, have then been added to further refine the metal coordinates within the protein frame and to improve the structure resolution. A dramatic resolution improvement of the metal coordinates together with a sizable resolution improvement in the regions close to the paramagnetic centers, where the number of NOEs is low, is observed. The good quality of the solution structure permitted a meaningful comparison with the solid-state structure of calcium-loaded calmodulin at 1.7 A resolution [Chattopadhyaya, R., Meador, W. E., Means, A. R., & Quiocho, F. A. (1992) J. Mol. Biol. 228, 1177]. The Ce2-TR1C complex is overall more compact than the Ca form.
Collapse
Affiliation(s)
- D Bentrop
- Department of Chemistry, University of Florence, Via Gino Capponi 7, 50121 Florence, Italy
| | | | | | | | | | | |
Collapse
|