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Banci L, Camponeschi F, Ciofi-Baffoni S, Piccioli M. The NMR contribution to protein-protein networking in Fe-S protein maturation. J Biol Inorg Chem 2018; 23:665-685. [PMID: 29569085 PMCID: PMC6006191 DOI: 10.1007/s00775-018-1552-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/12/2018] [Indexed: 12/12/2022]
Abstract
Iron–sulfur proteins were among the first class of metalloproteins that were actively studied using NMR spectroscopy tailored to paramagnetic systems. The hyperfine shifts, their temperature dependencies and the relaxation rates of nuclei of cluster-bound residues are an efficient fingerprint of the nature and the oxidation state of the Fe–S cluster. NMR significantly contributed to the analysis of the magnetic coupling patterns and to the understanding of the electronic structure occurring in [2Fe–2S], [3Fe–4S] and [4Fe–4S] clusters bound to proteins. After the first NMR structure of a paramagnetic protein was obtained for the reduced E. halophila HiPIP I, many NMR structures were determined for several Fe–S proteins in different oxidation states. It was found that differences in chemical shifts, in patterns of unobserved residues, in internal mobility and in thermodynamic stability are suitable data to map subtle changes between the two different oxidation states of the protein. Recently, the interaction networks responsible for maturing human mitochondrial and cytosolic Fe–S proteins have been largely characterized by combining solution NMR standard experiments with those tailored to paramagnetic systems. We show here the contribution of solution NMR in providing a detailed molecular view of “Fe–S interactomics”. This contribution was particularly effective when protein–protein interactions are weak and transient, and thus difficult to be characterized at high resolution with other methodologies.
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Affiliation(s)
- Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy. .,Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Florence, Italy.
| | - Francesca Camponeschi
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Florence, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy.,Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Florence, Italy
| | - Mario Piccioli
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019, Florence, Italy. .,Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Florence, Italy.
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2
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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3
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Site-directed mutagenesis of HgcA and HgcB reveals amino acid residues important for mercury methylation. Appl Environ Microbiol 2015; 81:3205-17. [PMID: 25724962 DOI: 10.1128/aem.00217-15] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 02/24/2015] [Indexed: 11/20/2022] Open
Abstract
Methylmercury is a potent neurotoxin that is produced by anaerobic microorganisms from inorganic mercury by a recently discovered pathway. A two-gene cluster, consisting of hgcA and hgcB, encodes two of the proteins essential for this activity. hgcA encodes a corrinoid protein with a strictly conserved cysteine proposed to be the ligand for cobalt in the corrinoid cofactor, whereas hgcB encodes a ferredoxin-like protein thought to be an electron donor to HgcA. Deletion of either gene eliminates mercury methylation by the methylator Desulfovibrio desulfuricans ND132. Here, site-directed mutants of HgcA and HgcB were constructed to determine amino acid residues essential for mercury methylation. Mutations of the strictly conserved residue Cys93 in HgcA, the proposed ligand for the corrinoid cobalt, to Ala or Thr completely abolished the methylation capacity, but a His substitution produced measurable methylmercury. Mutations of conserved amino acids near Cys93 had various impacts on the methylation capacity but showed that the structure of the putative "cap helix" region harboring Cys93 is crucial for methylation function. In the ferredoxin-like protein HgcB, only one of two conserved cysteines found at the C terminus was necessary for methylation, but either cysteine sufficed. An additional, strictly conserved cysteine, Cys73, was also determined to be essential for methylation. This study supports the previously predicted importance of Cys93 in HgcA for methylation of mercury and reveals additional residues in HgcA and HgcB that facilitate the production of this neurotoxin.
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4
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X-ray vs. NMR structure of N-terminal domain of δ-subunit of RNA polymerase. J Struct Biol 2014; 187:174-186. [DOI: 10.1016/j.jsb.2014.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/23/2014] [Accepted: 06/07/2014] [Indexed: 11/21/2022]
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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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6
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Sikic K, Tomic S, Carugo O. Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. Open Biochem J 2010; 4:83-95. [PMID: 21293729 PMCID: PMC3032220 DOI: 10.2174/1874091x01004010083] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 05/20/2010] [Accepted: 06/14/2010] [Indexed: 11/22/2022] Open
Abstract
Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in the files of the Protein Data Bank, in order to find out to which extent these information can be aggregated in bioinformatics. A non-redundant data set containing 109 NMR – X-ray structure pairs of nearly identical proteins was derived from the Protein Data Bank. A series of comparisons were performed by focusing the attention towards both global features and local details. It was observed that: (1) the RMDS values between NMR and crystal structures range from about 1.5 Å to about 2.5 Å; (2) the correlation between conformational deviations and residue type reveals that hydrophobic amino acids are more similar in crystal and NMR structures than hydrophilic amino acids; (3) the correlation between solvent accessibility of the residues and their conformational variability in solid state and in solution is relatively modest (correlation coefficient = 0.462); (4) beta strands on average match better between NMR and crystal structures than helices and loops; (5) conformational differences between loops are independent of crystal packing interactions in the solid state; (6) very seldom, side chains buried in the protein interior are observed to adopt different orientations in the solid state and in solution.
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Affiliation(s)
- Kresimir Sikic
- Departement of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna University, Austria
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7
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Lula I, Denadai AL, Resende JM, de Sousa FB, de Lima GF, Pilo-Veloso D, Heine T, Duarte HA, Santos RAS, Sinisterra RD. Study of angiotensin-(1-7) vasoactive peptide and its beta-cyclodextrin inclusion complexes: complete sequence-specific NMR assignments and structural studies. Peptides 2007; 28:2199-210. [PMID: 17904691 DOI: 10.1016/j.peptides.2007.08.011] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2007] [Revised: 08/06/2007] [Accepted: 08/06/2007] [Indexed: 11/19/2022]
Abstract
We report the complete sequence-specific hydrogen NMR assignments of vasoactive peptide angiotensin-(1-7) (Ang-(1-7)). Assignments of the majority of the resonances were accomplished by COSY, TOCSY, and ROESY peak coordinates at 400MHz and 600MHz. Long-side-chain amino acid spin system identification was facilitated by long-range coherence transfer experiments (TOCSY). Problems with overlapped resonance signals were solved by analysis of heteronuclear 2D experiments (HSQC and HMBC). Nuclear Overhauser effects (NOE) results were used to probe peptide conformation. We show that the inclusion of the angiotensin-(1-7) tyrosine residue is favored in inclusion complexes with beta-cyclodextrin. QM/MM simulations at the DFTB/UFF level confirm the experimental NMR findings and provide detailed structural information on these compounds in aqueous solution.
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Affiliation(s)
- Ivana Lula
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, 31270-901 Belo Horizonte, Minas Gerais, Brazil
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Yang LW, Eyal E, Chennubhotla C, Jee J, Gronenborn AM, Bahar I. Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions. Structure 2007; 15:741-9. [PMID: 17562320 PMCID: PMC2760440 DOI: 10.1016/j.str.2007.04.014] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Revised: 04/18/2007] [Accepted: 04/19/2007] [Indexed: 11/24/2022]
Abstract
For a representative set of 64 nonhomologous proteins, each containing a structure solved by NMR and X-ray crystallography, we analyzed the variations in atomic coordinates between NMR models, the temperature (B) factors measured by X-ray crystallography, and the fluctuation dynamics predicted by the Gaussian network model (GNM). The NMR and X-ray data exhibited a correlation of 0.49. The GNM results, on the other hand, yielded a correlation of 0.59 with X-ray data and a distinctively better correlation (0.75) with NMR data. The higher correlation between GNM and NMR data, compared to that between GNM and X-ray B factors, is shown to arise from the differences in the spectrum of modes accessible in solution and in the crystal environment. Mainly, large-amplitude motions sampled in solution are restricted, if not inaccessible, in the crystalline environment of X-rays. Combined GNM and NMR analysis emerges as a useful tool for assessing protein dynamics.
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Affiliation(s)
- Lee-Wei Yang
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3051 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Eran Eyal
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3051 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Chakra Chennubhotla
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3051 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - JunGoo Jee
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3051 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Angela M. Gronenborn
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3051 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Ivet Bahar
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Biomedical Science Tower 3, 3051 Fifth Avenue, Pittsburgh, PA 15213, USA
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Giastas P, Pinotsis N, Efthymiou G, Wilmanns M, Kyritsis P, Moulis JM, Mavridis IM. The structure of the 2[4Fe-4S] ferredoxin from Pseudomonas aeruginosa at 1.32-A resolution: comparison with other high-resolution structures of ferredoxins and contributing structural features to reduction potential values. J Biol Inorg Chem 2006; 11:445-58. [PMID: 16596388 DOI: 10.1007/s00775-006-0094-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 02/09/2006] [Indexed: 10/24/2022]
Abstract
The structure of the 2[4Fe-4S] ferredoxin (PaFd) from Pseudomonas aeruginosa, which belongs to the Allochromatium vinosum (Alvin) subfamily, has been determined by X-ray crystallography at 1.32-A resolution, which is the highest up to now for a member of this subfamily of Fds. The main structural features of PaFd are similar to those of AlvinFd. However, the significantly higher resolution of the PaFd structure makes possible a reliable comparison with available high-resolution structures of [4Fe-4S]-containing Fds, in an effort to rationalize the unusual electrochemical properties of Alvin-like Fds. Three major factors contributing to the reduction potential values of [4Fe-4S]2+/+ clusters of Fds, namely, the surface accessibility of the clusters, the N-H...S hydrogen-bonding network, and the volume of the cavities hosting the clusters, are extensively discussed. The volume of the cavities is introduced in the present work for the first time, and can in part explain the very negative potential of cluster I of Alvin-like Fds.
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Affiliation(s)
- Petros Giastas
- Institute of Physical Chemistry, NCSR Demokritos, Aghia Paraskevi, 15310, PO Box 60228, Athens, Greece
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Garbuzynskiy SO, Melnik BS, Lobanov MY, Finkelstein AV, Galzitskaya OV. Comparison of X-ray and NMR structures: Is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures? Proteins 2005; 60:139-47. [PMID: 15856480 DOI: 10.1002/prot.20491] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have compared structures of 78 proteins determined by both NMR and X-ray methods. It is shown that X-ray and NMR structures of the same protein have more differences than various X-ray structures obtained for the protein, and even more than various NMR structures of the protein. X-ray and NMR structures of 18 of these 78 proteins have obvious large-scale structural differences that seem to reflect a difference of crystal and solution structures. The other 60 pairs of structures have only small-scale differences comparable with differences between various X-ray or various NMR structures of a protein; we have analyzed these structures more attentively. One of the main differences between NMR and X-ray structures concerns the number of contacts per residue: (1) NMR structures presented in PDB have more contacts than X-ray structures at distances below 3.0 A and 4.5-6.5 A, and fewer contacts at distances of 3.0-4.5 A and 6.5-8.0 A; (2) this difference in the number of contacts is greater for internal residues than for external ones, and it is larger for beta-containing proteins than for all-alpha proteins. Another significant difference is that the main-chain hydrogen bonds identified in X-ray and NMR structures often differ. Their correlation is 69% only. However, analogous difference is found for refined and rerefined NMR structures, allowing us to suggest that the observed difference in interresidue contacts of X-ray and NMR structures of the same proteins is due mainly to a difference in mathematical treatment of experimental results.
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Affiliation(s)
- Sergiy O Garbuzynskiy
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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11
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The difference between protein structures obtained by x-ray analysis and nuclear magnetic resonance. Mol Biol 2005. [DOI: 10.1007/s11008-005-0016-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Affiliation(s)
- I Bertini
- Magnetic Resonance Center (CERM), University of Florence, Florence 50019, Italy
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13
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Affiliation(s)
- G N La Mar
- Department of Chemistry, University of California, Davis, California 95616, USA
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14
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Pieulle L, Charon MH, Bianco P, Bonicel J, Pétillot Y, Hatchikian EC. Structural and kinetic studies of the pyruvate-ferredoxin oxidoreductase/ferredoxin complex from Desulfovibrio africanus. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 264:500-8. [PMID: 10491097 DOI: 10.1046/j.1432-1327.1999.00648.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The pyruvate-ferredoxin oxidoreductase (PFOR)/ferredoxin (Fd) system of Desulfovibrio africanus has been investigated with the aim of understanding more fully protein-protein interaction and the kinetic characteristics of electron transfer between the two redox partners. D. africanus contains three Fds (Fd I, Fd II and Fd III) able to function as electron acceptors for PFOR. The complete amino acid sequence of Fd II was determined by automatic Edman degradation. It revealed a striking similarity to that of Fd I. The protein consists of 64 residues and its amino acid sequence is in agreement with a molecular mass of 6822.5 Da as measured by electrospray MS. Fd II contains five cysteine residues of which the first four (Cys11, Cys14, Cys17 and Cys54) are likely ligands for the single [4Fe-4S] cluster. A covalently cross-linked complex between PFOR and Fd I or Fd II was obtained by using a water soluble carbodiimide. This complex exhibited a stoichiometry of one ferredoxin for one PFOR subunit and is dependent on the ionic strength. The second-order rate constants for electron transfer between PFOR and Fds determined electrochemically using cyclic voltammetry are 7 x 107 M-1.s-1 for Fd I and 2 x 107 M-1.s-1 for Fd II and Fd III. The Km values of PFOR for Fd I and Fd II measured both by the electrochemical and the spectrophotometric method have been found to be 3 microM and 5 microM, respectively. The three-dimensional modelling of Fd II and surface analysis of Fd I, Fd II and PFOR suggest that a protein-protein complex is likely to be formed between aspartic acid/glutamic acid invariant residues of Fds and lysine residues surrounding the distal [4Fe-4S] cluster of PFOR. All of these studies are indicative of the involvement of electrostatic interactions between the two redox partners.
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Affiliation(s)
- L Pieulle
- Unité de Bioénergétique et Ingéniérie des Protéines, Institut de Biologie Structurale et Microbiologie, CNRS, Marseille, France
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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]
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