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Bertini I, Felli IC, Luchinat C, Parigi G, Pierattelli R. Towards a protocol for solution structure determination of copper(II) proteins: the case of Cu(II)Zn(II) superoxide dismutase. Chembiochem 2016; 8:1422-9. [PMID: 17583552 DOI: 10.1002/cbic.200700006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have developed an optimized protocol to solve the solution structure of copper(II) proteins. After assignment, proton-proton NOEs are used for the shell where 1H spectra are conveniently observed. In a shell closer to the metal ion, 13C NMR spectra with band-selective homonuclear decoupling provide the assignment of all nuclei except for those of the metal ligands. A convenient method for the measurement of 13C longitudinal-relaxation rates (R1) of carbonyls and carboxylate moieties is proposed. 1H NOEs and 1H and 13C R1 data are sufficient to produce a good/reasonable solution structure, as demonstrated for a monomeric species of superoxide dismutase, a 153-residue protein.
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Affiliation(s)
- Ivano Bertini
- CERM and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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Yamaguchi T, Akao K, Takashina A, Asamura S, Unno M, Szilagyi RK, Kohzuma T. X-ray crystallographic evidence for the simultaneous presence of axial and rhombic sites in cupredoxins: atomic resolution X-ray crystal structure analysis of pseudoazurin and DFT modelling. RSC Adv 2016. [DOI: 10.1039/c6ra19282c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The simultaneous presence of axial (blue) and rhombic (green) Cu sites in pseudoazurin is described from experiments and computational modelling.
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Affiliation(s)
- T. Yamaguchi
- Institute of Quantum Beam Science
- Ibaraki University
- Mito
- Japan
| | - K. Akao
- Institute of Quantum Beam Science
- Ibaraki University
- Mito
- Japan
| | - A. Takashina
- Institute of Quantum Beam Science
- Ibaraki University
- Mito
- Japan
| | - S. Asamura
- Institute of Quantum Beam Science
- Ibaraki University
- Mito
- Japan
| | - M. Unno
- Institute of Quantum Beam Science
- Ibaraki University
- Mito
- Japan
- Frontier Research Center for Applied Atomic Sciences
| | - R. K. Szilagyi
- Department of Chemistry and Biochemistry
- Montana State University
- Bozeman
- USA
- MTA-ELTE “Momentum” Chemical Structure/Function Laboratory
| | - T. Kohzuma
- Institute of Quantum Beam Science
- Ibaraki University
- Mito
- Japan
- Frontier Research Center for Applied Atomic Sciences
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3
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Tierney DL. Jahn-Teller dynamics in a series of high-symmetry Co(II) chelates determine paramagnetic relaxation enhancements. J Phys Chem A 2012; 116:10959-72. [PMID: 23095055 DOI: 10.1021/jp309245e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
NMR paramagnetic relaxation enhancements (PREs) of a series of structurally characterized, trigonal bis-trispyrazolylborate (Tp) chelates of high-spin Co(II), spanning 100-850 MHz in field, are reported. Prior knowledge of the metal-nucleus distances allows numerical extraction of position-dependent electron spin relaxation rates (τ(c)(-1)) from direct measurement of the individual PREs of the four symmetry distinct protons in Co(Tp)(2), using available closed-form expressions. The data for this electronically complex system where spin-orbit coupling defines the ground state electronic structure are analyzed in terms of the Solomon-Bloembergen-Morgan (SBM) relations, as well as available zero-field splitting limit theories. A simple angular correction is shown to be sufficient to reconcile the individual τ(c)(T) data for the four classes of protons. The data identify a previously unrecognized dynamic Jahn-Teller effect in these historically important complexes, with a barrier of ~230 cm(-1), pointing to a level of dynamics in trispyrazolylborate chemistry that has not been described before, and further show that it is the Jahn-Teller that is responsible for the PREs in fluid solution. A field-dependent component is also identified for the two protons nearest g(//), which is suggested to arise due to Zeeman mixing of excited state character into the ground level.
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Affiliation(s)
- David L Tierney
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, New Mexico 87131, United States.
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4
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George GN, Pickering IJ, Pushie MJ, Nienaber K, Hackett MJ, Ascone I, Hedman B, Hodgson KO, Aitken JB, Levina A, Glover C, Lay PA. X-ray-induced photo-chemistry and X-ray absorption spectroscopy of biological samples. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:875-86. [PMID: 23093745 PMCID: PMC3480274 DOI: 10.1107/s090904951203943x] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Accepted: 09/16/2012] [Indexed: 05/03/2023]
Abstract
As synchrotron light sources and optics deliver greater photon flux on samples, X-ray-induced photo-chemistry is increasingly encountered in X-ray absorption spectroscopy (XAS) experiments. The resulting problems are particularly pronounced for biological XAS experiments. This is because biological samples are very often quite dilute and therefore require signal averaging to achieve adequate signal-to-noise ratios, with correspondingly greater exposures to the X-ray beam. This paper reviews the origins of photo-reduction and photo-oxidation, the impact that they can have on active site structure, and the methods that can be used to provide relief from X-ray-induced photo-chemical artifacts.
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Affiliation(s)
- Graham N. George
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Ingrid J. Pickering
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - M. Jake Pushie
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Kurt Nienaber
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Mark J. Hackett
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E2
| | - Isabella Ascone
- ENSCP Chimie ParisTech, LCF, CNRS, UMR 7223, 75005 Paris, France
| | - Britt Hedman
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jade B. Aitken
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- Australian Synchrotron, Clayton, VIC 3168, Australia
- Institute of Materials Structure Science, KEK, Tsukuba, Ibaraki 305-0801, Japan
| | - Aviva Levina
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | | | - Peter A. Lay
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
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5
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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
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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.
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Affiliation(s)
- D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom.
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Zhang Y, Oldfield E. NMR hyperfine shifts in blue copper proteins: a quantum chemical investigation. J Am Chem Soc 2008; 130:3814-23. [PMID: 18314973 DOI: 10.1021/ja075978b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the results of the first quantum chemical investigations of 1H NMR hyperfine shifts in the blue copper proteins (BCPs): amicyanin, azurin, pseudoazurin, plastocyanin, stellacyanin, and rusticyanin. We find that very large structural models that incorporate extensive hydrogen bond networks, as well as geometry optimization, are required to reproduce the experimental NMR hyperfine shift results, the best theory vs experiment predictions having R2 = 0.94, a slope = 1.01, and a SD = 40.5 ppm (or approximately 4.7% of the overall approximately 860 ppm shift range). We also find interesting correlations between the hyperfine shifts and the bond and ring critical point properties computed using atoms-in-molecules theory, in addition to finding that hyperfine shifts can be well-predicted by using an empirical model, based on the geometry-optimized structures, which in the future should be of use in structure refinement.
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Affiliation(s)
- Yong Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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