1
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Müntener T, Joss D, Häussinger D, Hiller S. Pseudocontact Shifts in Biomolecular NMR Spectroscopy. Chem Rev 2022; 122:9422-9467. [PMID: 35005884 DOI: 10.1021/acs.chemrev.1c00796] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.
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Affiliation(s)
- Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Daniel Joss
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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2
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Affiliation(s)
- Frank Weinhold
- Theoretical Chemistry and Department of Chemistry University of Wisconsin Madison Wisconsin 53706 USA
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3
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Schnack-Petersen AK, Simmermacher M, Fasshauer E, Jensen HJA, Sauer SPA. The Second-Order-Polarization-Propagator-Approximation (SOPPA) in a four-component spinor basis. J Chem Phys 2020; 152:134113. [DOI: 10.1063/5.0002389] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Mats Simmermacher
- School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom
| | - Elke Fasshauer
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Hans Jørgen Aa. Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
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4
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Vušak D, Pejić J, Jurković M, Szalontai G, Sabolović J. Coordination polymers of paramagnetic bis(leucinato)copper( ii) diastereomers: experimental and computational study of the stereoisomerism and conformations. CrystEngComm 2020. [DOI: 10.1039/d0ce00585a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The syntheses, X-ray diffraction, solid state NMR and molecular modeling determined (dis)similarities between the coordination polymers of two bis(leucinato)copper(ii) diastereomers.
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Affiliation(s)
- Darko Vušak
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Jelena Pejić
- Institute for Medical Research and Occupational Health
- HR-10000 Zagreb
- Croatia
| | - Mia Jurković
- Department of Chemistry
- Faculty of Science
- University of Zagreb
- HR-10000 Zagreb
- Croatia
| | - Gábor Szalontai
- NMR Laboratory
- Institute of Chemistry
- Faculty of Engineering
- University of Pannonia
- H-8201 Veszprém
| | - Jasmina Sabolović
- Institute for Medical Research and Occupational Health
- HR-10000 Zagreb
- Croatia
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5
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Markley JL, Westler WM. Biomolecular NMR: Past and future. Arch Biochem Biophys 2017; 628:3-16. [PMID: 28495511 PMCID: PMC5701516 DOI: 10.1016/j.abb.2017.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/04/2017] [Accepted: 05/07/2017] [Indexed: 12/28/2022]
Abstract
The editors of this special volume suggested this topic, presumably because of the perspective lent by our combined >90-year association with biomolecular NMR. What follows is our personal experience with the evolution of the field, which we hope will illustrate the trajectory of change over the years. As for the future, one can confidently predict that it will involve unexpected advances. Our narrative is colored by our experience in using the NMR Facility for Biomedical Studies at Carnegie-Mellon University (Pittsburgh) and in developing similar facilities at Purdue (1977-1984) and the University of Wisconsin-Madison (1984-). We have enjoyed developing NMR technology and making it available to collaborators and users of these facilities. Our group's association with the Biological Magnetic Resonance data Bank (BMRB) and with the Worldwide Protein Data Bank (wwPDB) has also been rewarding. Of course, many groups contributed to the early growth and development of biomolecular NMR, and our brief personal account certainly omits many important milestones.
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Affiliation(s)
- John L Markley
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - William Milo Westler
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
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6
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Barragan AM, Schulten K, Solov'yov IA. Mechanism of the Primary Charge Transfer Reaction in the Cytochrome bc 1 Complex. J Phys Chem B 2016; 120:11369-11380. [PMID: 27661199 DOI: 10.1021/acs.jpcb.6b07394] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bc1 complex is a critical enzyme for the ATP production in photosynthesis and cellular respiration. Its biochemical function relies on the so-called Q-cycle, which is well established and operates via quinol substrates that bind inside the protein complex. Despite decades of research, the quinol-protein interaction, which initiates the Q-cycle, has not yet been completely described. Furthermore, the initial charge transfer reactions of the Q-cycle lack a physical description. The present investigation utilizes classical molecular dynamics simulations in tandem with quantum density functional theory calculations, to provide a complete and consistent quantitative description of the primary events that occur within the bc1 complex upon quinol binding. In particular, the electron and proton transfer reactions that trigger the Q-cycle in the bc1 complex from Rhodobacter capsulatus are studied. The coupled nature of these charge transfer reactions was revealed by obtaining the transition energy path connecting configurations of the Qo-site prior and after the transfers. The analysis of orbitals and partial charge distribution of the different states of the Qo-site has further supported the conclusion. Finally, key structural elements of the bc1 complex that trigger the charge transfer reactions were established, manifesting the importance of the environment in the process, which is furthermore evidenced by free energy calculations.
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Affiliation(s)
- Angela M Barragan
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Klaus Schulten
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 West Green Street, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Campusvej 55, DK-5230 Odense M, Denmark
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7
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Lin B, Ma G, Liu Y. Mechanism of the Glutathione Persulfide Oxidation Process Catalyzed by Ethylmalonic Encephalopathy Protein 1. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Beibei Lin
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Guangcai Ma
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, Shandong 250100, China
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8
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Bren KL. Going with the Electron Flow: Heme Electronic Structure and Electron Transfer in Cytochrome
c. Isr J Chem 2016. [DOI: 10.1002/ijch.201600021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kara L. Bren
- Department of Chemistry University of Rochester Rochester NY 14627-0216 USA
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9
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Koppenol-Raab M, Harwig MC, Posey AE, Egner JM, MacKenzie KR, Hill RB. A Targeted Mutation Identified through pKa Measurements Indicates a Postrecruitment Role for Fis1 in Yeast Mitochondrial Fission. J Biol Chem 2016; 291:20329-44. [PMID: 27496949 DOI: 10.1074/jbc.m116.724005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Indexed: 12/25/2022] Open
Abstract
The tail-anchored protein Fis1 is implicated as a passive tether in yeast mitochondrial fission. We probed the functional role of Fis1 Glu-78, whose elevated side chain pKa suggests participation in protein interactions. Fis1 binds partners Mdv1 or Dnm1 tightly, but mutation E78A weakens Fis1 interaction with Mdv1, alters mitochondrial morphology, and abolishes fission in a growth assay. In fis1Δ rescue experiments, Fis1-E78A causes a novel localization pattern in which Dnm1 uniformly coats the mitochondria. By contrast, Fis1-E78A at lower expression levels recruits Dnm1 into mitochondrial punctate structures but fails to support normal fission. Thus, Fis1 makes multiple interactions that support Dnm1 puncta formation and may be essential after this step, supporting a revised model for assembly of the mitochondrial fission machinery. The insights gained by mutating a residue with a perturbed pKa suggest that side chain pKa values inferred from routine NMR sample pH optimization could provide useful leads for functional investigations.
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Affiliation(s)
| | - Megan Cleland Harwig
- the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and
| | - Ammon E Posey
- From the Department of Biology and the Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218
| | - John M Egner
- the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and
| | - Kevin R MacKenzie
- the Department of Pathology, Baylor College of Medicine, Houston, Texas 77030
| | - R Blake Hill
- the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and
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10
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Husen P, Solov'yov IA. Spontaneous Binding of Molecular Oxygen at the Qo-Site of the bc1 Complex Could Stimulate Superoxide Formation. J Am Chem Soc 2016; 138:12150-8. [PMID: 27447781 DOI: 10.1021/jacs.6b04849] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A key part of the respiratory and photosynthetic pathways is the bc1 protein complex embedded in the inner membrane of mitochondria and the plasma membrane of photosynthetic bacteria. The protein complex pumps protons across the membrane to maintain an electrostatic potential, which is in turn used to drive ATP synthesis. This molecular machinery, however, is suspected to be a source of superoxide, which is toxic to the cell, even in minuscular quantities, and believed to be a factor in aging. Through molecular dynamics simulations, we investigate here the migration of molecular oxygen in the bc1 complex in order to identify possible reaction sites that could lead to superoxide formation. It is found, in particular, that oxygen penetrates spontaneously the Qo binding site of the bc1 complex in the presence of an intermediate semiquinone radical, thus making the Qo-site a strong candidate for being a center of superoxide production.
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Affiliation(s)
- Peter Husen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Odense 5230, Denmark
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Odense 5230, Denmark
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11
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Szalontai G, Csonka R, Speier G, Kaizer J, Sabolović J. Solid-State NMR Study of Paramagnetic Bis(alaninato-κ2N,O)copper(II) and Bis(1-amino(cyclo)alkane-1-carboxylato-κ2N,O)copper(II) Complexes: Reflection of Stereoisomerism and Molecular Mobility in 13C and 2H Fast Magic Angle Spinning Spectra. Inorg Chem 2015; 54:4663-77. [DOI: 10.1021/ic502987e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Gábor Szalontai
- Department of Chemistry, Faculty of Engineering, University of Pannonia, Egyetem utca 10, H-8201 Veszprém, Hungary
| | - Róbert Csonka
- Department of Chemistry, Faculty of Engineering, University of Pannonia, Egyetem utca 10, H-8201 Veszprém, Hungary
| | - Gábor Speier
- Department of Chemistry, Faculty of Engineering, University of Pannonia, Egyetem utca 10, H-8201 Veszprém, Hungary
| | - József Kaizer
- Department of Chemistry, Faculty of Engineering, University of Pannonia, Egyetem utca 10, H-8201 Veszprém, Hungary
| | - Jasmina Sabolović
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, P.O. Box 291,
HR-10001 Zagreb, Croatia
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12
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Kong X, Terskikh VV, Khade RL, Yang L, Rorick A, Zhang Y, He P, Huang Y, Wu G. Solid-state ¹⁷O NMR spectroscopy of paramagnetic coordination compounds. Angew Chem Int Ed Engl 2015; 54:4753-7. [PMID: 25694203 PMCID: PMC4418630 DOI: 10.1002/anie.201409888] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 11/09/2022]
Abstract
High-quality solid-state (17)O (I=5/2) NMR spectra can be successfully obtained for paramagnetic coordination compounds in which oxygen atoms are directly bonded to the paramagnetic metal centers. For complexes containing V(III) (S=1), Cu(II) (S=1/2), and Mn(III) (S=2) metal centers, the (17)O isotropic paramagnetic shifts were found to span a range of more than 10,000 ppm. In several cases, high-resolution (17)O NMR spectra were recorded under very fast magic-angle spinning (MAS) conditions at 21.1 T. Quantum-chemical computations using density functional theory (DFT) qualitatively reproduced the experimental (17)O hyperfine shift tensors.
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Affiliation(s)
- Xianqi Kong
- Department of Chemistry, Queen's University Kingston, Ontario, K7L 3N6 (Canada)
| | - Victor V. Terskikh
- Department of Chemistry, University of Ottawa Ottawa, Ontario, K1N 6N5 (Canada)
| | - Rahul L. Khade
- Department of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology Castle Point on Hudson, Hoboken, New Jersey 07030 (USA)
| | - Liu Yang
- Department of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology Castle Point on Hudson, Hoboken, New Jersey 07030 (USA)
| | - Amber Rorick
- Department of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology Castle Point on Hudson, Hoboken, New Jersey 07030 (USA)
| | - Yong Zhang
- Department of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology Castle Point on Hudson, Hoboken, New Jersey 07030 (USA)
| | - Peng He
- Department of Chemistry, University of Western Ontario London, Ontario, N6A 5B7 (Canada)
| | - Yining Huang
- Department of Chemistry, University of Western Ontario London, Ontario, N6A 5B7 (Canada)
| | - Gang Wu
- Department of Chemistry, Queen's University Kingston, Ontario, K7L 3N6 (Canada)
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13
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Kong X, Terskikh VV, Khade RL, Yang L, Rorick A, Zhang Y, He P, Huang Y, Wu G. Solid-State17O NMR Spectroscopy of Paramagnetic Coordination Compounds. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Piccioli M, Turano P. Transient iron coordination sites in proteins: Exploiting the dual nature of paramagnetic NMR. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2014.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Barragan AM, Crofts AR, Schulten K, Solov'yov IA. Identification of ubiquinol binding motifs at the Qo-site of the cytochrome bc1 complex. J Phys Chem B 2014; 119:433-47. [PMID: 25372183 PMCID: PMC4297238 DOI: 10.1021/jp510022w] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Enzymes of the bc1 complex family power
the biosphere through their central role in respiration and photosynthesis.
These enzymes couple the oxidation of quinol molecules by cytochrome c to the transfer of protons across the membrane, to generate
a proton-motive force that drives ATP synthesis. Key for the function
of the bc1 complex is the initial redox
process that involves a bifurcated electron transfer in which the
two electrons from a quinol substrate are passed to different electron
acceptors in the bc1 complex. The electron
transfer is coupled to proton transfer. The overall mechanism of quinol
oxidation by the bc1 complex is well enough
characterized to allow exploration at the atomistic level, but details
are still highly controversial. The controversy stems from the uncertain
binding motifs of quinol at the so-called Qo active site of the bc1 complex.
Here we employ a combination of classical all atom molecular dynamics
and quantum chemical calculations to reveal the binding modes of quinol
at the Qo-site of the bc1 complex from Rhodobacter capsulatus. The calculations suggest a novel configuration of amino acid residues
responsible for quinol binding and support a mechanism for proton-coupled
electron transfer from quinol to iron–sulfur cluster through
a bridging hydrogen bond from histidine that stabilizes the reaction
complex.
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Affiliation(s)
- Angela M Barragan
- Department of Physics, University of Illinois at Urbana-Champaign , 1110 W. Green Street, Urbana, Illinois 61801, United States
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16
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Szalontai G, Sabolović J, Marković M, Szabolcs Balogh A. Solid-State NMR Characterization of Paramagnetic Bis(L-valinato)copper(II) Stereoisomers - Effect of Conformational Disorder and Molecular Mobility on13C and2H Fast Magic-Angle Spinning Spectra. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402134] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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17
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 560] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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18
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Iijima T, Yamase T, Tansho M, Shimizu T, Nishimura K. Electron Localization of Polyoxomolybdates with ε-Keggin Structure Studied by Solid-State 95Mo NMR and DFT Calculation. J Phys Chem A 2014; 118:2431-41. [DOI: 10.1021/jp409969g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Takahiro Iijima
- Institute for Molecular Science, Okazaki, 444-8585, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki, 444-8585, Japan
| | - Toshihiro Yamase
- Tokyo Institute of Technology, Nagatsuta,
Yokohama 226-8503, Japan
- MO Device Corporation, Kanazawa 920-0335, Japan
| | - Masataka Tansho
- National Institute for Materials Science, Tsukuba 305-0003, Japan
| | - Tadashi Shimizu
- National Institute for Materials Science, Tsukuba 305-0003, Japan
| | - Katsuyuki Nishimura
- Institute for Molecular Science, Okazaki, 444-8585, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki, 444-8585, Japan
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19
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Carvalho ATP, Swart M. Electronic Structure Investigation and Parametrization of Biologically Relevant Iron–Sulfur Clusters. J Chem Inf Model 2014; 54:613-20. [DOI: 10.1021/ci400718m] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexandra T. P. Carvalho
- Institut
de Química Computacional i Catàlisi and Departament
de Química, Universitat de Girona, 17071 Girona, Spain
- Department
of Cell and Molecular Biology, Computational and Systems Biology, Box 596, 751 24 Uppsala, Sweden
| | - Marcel Swart
- Institut
de Química Computacional i Catàlisi and Departament
de Química, Universitat de Girona, 17071 Girona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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20
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Ciofi-Baffoni S, Gallo A, Muzzioli R, Piccioli M. The IR-¹⁵N-HSQC-AP experiment: a new tool for NMR spectroscopy of paramagnetic molecules. JOURNAL OF BIOMOLECULAR NMR 2014; 58:123-8. [PMID: 24414179 DOI: 10.1007/s10858-013-9810-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 12/27/2013] [Indexed: 05/22/2023]
Abstract
A crucial factor for the understanding of structure-function relationships in metalloproteins is the identification of NMR signals from residues surrounding the metal cofactor. When the latter is paramagnetic, the NMR information in the proximity of the metal center may be scarce, because fast nuclear relaxation quenches signal intensity and coherence transfer efficiency. To identify residues at a short distance from a paramagnetic center, we developed a modified version of the ¹⁵N-HSQC experiment where (1) an inversion recovery filter is added prior to HSQC, (2) the INEPT period has been optimized according to fast relaxation of interested spins, (3) the inverse INEPT has been eliminated and signals acquired as antiphase doublets. The experiment has been successfully tested on a human [Fe₂S₂] protein which is involved in the biogenesis of iron-sulfur proteins. Thirteen HN resonances, unobserved with conventional HSQC experiments, could be identified. The structural arrangement of the protein scaffold in the proximity of the Fe/S cluster is fundamental to comprehend the molecular processes responsible for the transfer of Fe/S groups in the iron-sulfur protein assembly machineries.
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Affiliation(s)
- Simone Ciofi-Baffoni
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
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21
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Kumara Swamy SK, Karczmarska A, Makowska-Janusik M, Kassiba A, Dittmer J. Solid-State NMR Correlation Experiments and Distance Measurements in Paramagnetic Metalorganics Exemplified by Cu-Cyclam. Chemphyschem 2013; 14:1864-70. [DOI: 10.1002/cphc.201300119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Indexed: 11/11/2022]
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22
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Carvalho ATP, Teixeira AFS, Ramos MJ. Parameters for molecular dynamics simulations of iron-sulfur proteins. J Comput Chem 2013; 34:1540-8. [PMID: 23609049 DOI: 10.1002/jcc.23287] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 03/01/2013] [Accepted: 03/05/2013] [Indexed: 11/06/2022]
Abstract
Iron-sulfur proteins involved in electron transfer reactions have finely tuned redox potentials, which allow them to be highly efficient and specific. Factors such as metal center solvent exposure, interaction with charged residues, or hydrogen bonds between the ligand residues and amide backbone groups have all been pointed out to cause such specific redox potentials. Here, we derived parameters compatible with the AMBER force field for the metal centers of iron-sulfur proteins and applied them in the molecular dynamics simulations of three iron-sulfur proteins. We used density-functional theory (DFT) calculations and Seminario's method for the parameterization. Parameter validation was obtained by matching structures and normal frequencies at the quantum mechanics and molecular mechanics levels of theory. Having guaranteed a correct representation of the protein coordination spheres, the amide H-bonds and the water exposure to the ligands were analyzed. Our results for the pattern of interactions with the metal centers are consistent to those obtained by nuclear magnetic resonance spectroscopy (NMR) experiments and DFT calculations, allowing the application of molecular dynamics to the study of those proteins.
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Affiliation(s)
- Alexandra T P Carvalho
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Girona 17071, Spain.
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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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24
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Zhang JK, Wang PC, Wang XW, Wang L, Chen JC, Zheng ZW, Niu YP. Vinyl addition polymerization of norbornene catalyzed by β-iminoamine Ni(II) complexes/methylaluminoxane systems. J Organomet Chem 2011. [DOI: 10.1016/j.jorganchem.2011.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Roquette P, Maronna A, Reinmuth M, Kaifer E, Enders M, Himmel HJ. Combining NMR of Dynamic and Paramagnetic Molecules: Fluxional High-Spin Nickel(II) Complexes Bearing Bisguanidine Ligands. Inorg Chem 2011; 50:1942-55. [DOI: 10.1021/ic102420x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Pascal Roquette
- Contribution from the Department of Inorganic Chemistry, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Astrid Maronna
- Contribution from the Department of Inorganic Chemistry, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Matthias Reinmuth
- Contribution from the Department of Inorganic Chemistry, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Elisabeth Kaifer
- Contribution from the Department of Inorganic Chemistry, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Markus Enders
- Contribution from the Department of Inorganic Chemistry, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Hans-Jörg Himmel
- Contribution from the Department of Inorganic Chemistry, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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26
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Westler WM, Lin IJ, Perczel A, Weinhold F, Markley JL. Hyperfine-shifted 13C resonance assignments in an iron-sulfur protein with quantum chemical verification: aliphatic C-H···S 3-center-4-electron interactions. J Am Chem Soc 2011; 133:1310-6. [PMID: 21207994 PMCID: PMC3033705 DOI: 10.1021/ja1049059] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Although the majority of noncovalent interactions associated with hydrogen and heavy atoms in proteins and other biomolecules are classical hydrogen bonds between polar N−H or O−H moieties and O atoms or aromatic π electrons, high-resolution X-ray crystallographic models deposited in the Protein Data Bank show evidence for weaker C−H···O hydrogen bonds, including ones involving sp3-hybridized carbon atoms. Little evidence is available in proteins for the (even) weaker C−H···S interactions described in the crystallographic literature on small molecules. Here, we report experimental evidence and theoretical verification for the existence of nine aliphatic (sp3-hybridized) C−H···S 3-center−4-electron interactions in the protein Clostridium pasteurianum rubredoxin. Our evidence comes from the analysis of carbon-13 NMR chemical shifts assigned to atoms near the iron at the active site of this protein. We detected anomalous chemical shifts for these carbon-13 nuclei and explained their origin in terms of unpaired spin density from the iron atom being delocalized through interactions of the type: C−H···S−Fe, where S is the sulfur of one of the four cysteine side chains covalently bonded to the iron. These results suggest that polarized sulfur atoms in proteins can engage in multiple weak interactions with surrounding aliphatic groups. We analyze the strength and angular dependence of these interactions and conclude that they may contribute small, but significant, stabilization to the molecule.
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Affiliation(s)
- William M Westler
- National Magnetic Resonance Facility at Madison, University of Wisconsin, Madison, Wisconsin 53706, United States.
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27
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Lin IJ, Xia B, King DS, Machonkin TE, Westler WM, Markley JL. Hyperfine-shifted (13)C and (15)N NMR signals from Clostridium pasteurianum rubredoxin: extensive assignments and quantum chemical verification. J Am Chem Soc 2010; 131:15555-63. [PMID: 19799419 PMCID: PMC2766250 DOI: 10.1021/ja905928x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Stable isotope-labeling methods, coupled with novel techniques for detecting fast-relaxing NMR signals, now permit detailed investigations of paramagnetic centers of metalloproteins. We have utilized these advances to carry out comprehensive assignments of the hyperfine-shifted 13C and 15N signals of the rubredoxin from Clostridium pasteurianum (CpRd) in both its oxidized and reduced states. We used residue-specific labeling (by chemical synthesis) and residue-type-selective labeling (by biosynthesis) to assign signals detected by one-dimensional 15N NMR spectroscopy, to nitrogen atoms near the iron center. We refined and extended these 15N assignments to the adjacent carbonyl carbons by means of one-dimensional 13C[15N] decoupling difference experiments. We collected paramagnetic-optimized SuperWEFT 13C[13C] constant time COSY (SW-CT-COSY) data to complete the assignment of 13C signals of reduced CpRd. By following these 13C signals as the protein was gradually oxidized, we transferred these assignments to carbons in the oxidized state. We have compared these assignments with hyperfine chemical shifts calculated from available X-ray structures of CpRd in its oxidized and reduced forms. The results allow the evaluation of the X-ray structural models as representative of the solution structure of the protein, and they provide a framework for future investigation of the active site of this protein. The methods developed here should be applicable to other proteins that contain a paramagnetic center with high spin and slow electron exchange.
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Affiliation(s)
- I-Jin Lin
- Graduate Program in Biophysics, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, USA
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28
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An NMR structural study of nickel-substituted rubredoxin. J Biol Inorg Chem 2009; 15:409-20. [PMID: 19997764 DOI: 10.1007/s00775-009-0613-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2009] [Accepted: 11/10/2009] [Indexed: 10/20/2022]
Abstract
The Ni(II) and Zn(II) derivatives of Desulfovibrio vulgaris rubredoxin (DvRd) have been studied by NMR spectroscopy to probe the structure at the metal centre. The beta CH(2) proton pairs from the cysteines that bind the Ni(II) atom have been identified using 1D nuclear Overhauser enhancement (NOE) difference spectra and sequence specifically assigned via NOE correlations to neighbouring protons and by comparison with the published X-ray crystal structure of a Ni(II) derivative of Clostridium pasteurianum rubredoxin. The solution structures of DvRd(Zn) and DvRd(Ni) have been determined and the paramagnetic form refined using pseudocontact shifts. The determination of the magnetic susceptibility anisotropy tensor allowed the contact and pseudocontact contributions to the observed chemical shifts to be obtained. Analysis of the pseudocontact and contact chemical shifts of the cysteine H beta protons and backbone protons close to the metal centre allowed conclusions to be drawn as to the geometry and hydrogen-bonding pattern at the metal binding site. The importance of NH-S hydrogen bonds at the metal centre for the delocalization of electron spin density is confirmed for rubredoxins and can be extrapolated to metal centres in Cu proteins: amicyanin, plastocyanin, stellacyanin, azurin and pseudoazurin.
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29
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Dikanov SA, Samoilova RI, Kappl R, Crofts AR, Hüttermann J. The reduced [2Fe-2S] clusters in adrenodoxin and Arthrospira platensis ferredoxin share spin density with protein nitrogens, probed using 2D ESEEM. Phys Chem Chem Phys 2009; 11:6807-19. [PMID: 19639155 PMCID: PMC2773023 DOI: 10.1039/b904597j] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have used X-band ESEEM to study the reduced [2Fe-2S] cluster in adrenodoxin and Arthrospira platensis ferredoxin. By use of a 2D approach (HYSCORE), we have shown that the cluster is involved in weak magnetic interactions with several nitrogens in each protein. Despite substantial differences in the shape and orientational dependence of individual cross-peaks, the major spectral features in both proteins are attributable to two peptide nitrogens (N1 and N2) with similar hyperfine couplings approximately 1.1 and approximately 0.70 MHz. The couplings determined represent a small fraction (0.0003-0.0005) of the unpaired spin density of the reduced cluster transferred to these nitrogens over H-bond bridges or the covalent bonds of cysteine ligands. Simulation of the HYSCORE spectra has allowed us to estimate the orientation of the nuclear quadrupole tensors of N1 and N2 in the g-tensor coordinate system. The most likely candidates for the role of N1 and N2 have been identified in the protein environment by comparing magnetic-resonance data with crystallographic structures of the oxidized proteins. A possible influence of redox-linked structural changes on ESEEM data is analyzed using available structures for related proteins in two redox states.
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Affiliation(s)
- Sergei A Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois, Urbana, IL 61801, USA.
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30
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Tang JA, Kogut E, Norton D, Lough AJ, McGarvey BR, Fekl U, Schurko RW. Impact of reduction on the properties of metal bisdithiolenes: multinuclear solid-state NMR and structural studies on Pt(tfd)2 and its reduced forms. J Phys Chem B 2009; 113:3298-313. [PMID: 19236015 DOI: 10.1021/jp807530d] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transition-metal dithiolene complexes have interesting structures and fascinating redox properties, making them promising candidates for a number of applications, including superconductors, photonic devices, chemical sensors, and catalysts. However, not enough is known about the molecular electronic origins of these properties. Multinuclear solid-state NMR spectroscopy and first-principles calculations are used to examine the molecular and electronic structures of the redox series [Pt(tfd)(2)](z-) (tfd = S(2)C(2)(CF(3))(2); z = 0, 1, 2; the anionic species have [NEt(4)](+) countercations). Single-crystal X-ray structures for the neutral (z = 0) and the fully reduced forms (z = 2) were obtained. The two species have very similar structures but differ slightly in their intraligand bond lengths. (19)F-(195)Pt CP/CPMG and (195)Pt magic-angle spinning (MAS) NMR experiments are used to probe the diamagnetic (z = 0, 2) species, revealing large platinum chemical shielding anisotropies (CSA) with distinct CS tensor properties, despite the very similar structural features of these species. Density functional theory (DFT) calculations are used to rationalize the large platinum CSAs and CS tensor orientations of the diamagnetic species using molecular orbital (MO) analysis, and are used to explain their distinct molecular electronic structures in the context of the NMR data. The paramagnetic species (z = 1) is examined using both EPR spectroscopy and (13)C and (19)F MAS NMR spectroscopy. Platinum g-tensor components were determined by using solid-state EPR experiments. The unpaired electron spin densities at (13)C and (19)F nuclei were measured by employing variable-temperature (13)C and (19)F NMR experiments. DFT and ab initio calculations are able to qualitatively reproduce the experimentally measured g-tensor components and spin densities. The combination of experimental and theoretical data confirm localization of unpaired electron density in the pi-system of the dithiolene rings.
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Affiliation(s)
- Joel A Tang
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada
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31
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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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32
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Casabianca LB, de Dios AC. Ab initiocalculations of NMR chemical shifts. J Chem Phys 2008; 128:052201. [DOI: 10.1063/1.2816784] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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33
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Fernández P, Pritzkow H, Carbó JJ, Hofmann P, Enders M. 1H NMR Investigation of Paramagnetic Chromium(III) Olefin Polymerization Catalysts: Experimental Results, Shift Assignment and Prediction by Quantum Chemical Calculations. Organometallics 2007. [DOI: 10.1021/om070173y] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pablo Fernández
- Anorganisch- and Organisch-Chemisches Institut der Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany, and Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel lí Domingo s/n, 43007 Tarragona, Spain
| | - Hans Pritzkow
- Anorganisch- and Organisch-Chemisches Institut der Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany, and Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel lí Domingo s/n, 43007 Tarragona, Spain
| | - Jorge J. Carbó
- Anorganisch- and Organisch-Chemisches Institut der Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany, and Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel lí Domingo s/n, 43007 Tarragona, Spain
| | - Peter Hofmann
- Anorganisch- and Organisch-Chemisches Institut der Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany, and Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel lí Domingo s/n, 43007 Tarragona, Spain
| | - Markus Enders
- Anorganisch- and Organisch-Chemisches Institut der Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany, and Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Marcel lí Domingo s/n, 43007 Tarragona, Spain
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34
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Russ JL, Gu J, Tsai KH, Glass T, Duchamp JC, Dorn HC. Nitroxide/Substrate Weak Hydrogen Bonding: Attitude and Dynamics of Collisions in Solution. J Am Chem Soc 2007; 129:7018-27. [PMID: 17497854 DOI: 10.1021/ja064632i] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The study of intermolecular collisions and bonding interactions in solutions is of critical importance in understanding and predicting solute/solvent properties. Previous work has established that stable paramagnetic nitroxide molecules are excellent probes of intermolecular interactions for hydrogen bonding in polar solvents. In this study, 1H, 2H, 13C, 15N NMR and liquid/liquid intermolecular transfer dynamic nuclear polarization (L2IT DNP) results are obtained for the paramagnetic probe molecule, TEMPO, interacting with the common aprotic and protic polar solvents, CH3CN and CH3CONH2, yielding a profile of both dipolar and scalar interactions. A significant scalar contact hyperfine is observed for the N-O...H-C interaction (13CH3 hyperfine, a/h=0.66 MHz) in the CH3CN/TEMPO system, whereas the N-O...H-C and N-O...H-N interactions for the TEMPO/CH3CONH2 system yield 13CH3 and 15N hyperfine couplings of a/h=0.16 and -0.50 MHz, respectively. The distance and attitude of the scalar interaction for the nitroxide hydrogen bonding at the methyl group in CH3CN and the amino group in CH3CONH2 are computed using density functional theory (DFT), yielding good agreement with the experimental results. These results show that the hyperfine coupling provides a sensitive probe of weak hydrogen-bonding interactions in solution.
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Affiliation(s)
- Jennifer L Russ
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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35
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Hrobárik P, Reviakine R, Arbuznikov AV, Malkina OL, Malkin VG, Köhler FH, Kaupp M. Density functional calculations of NMR shielding tensors for paramagnetic systems with arbitrary spin multiplicity: validation on 3d metallocenes. J Chem Phys 2007; 126:024107. [PMID: 17228943 DOI: 10.1063/1.2423003] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The calculation of nuclear shieldings for paramagnetic molecules has been implemented in the ReSpect program, which allows the use of modern density functional methods with accurate treatments of spin-orbit effects for all relevant terms up to order Omicron(alpha4) in the fine structure constant. Compared to previous implementations, the methodology has been extended to compounds of arbitrary spin multiplicity. Effects of zero-field splittings in high-spin systems are approximately accounted for. Validation of the new implementation is carried out for the 13C and 1H NMR signal shifts of the 3d metallocenes 4VCp2, 3CrCp2, 2MnCp2, 6MnCp2, 2CoCp2, and 3NiCp2. Zero-field splitting effects on isotropic shifts tend to be small or negligible. Agreement with experimental isotropic shifts is already good with the BP86 gradient-corrected functional and is further improved by admixture of Hartree-Fock exchange in hybrid functionals. Decomposition of the shieldings confirms the dominant importance of the Fermi-contact shifts, but contributions from spin-orbit dependent terms are frequently also non-negligible. Agreement with 13C NMR shift tensors from solid-state experiments is of similar quality as for isotropic shifts.
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Affiliation(s)
- Peter Hrobárik
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84536 Bratislava, Slovakia
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36
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Kervern G, Pintacuda G, Zhang Y, Oldfield E, Roukoss C, Kuntz E, Herdtweck E, Basset JM, Cadars S, Lesage A, Copéret C, Emsley L. Solid-State NMR of a Paramagnetic DIAD-FeII Catalyst: Sensitivity, Resolution Enhancement, and Structure-Based Assignments. J Am Chem Soc 2006; 128:13545-52. [PMID: 17031968 DOI: 10.1021/ja063510n] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A general protocol for the structural characterization of paramagnetic molecular solids using solid-state NMR is provided and illustrated by the characterization of a high-spin Fe(II) catalyst precursor. We show how good NMR performance can be obtained on a molecular powder sample at natural abundance by using very fast (>30 kHz) magic angle spinning (MAS), even though the individual NMR resonances have highly anisotropic shifts and very short relaxation times. The results include the optimization of broadband heteronuclear (proton-carbon) recoupling sequences for polarization transfer; the observation of single or multiple quantum correlation spectra between coupled spins as a tool for removing the inhomogeneous bulk magnetic susceptibility (BMS) broadening; and the combination of NMR experiments and density functional theory calculations, to yield assignments.
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Affiliation(s)
- Gwendal Kervern
- Laboratoire de Chimie, UMR 5182 CNRS-ENS Lyon, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
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37
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LeMaster DM, Minnich M, Parsons PJ, Anderson JS, Hernández G. Tetrathiolate coordination of germanium(IV) in a protein active site. J Inorg Biochem 2006; 100:1410-2. [PMID: 16712938 DOI: 10.1016/j.jinorgbio.2006.03.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Revised: 03/20/2006] [Accepted: 03/21/2006] [Indexed: 11/24/2022]
Abstract
The tetracysteine metal coordination site of the rubredoxins from Clostridium pasteurianum (Cp) and Pyrococcus furiosus (Pf) are shown to stably bind the inorganic Ge(IV) ion. This is the first characterized coordination complex of tetravalent germanium with a biological macromolecule. Zn(II), Ga(III) and Ge(IV) substitution yields differential NMR chemical shifts for the 1H and 15N amide resonances throughout much of the protein structure. The differential shifts for the six backbone amides that hydrogen bond to the metal-coordinated sulfurs indicate that the pseudo 2-fold symmetry of the active site is more closely maintained in the hyperthermophile Pf rubredoxin than in its mesophile Cp homolog. These three metal substitutions form an isoelectronic series of small diamagnetic proteins for which reference structures are known to 1A resolution. These series provide a promising system to analyze theoretical predictions of the effects of differential charge distribution on chemical shifts from both proximal and long range interactions.
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Affiliation(s)
- David M LeMaster
- Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA
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38
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Rodríguez JC, Wilks A, Rivera M. Backbone NMR Assignments and H/D Exchange Studies on the Ferric Azide- and Cyanide-Inhibited Forms of Pseudomonas aeruginosa Heme Oxygenase,. Biochemistry 2006; 45:4578-92. [PMID: 16584193 DOI: 10.1021/bi0600188] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 198 amino acid long heme oxygenase from Pseudomonas aeruginosa (pa-HO) was studied by multinuclear and multidimensional NMR spectroscopy in its paramagnetic cyanide-inhibited (pa-HO-CN) and azide-inhibited (pa-HO-N3) forms. Nearly complete backbone assignments (>93%) of all non-proline residues have been obtained, with the majority of the nonassigned residues corresponding to the first 10 amino terminal residues. Resonances strongly affected by heme iron paramagnetism were assigned with the aid of selective amino acid labeling and experiments tailored to detect fast relaxing signals, whereas the rest of the polypeptide was assigned using conventional three-dimensional NMR experiments. Amide chemical shift assignments were used to monitor the rate of exchange of backbone protons in hydrogen-deuterium exchange experiments. The polypeptide in the pa-HO-N3 complex was found to be significantly less prone to exchange than the polypeptide in pa-HO-CN, which we interpret to indicate that pa-HO-N3 is conformationally less flexible than pa-HO-CN. The differences in protection factors extend to regions of the protein remote from the heme iron and distal ligand. Mapping the differences in protection factors into the X-ray crystal structure of pa-HO [Friedman, J., Lad, L., Li, H., Wilks, A. Poulos, T. L. (2004) Biochemistry 43, 5239-5345] suggests that the distinct chemical properties imparted by the coordination of azide or cyanide to the heme iron [Zeng, Y. Caignan, G. A., Bunce, R. A., Rodríguez, J. C., Wilks, A., Rivera, M. (2005) J. Am. Chem. Soc. 127, 9794-9807] are transmitted to the polypeptide by a network of structural water molecules extending from the active site to the surface of the enzyme. Finally, while the 1H amide resonance of Gly125 was too broad to detect, the corresponding 15N resonance exhibits a large downfield shift, large line width, steep temperature dependence, and a larger than usual upfield deuterium isotope effect. These properties indicate unpaired spin delocalization from the heme iron into the Gly 15N atom via formation of a hydrogen bond between the coordinated azide nitrogen and the Gly125 N-H.
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Affiliation(s)
- Juan Carlos Rodríguez
- Department of Chemistry, The University of Kansas, Multidisciplinary Research Building, 2030 Becker Drive, Lawrence, Kansas 66047, USA
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39
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Enders M. Single-Site Organochromium Catalysts: Synthesis, Characterisation by Paramagnetic NMR and Olefin Polymerisation. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/masy.200690065] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Balayssac S, Jiménez B, Piccioli M. Assignment strategy for fast relaxing signals: complete aminoacid identification in thulium substituted calbindin D 9K. JOURNAL OF BIOMOLECULAR NMR 2006; 34:63-73. [PMID: 16518694 DOI: 10.1007/s10858-005-5359-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Accepted: 11/14/2005] [Indexed: 05/07/2023]
Abstract
Paramagnetic proteins generally contain regions with diverse relaxation properties. Nuclei in regions far from the metal center may behave like those in diamagnetic proteins, but those closer to the metal experience rapid relaxation with accompanying line broadening. We have used a set of NMR experiments optimized to capture data from these various concentric regions in assigning the signals from a paramagnetic Calbindin D 9K derivative in which one of the two calcium ions has been replaced by thulium(III). Normal double- and triple-resonance experiments with 1H detection were used in collecting data from nuclei in the diamagnetic-like region; these approaches identified signals from fewer than 50% of the amino acid residues (those with d > 17.5 A from thulium(III)). Paramagnetism-optimized two-dimensional NMR experiments with 1H detection were used in collecting data from nuclei in the next nearer region (d > 15 A). Standard (d > 14 A) and optimized (d > 9 A) 13C direct-detection experiments were used to capture data from nuclei in the next layer. Finally nuclei closest to the metal were detected by one-dimensional 13C (d > 5 A) and one-dimensional 15N data collection (d > 4.2 A). NMR signals were assigned on the basis of through-bond correlations and, for signals closest to the metal, pseudocontact shifts. The latter were determined from chemical shift differences between assigned signals in thulium(III) and lanthanum(III) derivatives of Calbindin D 9K and they were interpreted on the basis of a structural model for the lanthanide-substituted protein. This approach yielded assignments of at least one resonance per amino acid residue, including those in the thulium(III) coordination sphere.
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Affiliation(s)
- Stéphane Balayssac
- Department of Chemistry, Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
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41
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Lin IJ, Gebel EB, Machonkin TE, Westler WM, Markley JL. Changes in hydrogen-bond strengths explain reduction potentials in 10 rubredoxin variants. Proc Natl Acad Sci U S A 2005; 102:14581-6. [PMID: 16199518 PMCID: PMC1239895 DOI: 10.1073/pnas.0505521102] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rubredoxin from Clostridium pasteurianum (CpRd) provides an excellent system for investigating how the protein sequence modulates the reduction potential of the active site in an iron-sulfur protein. (15)N NMR spectroscopy has allowed us to determine with unprecedented accuracy the strengths of all six key hydrogen bonds between protein backbone amides and the sulfur atoms of the four cysteine residues that ligate the iron in the oxidized (Fe(III)) and reduced (Fe(II)) forms of wild-type CpRd and nine mutants (V44G, V44A, V44I, V44L, V8G, V8A, V8I, V8L, and V8G/V44G). The length (or strength) of each hydrogen bond was inferred from the magnitude of electron spin delocalized across the hydrogen bond from the iron atom onto the nitrogen. The aggregate lengths of these six hydrogen bonds are shorter in both oxidation states in variants with higher reduction potential than in those with lower reduction potential. Differences in aggregate hydrogen bonding upon reduction correlate linearly with the published reduction potentials for the 10 CpRd variants, which span 126 mV. Sequence effects on the reduction potential can be explained fully by their influence on hydrogen-bond strengths.
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Affiliation(s)
- I-Jin Lin
- Graduate Program in Biophysics, National Magnetic Resonance Facility at Madison, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706, USA
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42
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Jain NU, Tjioe E, Savidor A, Boulie J. Redox-dependent structural differences in putidaredoxin derived from homologous structure refinement via residual dipolar couplings. Biochemistry 2005; 44:9067-78. [PMID: 15966730 DOI: 10.1021/bi050152c] [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: 11/29/2022]
Abstract
Structural differences in the [2Fe-2S] ferredoxin, putidaredoxin (Pdx), from the camphor hydroxylation pathway of Pseudomonas putida have been investigated as a function of oxidation state of the iron cluster. Pdx is involved in biological electron transfer to cytochrome P450(cam) (CYP101). Redox-dependent differences have been observed previously for Pdx in terms of binding affinities to CYP101, NMR spectral differences, and dynamic properties. To further characterize these differences, structure refinement of both oxidized and reduced Pdx has been carried out using a hybrid approach utilizing paramagnetic distance restraints and NMR orientational restraints in the form of backbone (15)N residual dipolar couplings. Use of these new restraints has improved the structure of oxidized Pdx considerably over the earlier solution NMR structure without RDC restraints, with the new structure now much closer in overall fold to the recently published X-ray crystal structures. We now observe better defined relative orientations of the major secondary structure elements as also of the conformation of the metal binding loop region. Extension of this approach to structure calculation of reduced Pdx has identified structural differences that are primarily localized for residues in the C-terminal interaction domain consisting of the functionally important residue Trp 106 and regions near the metal binding loop in Pdx. These redox-dependent structural differences in Pdx correlate to dynamic changes observed before and may be linked to differences in binding and electron transfer properties between oxidized and reduced Pdx.
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Affiliation(s)
- Nitin U Jain
- Biochemistry, Cellular and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee 37996-0840, USA.
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43
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Abstract
This article deals with the solution structure determination of paramagnetic metalloproteins by NMR spectroscopy. These proteins were believed not to be suitable for NMR investigations for structure determination until a decade ago, but eventually novel experiments and software protocols were developed, with the aim of making the approach suitable for the goal and as user-friendly and safe as possible. In the article, we also give hints for the optimization of experiments with respect to each particular metal ion, with the aim of also providing a handy tool for nonspecialists. Finally, a section is dedicated to the significant progress made on 13C direct detection, which reduces the negative effects of paramagnetism and may constitute a new chapter in the whole field of NMR spectroscopy.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.
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44
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Machonkin TE, Westler WM, Markley JL. Paramagnetic NMR spectroscopy and density functional calculations in the analysis of the geometric and electronic structures of iron-sulfur proteins. Inorg Chem 2005; 44:779-97. [PMID: 15859246 DOI: 10.1021/ic048624j] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Paramagnetic NMR spectroscopy has been underutilized in the study of metalloproteins. One difficulty of the technique is that paramagnetic relaxation broadens signals from nuclei near paramagnetic centers. In systems with low electronic relaxation rates, this makes such signals difficult to observe or impossible to assign by traditional methods. We show how the challenges of detecting and assigning signals from nuclei near the metal center can be overcome through the combination of uniform and selective 2H, 13C, and 15N isotopic labeling with NMR experiments that utilize direct one-dimensional (2H, 13C, and 15N) and two-dimensional (13C-X) detection. We have developed methods for calculating NMR chemical shifts and relaxation rates by density functional theory (DFT) approaches. We use the correspondence between experimental NMR parameters and those calculated from structural models of iron-sulfur clusters derived from X-ray crystallography to validate the computational approach and to investigate how structural differences are manifested in these values. We have applied this strategy to three iron-sulfur proteins: Clostridium pasteurianum rubredoxin, Anabaena [2Fe-2S] ferredoxin, and human [2Fe-2S] ferredoxin. Provided that an accurate structural model of the iron-sulfur cluster and surrounding residues is available from diffraction data, our results show that DFT calculations can return NMR observables with excellent accuracy. This suggests that it might be possible to use calculations to refine structures or to generate structural models of active sites when crystal structures are unavailable. The approach has yielded insights into the electronic structures of these iron-sulfur proteins. In rubredoxin, the results show that substantial unpaired electron spin is delocalized across NH...S hydrogen bonds and that the reduction potential can be changed by 77 mV simply by altering the strength of one of these hydrogen bonds. In reduced [2Fe-2S] ferredoxins, hyperfine shift data have provided quantitative information on the degree of valence trapping. The approach described here for iron-sulfur proteins offers new avenues for detailed studies of these and other metalloprotein systems.
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Affiliation(s)
- Timothy E Machonkin
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
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45
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Oldfield E. Quantum chemical studies of protein structure. Philos Trans R Soc Lond B Biol Sci 2005; 360:1347-61. [PMID: 16147526 PMCID: PMC1569496 DOI: 10.1098/rstb.2003.1421] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2003] [Accepted: 09/24/2003] [Indexed: 11/12/2022] Open
Abstract
Quantum chemical methods now permit the prediction of many spectroscopic observables in proteins and related model systems, in addition to electrostatic properties, which are found to be in excellent accord with those determined from experiment. I discuss the developments over the past decade in these areas, including predictions of nuclear magnetic resonance chemical shifts, chemical shielding tensors, scalar couplings and hyperfine (contact) shifts, the isomer shifts and quadrupole splittings in Mössbauer spectroscopy, molecular energies and conformations, as well as a range of electrostatic properties, such as charge densities, the curvatures, Laplacians and Hessians of the charge density, electrostatic potentials, electric field gradients and electrostatic field effects. The availability of structure/spectroscopic correlations from quantum chemistry provides a basis for using numerous spectroscopic observables in determining aspects of protein structure, in determining electrostatic properties which are not readily accessible from experiment, as well as giving additional confidence in the use of these techniques to investigate questions about chemical bonding and chemical reactions.
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Affiliation(s)
- Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, 61801, USA.
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46
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Zhang Y, Sun H, Oldfield E. Solid-State NMR Fermi Contact and Dipolar Shifts in Organometallic Complexes and Metalloporphyrins. J Am Chem Soc 2005; 127:3652-3. [PMID: 15771472 DOI: 10.1021/ja043461j] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have used density functional theory methods to investigate the solid-state "magic-angle" spinning (MAS) NMR and single-crystal NMR/ENDOR spectra of paramagnetic organometallic complexes and metalloporphyrins. The solid-state MAS NMR chemical shifts (including both diamagnetic and hyperfine contributions) are predicted with a slope of 1.007 and an R2 = 0.967, corresponding to a 28 ppm (or 6.3%) error over the entire 442 ppm range. Single-crystal ENDOR hyperfine values, including both isotropic Fermi contact and dipolar couplings, are predicted with a slope of 1.009 and an R2 = 0.998, corresponding to a 0.93 MHz (or 1.2%) error over the entire 78.37 MHz range. In addition, single-crystal NMR shifts (including both hyperfine terms) are predicted with an R2 = 0.961. The ability to compute solid-state MAS NMR and single-crystal NMR/ENDOR data should facilitate the use of these techniques in investigating paramagnetic metal complexes and should be of particular use in studying paramagnetic metalloproteins, where structures are less accurately known.
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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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47
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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.
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Affiliation(s)
- Timothy E Machonkin
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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48
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Prestegard JH, Bougault CM, Kishore AI. Residual Dipolar Couplings in Structure Determination of Biomolecules. Chem Rev 2004; 104:3519-40. [PMID: 15303825 DOI: 10.1021/cr030419i] [Citation(s) in RCA: 340] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA.
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49
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Cheng RJ, Chen PY, Lovell T, Liu T, Noodleman L, Case DA. Symmetry and bonding in metalloporphyrins. A modern implementation for the bonding analyses of five- and six-coordinate high-spin iron(III)-porphyrin complexes through density functional calculation and NMR spectroscopy. J Am Chem Soc 2003; 125:6774-83. [PMID: 12769588 DOI: 10.1021/ja021344n] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bonding interactions between the iron and the porphyrin macrocycle of five- and six-coordinate high-spin iron(III)-porphyrin complexes are analyzed within the framework of approximate density functional theory with the use of the quantitative energy decomposition scheme in combination with removal of the vacant pi orbitals of the porphyrin from the valence space. Although the relative extent of the iron-porphyrin interactions can be evaluated qualitatively through the spin population and orbital contribution analyses, the bond strengths corresponding to different symmetry representations can be only approximated quantitatively by the orbital interaction energies. In contrast to previous suggestions, there are only limited Fe --> P pi back-bonding interactions in high-spin iron(III)-porphyrin complexes. It is the symmetry-allowed bonding interaction between d(z)2 and a(2u) orbitals that is responsible for the positive pi spin densities at the meso-carbons of five-coordinate iron(III)-porphyrin complexes. Both five- and six-coordinate complexes show significant P --> Fe pi donation, which is further enhanced by the movement of the metal toward the in-plane position for six-coordinate complexes. These bonding characteristics correlate very well with the NMR data reported experimentally. The extraordinary bonding interaction between d(z)2 and a(2u) orbitals in five-coordinate iron(III)-porphyrin complexes offers a novel symmetry-controlled mechanism for spin transfer between the axial ligand sigma system and the porphyrin pi system and may be critical to the electron transfer pathways mediated by hemoproteins.
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Affiliation(s)
- Ru-Jen Cheng
- Department of Chemistry, National Chung-Hsing University, Taichung, Taiwan 402, Republic of China.
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50
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Lin IJ, Gebel EB, Machonkin TE, Westler WM, Markley JL. Correlation between hydrogen bond lengths and reduction potentials in Clostridium pasteurianum rubredoxin. J Am Chem Soc 2003; 125:1464-5. [PMID: 12568591 DOI: 10.1021/ja028710n] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
15N NMR hyperfine-shift data were collected for wild-type and site-specific mutant (V44I, V44A, and V44G) Clostridium pasteurianum rubredoxins in the oxidized state. Whereas most of the (15)N NMR signals did not exhibit large systematic changes upon mutation of residue 44, the signal from the backbone nitrogen of residue 44 itself (arrows) shifted by approximately 400 ppm. These shifts were used to determine the lengths of the hydrogen bond between the backbone amide of residue 44 and the side-chain sulfur of cysteine-44, which is covalently ligated to the iron of the metal center. The results, which demonstrated that this hydrogen bond is shorter in mutants with higher reduction potential, point to the importance of hydrogen bonds in modulating the reduction potential of iron-sulfur proteins.
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Affiliation(s)
- I-Jin Lin
- Graduate Biophysics Program, Department of Biochemistry, , University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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