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Ahlawat S, Mote KR, Lakomek NA, Agarwal V. Solid-State NMR: Methods for Biological Solids. Chem Rev 2022; 122:9643-9737. [PMID: 35238547 DOI: 10.1021/acs.chemrev.1c00852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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2
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Charles P, Kalendra V, He Z, Khatami MH, Golbeck JH, van der Est A, Lakshmi KV, Bryant DA. Two-dimensional 67Zn HYSCORE spectroscopy reveals that a Zn-bacteriochlorophyll aP′ dimer is the primary donor (P840) in the type-1 reaction centers of Chloracidobacterium thermophilum. Phys Chem Chem Phys 2020; 22:6457-6467. [DOI: 10.1039/c9cp06556c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Using pulsed EPR spectroscopy and isotopic labeling we demonstrate that reaction centers of Chloracidobacterium thermophilum have an unusual primary donor that is a dimer of Zn-bacteriochlorophyll aP′ molecules.
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Affiliation(s)
- Philip Charles
- Departments of Chemistry and Physics and The Baruch ’60 Center for Biochemical Solar Energy Research
- Rensselaer Polytechnic Institute
- Troy
- USA
| | - Vidmantas Kalendra
- Departments of Chemistry and Physics and The Baruch ’60 Center for Biochemical Solar Energy Research
- Rensselaer Polytechnic Institute
- Troy
- USA
| | - Zhihui He
- Department of Biochemistry and Molecular Biology
- The Pennsylvania State University
- State College
- USA
| | | | - John H. Golbeck
- Department of Biochemistry and Molecular Biology
- The Pennsylvania State University
- State College
- USA
- Department of Chemistry
| | | | - K. V. Lakshmi
- Departments of Chemistry and Physics and The Baruch ’60 Center for Biochemical Solar Energy Research
- Rensselaer Polytechnic Institute
- Troy
- USA
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology
- The Pennsylvania State University
- State College
- USA
- Department of Chemistry and Biochemistry
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3
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Application of Heteronuclear NMR Spectroscopy to Bioinorganic and Medicinal Chemistry ☆. REFERENCE MODULE IN CHEMISTRY, MOLECULAR SCIENCES AND CHEMICAL ENGINEERING 2018. [PMCID: PMC7157447 DOI: 10.1016/b978-0-12-409547-2.10947-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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4
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Rossini AJ, Hanrahan MP, Thuo M. Rapid acquisition of wideline MAS solid-state NMR spectra with fast MAS, proton detection, and dipolar HMQC pulse sequences. Phys Chem Chem Phys 2016; 18:25284-25295. [DOI: 10.1039/c6cp04279a] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fast MAS and proton detection are applied to rapidly acquire wideline solid-state NMR spectra of spin-1/2 and half-integer quadrupolar nuclei.
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Affiliation(s)
- Aaron J. Rossini
- Iowa State University
- Department of Chemistry
- Ames
- USA
- US DOE Ames Laboratory
| | | | - Martin Thuo
- US DOE Ames Laboratory
- Ames
- USA
- Iowa State University
- Materials Science and Engineering Department
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5
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Renault M, García J, Cordeiro TN, Baldus M, Pons M. Protein oligomers studied by solid-state NMR--the case of the full-length nucleoid-associated protein histone-like nucleoid structuring protein. FEBS J 2013; 280:2916-28. [PMID: 23601147 DOI: 10.1111/febs.12297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 04/03/2013] [Accepted: 04/16/2013] [Indexed: 11/28/2022]
Abstract
Members of the histone-like nucleoid structuring protein (H-NS) family play roles both as architectural proteins and as modulators of gene expression in Gram-negative bacteria. The H-NS protein participates in modulatory processes that respond to environmental changes in osmolarity, pH, or temperature. H-NS oligomerization is essential for its activity. Structural models of different truncated forms are available. However, high-resolution structural details of full-length H-NS and its DNA-bound state have largely remained elusive. We report on progress in characterizing the biologically active H-NS oligomers with solid-state NMR. We compared uniformly ((13)C,(15)N)-labeled ssNMR preparations of the isolated N-terminal region (H-NS 1-47) and full-length H-NS (H-NS 1-137). In both cases, we obtained ssNMR spectra of good quality and characteristic of well-folded proteins. Analysis of the results of 2D and 3D (13)C-(13)C and (15)N-(13)C correlation experiments conducted at high magnetic field led to assignments of residues located in different topological regions of the free full-length H-NS. These findings confirm that the structure of the N-terminal dimerization domain is conserved in the oligomeric full-length protein. Small changes in the dimerization interface suggested by localized chemical shift variations between solution and solid-state spectra may be relevant for DNA recoginition.
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Affiliation(s)
- Marie Renault
- Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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6
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MacGregor AW, O'Dell LA, Schurko RW. New methods for the acquisition of ultra-wideline solid-state NMR spectra of spin-1/2 nuclides. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 208:103-113. [PMID: 21130011 DOI: 10.1016/j.jmr.2010.10.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 10/15/2010] [Accepted: 10/16/2010] [Indexed: 05/30/2023]
Abstract
The Wideband Uniform Rate Smooth Truncation - Carr-Purcell Meiboom-Gill (WURST-CPMG) pulse sequence was recently introduced as a new method of acquiring ultra-wideline solid-state NMR (SSNMR) patterns of quadrupolar nuclei (Chem. Phys. Lett. 464 (2008) 97). Herein, we describe the application of the WURST-CPMG pulse sequence to stationary samples (i.e., non-spinning or "static" samples) of various spin-1/2 nuclides ((119)Sn, (207)Pb, (199)Hg and (195)Pt) in order to examine its effectiveness for acquiring ultra-wideline SSNMR patterns. WURST-CPMG is compared to the CPMG and Cross Polarization (CP)-CPMG pulse sequences in select cases ((119)Sn and (207)Pb, respectively), and its usefulness in obtaining ultra-wideline SSNMR spectra in a piecewise fashion is explored. In addition, a preliminary investigation of pulses generated using optimal control theory (OCT) for the purpose of wideline excitation is presented; spectra acquired using these pulses are compared with standard, rectangular pulses of similar pulse powers. Both methods show much promise for acquiring high quality wideline patterns dominated by chemical shift anisotropy, with minimal distortions and significantly reduced experimental times.
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Affiliation(s)
- Alan W MacGregor
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4
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7
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Hung I, Gan Z. On the practical aspects of recording wideline QCPMG NMR spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 204:256-265. [PMID: 20359918 DOI: 10.1016/j.jmr.2010.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 03/02/2010] [Accepted: 03/02/2010] [Indexed: 05/29/2023]
Abstract
The practical aspects of applying CPMG for acquisition of wideline powder patterns are examined. It is shown that most distortions/modulations of spikelet spectra can be traced to the incoherent signal averaging from multiple coherence transfer pathways. A strategy for minimizing these distortions/modulations is described. Also, a few interesting observations regarding the implementation of the wideline WURST-QCPMG experiment are presented, namely the accumulation of second-order signal phase and the effects of varying the sweep rate and rf field of chirp pulses.
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Affiliation(s)
- Ivan Hung
- Center of Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, FL 32310, USA
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Mroué KH, Power WP. High-Field Solid-State 67Zn NMR Spectroscopy of Several Zinc−Amino Acid Complexes. J Phys Chem A 2009; 114:324-35. [PMID: 19919076 DOI: 10.1021/jp908325n] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Kamal H. Mroué
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - William P. Power
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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9
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Acquisition of ultra-wideline NMR spectra from quadrupolar nuclei by frequency stepped WURST–QCPMG. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2008.12.044] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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O’Dell LA, Schurko RW. QCPMG using adiabatic pulses for faster acquisition of ultra-wideline NMR spectra. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.08.095] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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11
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Lipton AS, Heck RW, Staeheli GR, Valiev M, De Jong WA, Ellis PD. A QM/MM Approach to Interpreting 67Zn Solid-State NMR Data in Zinc Proteins. J Am Chem Soc 2008; 130:6224-30. [DOI: 10.1021/ja711240t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew S. Lipton
- Biological Sciences Division and the Environmental Molecular Sciences Laboratory, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Robert W. Heck
- Biological Sciences Division and the Environmental Molecular Sciences Laboratory, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Greg R. Staeheli
- Biological Sciences Division and the Environmental Molecular Sciences Laboratory, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Marat Valiev
- Biological Sciences Division and the Environmental Molecular Sciences Laboratory, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Wibe A. De Jong
- Biological Sciences Division and the Environmental Molecular Sciences Laboratory, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Paul D. Ellis
- Biological Sciences Division and the Environmental Molecular Sciences Laboratory, Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352
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Abstract
We present here a 67Zn solid-state NMR investigation of several model complexes of zinc coordinated by four sulfurs. The lineshapes were obtained at a variety of magnetic fields from 11.7 T (500 MHz for 1H) to 21.15 T (900 MHz for 1H) and at ambient temperature down to 10 K. The quadrupole coupling constants, Cq's, ranged from 3.25 to 16.7 MHz throughout the series, while the average bond distances only spanned 2.34-2.36 A. Reasonable agreement with experiment was achieved in the molecular orbital calculations using DFT methods and the local density approximation to predict electric field gradients.
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Affiliation(s)
- Andrew S Lipton
- Macromolecular Structure & Dynamics Directorate, Fundamental Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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13
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Wazeer MI, Isab AA, Fettouhi M. New cadmium chloride complexes with imidazolidine-2-thione and its derivatives: X-ray structures, solid state and solution NMR and antimicrobial activity studies. Polyhedron 2007. [DOI: 10.1016/j.poly.2006.12.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Chapman RP, Bryce DL. A high-field solid-state 35/37Cl NMR and quantum chemical investigation of the chlorine quadrupolar and chemical shift tensors in amino acid hydrochlorides. Phys Chem Chem Phys 2007; 9:6219-30. [DOI: 10.1039/b712688c] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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15
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Bryce DL, Sward GD. Chlorine-35/37 NMR Spectroscopy of Solid Amino Acid Hydrochlorides: Refinement of Hydrogen-Bonded Proton Positions Using Experiment and Theory. J Phys Chem B 2006; 110:26461-70. [PMID: 17181306 DOI: 10.1021/jp065878c] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Trends in the chlorine chemical shift (CS) tensors of amino acid hydrochlorides are investigated in the context of new data obtained at 21.1 T and extensive quantum chemical calculations. The analysis of chlorine-35/37 NMR spectra of solid L-tryptophan hydrochloride obtained at two magnetic field strengths yields the chlorine electric field gradient (EFG) and CS tensors, and their relative orientations. The chlorine CS tensor is also determined for the first time for DL-arginine hydrochloride monohydrate. The drastic influence of 1H decoupling at 21.1 T on the spectral features of salts with particularly small 35Cl quadrupolar coupling constants (CQ) is demonstrated. The chlorine CS tensor spans (Omega) of hydrochloride salts of hydrophobic amino acids are found to be larger than those for salts of hydrophilic amino acids. A new combined experimental-theoretical procedure is described in which quantum chemical geometry optimizations of hydrogen-bonded proton positions around the chloride ions in a series of amino acid hydrochlorides are cross-validated against the experimental chlorine EFG and CS tensor data. The conclusion is reached that the relatively computationally inexpensive B3LYP/3-21G* method provides proton positions which are suitable for subsequent higher-level calculations of the chlorine EFG tensors. The computed value of is less sensitive to the proton positions. Following this cross-validation procedure, /CQ(35Cl)/ is generally predicted within 15% of the experimental value for a range of HCl salts. The results suggest the applicability of chlorine NMR interaction tensors in the refinement of proton positions in structurally similar compounds, e.g., chloride ion channels, for which neutron diffraction data are unavailable.
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Affiliation(s)
- David L Bryce
- Department of Chemistry and Centre for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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16
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Wong A, Ida R, Mo X, Gan Z, Poh J, Wu G. Solid-State 25Mg NMR Spectroscopic and Computational Studies of Organic Compounds. Square-Pyramidal Magnesium(II) Ions in Aqua(magnesium) Phthalocyanine and Chlorophyll a. J Phys Chem A 2006; 110:10084-90. [PMID: 16913682 DOI: 10.1021/jp061350w] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a solid-state (25)Mg NMR spectroscopic study of two magnesium-containing organic compounds: monopyridinated aqua(magnesium) phthalocyanine (MgPc.H(2)O.Py) and chlorophyll a (Chla). Each of these compounds contains a Mg(II) ion coordinating to four nitrogen atoms and a water molecule in a square-pyramidal geometry. Solid-state (25)Mg NMR spectra for MgPc.H(2)O.Py were obtained at 11.7 T (500 MHz for (1)H) for a (25)Mg-enriched sample (99.1% (25)Mg atom) using both Hahn-echo and quadrupole Carr-Purcell Meiboom-Gill (QCPMG) pulse sequences. Solid-state (25)Mg NMR spectra for Chla were recorded at (25)Mg natural abundance (10.1%) at 19.6 T (830 MHz for (1)H). The (25)Mg quadrupole parameters were determined from spectral analyses: MgPc.H(2)O.Py, C(Q) = 13.0 +/- 0.1 MHz and eta(Q) = 0.00 +/- 0.05; Chla, C(Q) = 12.9 +/- 0.1 MHz and eta(Q) = 1.00 +/- 0.05. This work represents the first time that Mg(II) ions in a square-pyramidal geometry have been characterized by solid-state (25)Mg NMR spectroscopy. Extensive quantum mechanical calculations for electric-field-gradient (EFG) and chemical shielding tensors were performed at restricted Hartee-Fock (RHF), density functional theory (DFT), and second-order Møller-Plesset perturbation theory (MP2) levels for both compounds. Computed (25)Mg nuclear quadrupole coupling constants at the RHF and MP2 levels show a reasonable basis-set convergence at the cc-pV5Z basis set (within 7% of the experimental value); however, B3LYP results display a drastic divergence beyond the cc-pVTZ basis set. A new crystal structure for MgPc.H(2)O.Py is also reported.
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Affiliation(s)
- Alan Wong
- Department of Chemistry, 90 Bader Lane, Queen's University, Kingston, Ontario, Canada
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Larsen FH, Farnan I, Lipton AS. Separation of 47Ti and 49Ti solid-state NMR lineshapes by static QCPMG experiments at multiple fields. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 178:228-36. [PMID: 16260159 DOI: 10.1016/j.jmr.2005.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2005] [Revised: 10/01/2005] [Accepted: 10/06/2005] [Indexed: 05/05/2023]
Abstract
Experimental procedures are proposed and demonstrated that separate the spectroscopic contribution from both (47)Ti and (49)Ti in solid-state nuclear magnetic resonance spectra. These take advantage of the different nuclear spin quantum numbers of these isotopes that lead to different "effective" radiofrequency fields for the central transition nutation frequencies when these nuclei occur in sites with a significant electric field gradient. Numerical simulations and solid-state NMR experiments were performed on the TiO(2) polymorphs anatase and rutile. For anatase, the separation of the two isotopes at high field (21.1T) facilitated accurate determination of the electric field gradient (EFG) and chemical shift anisotropy (CSA) tensors. This was accomplished by taking advantage of the quadrupolar interaction between the EFG at the titanium site and the different magnitudes of the nuclear quadrupole moments (Q) of the two isotopes. Rutile, having a larger quadrupolar coupling constant (C(Q)), was examined by (49)Ti-selective experiments at different magnetic fields to obtain spectra with different scalings of the two anisotropic tensors. A small chemical shielding anisotropy (CSA) of -30 ppm was determined.
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Affiliation(s)
- Flemming H Larsen
- Department of Food Science, Quality and Technology, The Royal Veterinary and Agricultural University, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark
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18
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Bryce DL, Sward GD, Adiga S. Solid-State 35/37Cl NMR Spectroscopy of Hydrochloride Salts of Amino Acids Implicated in Chloride Ion Transport Channel Selectivity: Opportunities at 900 MHz. J Am Chem Soc 2006; 128:2121-34. [PMID: 16464115 DOI: 10.1021/ja057253i] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The results of a detailed systematic chlorine solid-state NMR study of several hydrochloride salts of amino acids implicated in chloride ion transport channel selectivity are reported. (35)Cl and (37)Cl NMR spectra have been obtained for stationary and/or magic-angle spinning powdered samples of the following compounds on 500 and/or 900 MHz spectrometers: DL-arginine HCl monohydrate, L-lysine HCl, L-serine HCl, L-glutamic acid HCl, L-proline HCl, L-isoleucine HCl, L-valine HCl, L-phenylalanine HCl, and glycine HCl. Spectral analyses provide information on the anisotropic properties and relative orientations of the chlorine electric field gradient and chemical shift (CS) tensors, which are intimately related to the local molecular and electronic structure. Data obtained at 900 MHz provide unique examples of the effects of CS anisotropy on the NMR spectrum of a quadrupolar nucleus. The range of chlorine quadrupolar coupling constants (C(Q)) measured, -6.42 to 2.03 MHz, demonstrates the sensitivity of this parameter to the chloride ion environment and suggests the applicability of chlorine solid-state NMR as a novel experimental tool for defining chloride binding environments in larger ion channel systems. Salts of hydrophobic amino acids are observed to tend to exhibit larger values of C(Q) than salts of hydrophilic amino acids. A simple model for rationalizing the observed trend in C(Q) is proposed. For salts for which neutron diffraction structures are available, we identify a quantum chemical method which reproduces experimental values of C(Q) with a root-mean-square deviation of 0.1 MHz and a correlation coefficient of 0.9998. On the basis of this, chlorine NMR tensors are predicted for the Cl(-) binding site in ClC channels.
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Affiliation(s)
- David L Bryce
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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Marulanda D, Tasayco ML, McDermott A, Cataldi M, Arriaran V, Polenova T. Magic angle spinning solid-state NMR spectroscopy for structural studies of protein interfaces. resonance assignments of differentially enriched Escherichia coli thioredoxin reassembled by fragment complementation. J Am Chem Soc 2005; 126:16608-20. [PMID: 15600367 DOI: 10.1021/ja0464589] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
De novo site-specific backbone and side-chain resonance assignments are presented for U-15N(1-73)/U-13C,15N(74-108) reassembly of Escherichia coli thioredoxin by fragment complementation, determined using solid-state magic angle spinning NMR spectroscopy at 17.6 T. Backbone dihedral angles and secondary structure predicted from the statistical analysis of 13C and 15N chemical shifts are in general agreement with solution values for the intact full-length thioredoxin, confirming that the secondary structure is retained in the reassembled complex prepared as a poly(ethylene glycol) precipitate. The differential labeling of complementary thioredoxin fragments introduced in this work is expected to be beneficial for high-resolution structural studies of protein interfaces formed by protein assemblies by solid-state NMR spectroscopy.
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Affiliation(s)
- Dabeiba Marulanda
- Department of Chemistry and Biochemistry, Brown Laboratories, University of Delaware, Newark, Delaware 19716, USA
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Zhang Y, Mukherjee S, Oldfield E. 67Zn NMR Chemical Shifts and Electric Field Gradients in Zinc Complexes: A Quantum Chemical Investigation. J Am Chem Soc 2005; 127:2370-1. [PMID: 15724973 DOI: 10.1021/ja040242p] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used quantum chemical methods to predict 67Zn NMR chemical shifts as well as quadrupole coupling constants (CQ) in a series of biomimetic and inorganic zinc complexes. The 67Zn chemical shifts are predicted with an R2 = 0.975, corresponding to a 24.3 ppm or 6.7% error over the entire 365 ppm 67Zn chemical shift range. The 67Zn CQ values are predicted with an R2 = 0.991, corresponding to a 1.17 MHz or 3.0% error over the entire 38.75 MHz range. The 67Zn NMR shifts in a series of complexes containing N,O ligands are, in general, highly correlated with the number of oxygen ligands. The ability to compute 67Zn NMR shifts as well as CQ values opens up the possibility of using both of these properties in structure determination or refinement in proteins.
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Affiliation(s)
- Yong Zhang
- Departments of Chemistry and Biophysics, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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21
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Hung I, Rossini AJ, Schurko RW. Application of the Carr−Purcell Meiboom−Gill Pulse Sequence for the Acquisition of Solid-State NMR Spectra of Spin-1/2Nuclei. J Phys Chem A 2004. [DOI: 10.1021/jp0401123] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Hung I, Schurko RW. Solid-State 91Zr NMR of Bis(cyclopentadienyl)dichlorozirconium(IV). J Phys Chem B 2004. [DOI: 10.1021/jp040270u] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ivan Hung
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4
| | - Robert W. Schurko
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4
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Lipton AS, Heck RW, Sears JA, Ellis PD. Low temperature solid-state NMR experiments of half-integer quadrupolar nuclides: caveats and data analysis. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 168:66-74. [PMID: 15082250 DOI: 10.1016/j.jmr.2004.01.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2003] [Revised: 12/19/2003] [Indexed: 05/24/2023]
Abstract
Solid-state NMR spectroscopy of half-integer quadrupolar nuclides has received a lot of interest recently with the advent of new methodologies and higher magnetic fields. We present here the extension of our previous low temperature method to an 18.8T system. This new probe entailed a total redesign including a cross coil and variable capacitors that are operational at cryogenic temperatures. The limitations to sensitivity are also discussed; including a new diode network, the utilization of a cryogenic band pass filter, and the consequences of the RF profiles of the coil. Further, details of the spectroscopy of quadrupolar nuclei in a protein are discussed, such as the observation of the outer transitions and how to distinguish them from the desired +/-1/2 transition.
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Affiliation(s)
- Andrew S Lipton
- Macromolecular Structure and Dynamics Directorate, WR Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Affiliation(s)
- Gerard Parkin
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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25
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Siegel R, Nakashima TT, Wasylishen RE. Application of Multiple-Pulse Experiments to Characterize Broad NMR Chemical-Shift Powder Patterns from Spin-1/2 Nuclei in the Solid State. J Phys Chem B 2004. [DOI: 10.1021/jp031048c] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Renée Siegel
- Department of Chemistry, Gunning/Lemieux Chemistry Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Thomas T. Nakashima
- Department of Chemistry, Gunning/Lemieux Chemistry Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | - Roderick E. Wasylishen
- Department of Chemistry, Gunning/Lemieux Chemistry Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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26
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Ivanov D, Redfield AG. Field-cycling method with central transition readout for pure quadrupole resonance detection in dilute systems. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 166:19-27. [PMID: 14675815 DOI: 10.1016/j.jmr.2003.10.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We present a modification of a field-cycling method which uses the NMR signal of the central transition at high field to indirectly detect zero-field quadrupole transitions. The quadrupole transitions at zero-field are detected as changes in the overall intensity of the central transition signal after the field cycle, and the method is relatively immune to lineshape distortions of the central transition caused by receiver dead time, frequency response of the probe, longer pulse lengths, etc. Cross-polarization with protons is used to enhance the central-transition signal and to increase the recycling rate of the experiment. The technique is especially useful when mixtures of several species are present. In a frozen solution of phenylboronic acid, 11B quadrupole signals of the tetrahedral species at 600 kHz and planar-trigonal species at 1450 kHz are clearly resolved. The field-cycling approach allows high-sensitivity detection of low-frequency quadrupole transitions; the experiment is sensitive enough to study boronic-acid protease inhibitors bound to proteins and may possibly be extended to lower sensitivity nuclei. The experiments are performed using a low-temperature field-cycling apparatus, operated at 10-30 K, capable of pneumatically moving the sample from the high field of a commercial 500 MHz magnet to the area above the top of the magnet where the low field is controlled by a pair of Helmholz coils.
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Affiliation(s)
- Dmitri Ivanov
- Biophysics and Structural Biology Graduate Program, Brandeis University, Waltham, MA 02454, USA.
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27
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Lipton AS, Bergquist C, Parkin G, Ellis PD. Solid-State 67Zn NMR spectroscopic studies and ab initio molecular orbital calculations on a synthetic analogue of carbonic anhydrase. J Am Chem Soc 2003; 125:3768-72. [PMID: 12656608 DOI: 10.1021/ja021328q] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The tris(pyrazolyl)hydroborato zinc complexes [Tp(But,Me)]ZnX (where X = Br, Cl, and OH) have been examined by low-temperature solid-state (67)Zn NMR spectroscopy. The value of the quadrupole coupling constant, Cq, for the zinc increased monotonically with the electronegativity of the bound substituent X, e.g., Br < Cl << OH. Calculations on the methylimidazole complex [(MeImH)(3)Zn(OH)](+) as a model for the active site of carbonic anhydrase indicate that the computed electric field gradient tensor is in good agreement with the experimental and calculated values for [Tp(But,Me)]ZnOH.
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Affiliation(s)
- Andrew S Lipton
- Macromolecular Structure & Dynamics Directorate, WR Wiley Environmental Molecular Sciences Laboratory, Richland, Washington 99352, USA
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28
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Lupulescu A, Kotecha M, Frydman L. Relaxation-assisted separation of chemical sites in NMR spectroscopy of static solids. J Am Chem Soc 2003; 125:3376-83. [PMID: 12630893 DOI: 10.1021/ja021173m] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We discuss the potential use of relaxation times toward the resolution of inequivalent chemical sites in the NMR spectroscopy of powdered or disordered samples. This proposal is motivated by the significant differences that can often be detected in the relaxation behavior of sites in solids, particularly when focusing on NMR observations of quadrupolar nuclei possessing different coordination and/or dynamic environments. It is shown that in these cases the implementation of a non-negative least-squares analysis on relaxation data sets enables the bidimensional resolution of overlapping powder line shapes, even when dealing with static samples. In combination with signal-enhancement methodologies such as the quadrupolar Carr-Purcell Meiboom-Gill train, such relaxation-assisted separations open up valuable routes toward the high-resolution characterization of systems involving insensitive (e.g., low-gamma) nuclei. The principles and limitations of the 2D NMR approach resulting from these considerations are discussed, and their potential is exemplified with a variety of static and spinning investigations. Their extension to other nuclear systems where spectral resolution is problematic, such as protons in organic solids, is also briefly considered.
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Affiliation(s)
- Adonis Lupulescu
- Department of Chemical Physics, Weizmann Institute of Sciences, 76100 Rehovot, Israel
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29
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Rovnyak D, Filip C, Itin B, Stern AS, Wagner G, Griffin RG, Hoch JC. Multiple-quantum magic-angle spinning spectroscopy using nonlinear sampling. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 161:43-55. [PMID: 12660110 DOI: 10.1016/s1090-7807(02)00189-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
NMR spectroscopy is a relatively insensitive technique and many biomolecular applications operate near the limits of sensitivity and resolution. A particularly challenging example is detection of the quadrupolar nucleus 17O, due to its low natural abundance, large quadrupole couplings, and low gyromagnetic ratio. Yet the chemical shift of 17O spans almost 1000 ppm in organic molecules and it serves as a potentially unique reporter of hydrogen bonding in peptides, nucleic acids, and water, and as a valuable complement to 13C and 15N NMR. Recent developments including the multiple-quantum magic-angle spinning (MQMAS) experiment have enabled the detection of 17O in biological solids, but very long data acquisitions are required to achieve sufficient sensitivity and resolution. Here, we perform nonlinear sampling in the indirect dimension of MQMAS experiments to substantially reduce the total acquisition time and improve sensitivity and resolution. Nonlinear sampling prevents the use of the discrete Fourier transform; instead, we employ maximum entropy (MaxEnt) reconstruction. Nonlinearly sampled MQMAS spectra are shown to provide high resolution and sensitivity in several systems, including lithium sulfate monohydrate (LiSO(4)-H(2)17O) and L-asparagine monohydrate (H(2)17O). The combination of nonlinear sampling and MaxEnt reconstruction promises to make the application of 17O MQMAS practical in a wider range of biological systems.
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Affiliation(s)
- David Rovnyak
- MIT/Harvard Center for Magnetic Resonance, Massachusetts Institute of Technology, 150 Albany Street, Cambridge, MA 02139, USA
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30
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Ida R, Wu G. Theoretical Study of the 67Zn Electric-Field-Gradient Tensors in Zinc(II) Coordination Complexes. J Phys Chem A 2002. [DOI: 10.1021/jp0212141] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ramsey Ida
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
| | - Gang Wu
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada K7L 3N6
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31
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Abstract
Over the last decades, NMR spectroscopy has grown into an indispensable tool for chemical analysis, structure determination, and the study of dynamics in organic, inorganic, and biological systems. It is commonly used for a wide range of applications from the characterization of synthetic products to the study of molecular structures of systems such as catalysts, polymers, and proteins. Although most NMR experiments are performed on liquid-state samples, solid-state NMR is rapidly emerging as a powerful method for the study of solid samples and materials. This Review outlines some of the developments of solid-state NMR spectroscopy, including techniques such as cross-polarization, magic-angle spinning, multiple-pulse sequences, homo- and heteronuclear decoupling and recoupling techniques, multiple-quantum spectroscopy, and dynamic angle spinning, as well as their applications to structure determination. Modern solid-state NMR spectroscopic techniques not only produce spectra with a resolution close to that of liquid-state spectra, but also capitalize on anisotropic interactions, which are often unavailable for liquid samples. With this background, the future of solid-state NMR spectroscopy in chemistry appears to be promising, indeed.
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Affiliation(s)
- David D Laws
- Materials Sciences Division, Lawrence Berkeley National Laboratory and Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720, USA
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33
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Lipton AS, Wright TA, Bowman MK, Reger DL, Ellis PD. Solid-state (67)zn NMR spectroscopy in bioinorganic chemistry. Spectra of four- and six-coordinate zinc pyrazolylborate complexes obtained by management of proton relaxation rates with a paramagnetic dopant. J Am Chem Soc 2002; 124:5850-60. [PMID: 12010060 DOI: 10.1021/ja0127133] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Solid-state (67)Zn NMR spectra of model compounds for metalloproteins, such as [H(2)B(3,5-Me(2)pz)(2)](2)Zn (pz denotes pyrazolyl ring), have been obtained using low temperatures (10 K) to enhance the Boltzmann factor in combination with cross polarization (CP) from (1)H to (67)Zn. Attempts to observe spectra of other model compounds, such as [H(2)B(pz)(2)](2)Zn, were hindered by long relaxation times of the protons. To decrease the proton relaxation times, the high-spin six-coordinate complex [HB(3,4,5-Me(3)pz)(3)](2)Fe has been investigated as a dopant. NMR and EPR measurements have shown that this Fe(II) dopant effectively reduces the (1)H spin lattice relaxation time, T(1), of the zinc samples in the temperature range 5-10 K with minimal perturbations of the (1)H spin lattice relaxation time in the rotating frame, T(1)(rho). Using this methodology, we have determined the (67)Zn NMR parameters of four- and six-coordinate zinc(II) poly(pyrazolyl)borate complexes that are useful models for systems of biological importance. The (67)Zn NMR parameters are contrasted to the corresponding changes in the (113)Cd NMR parameters for the analogous compounds. Further, these investigations have demonstrated that a temperature-dependent phase transition occurs in the neighborhood of 185 K for [HB(3,5-Me(2)pz)(3)](2)Zn; the other poly(pyrazolyl)borate complexes we investigated did not show this temperature-dependent behavior. This conclusion is confirmed by a combination of room-temperature high-field (18.8 T) solid-state (67)Zn NMR spectroscopy and low-temperature X-ray methods. The utilization of paramagnetic dopants should enable low-temperature cross polarization experiments to be performed on a wide variety of nuclides that are important in bioinorganic chemistry, for example, (25)Mg, (43)Ca, and (67)Zn.
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Affiliation(s)
- Andrew S Lipton
- Macromolecular Structure & Dynamics Directorate, WR Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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34
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Larsen FH, Farnan I. 29Si and 17O (Q)CPMG-MAS solid-state NMR experiments as an optimum approach for half-integer nuclei having long T1 relaxation times. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)00520-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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35
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Grant CV, Frydman V, Harwood JS, Frydman L. 59Co solid-state NMR as a new probe for elucidating metal binding in polynucleotides. J Am Chem Soc 2002; 124:4458-62. [PMID: 11960475 DOI: 10.1021/ja012353j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although magnesium fulfills several essential biochemical roles, direct studies on this ion are complicated by its unfavorable spectroscopic characteristics. This contribution explores the possibility of monitoring magnesium-nucleic acid binding via a combination of [Co(NH3)6]3+ as surrogate for [Mg(H2O)6]2+, and of high-resolution solid-state 59Co NMR as a spectroscopic probe. Such strategy quenches fast cationic exchanges between bound and free states, while exploiting the superior NMR properties of the 59Co spin. Experiments on relatively small amounts of tRNA can then discern resonances corresponding to different metal binding environments. These characterizations were assisted by studies on model compounds and by multinuclear 31P-59Co recoupling experiments.
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Affiliation(s)
- Christopher V Grant
- Department of Chemical Physics, Weizmann Institute of Sciences, 76100 Rehovot, Israel
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36
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Ivanov D, Bachovchin WW, Redfield AG. Boron-11 pure quadrupole resonance investigation of peptide boronic acid inhibitors bound to alpha-lytic protease. Biochemistry 2002; 41:1587-90. [PMID: 11814352 DOI: 10.1021/bi011783j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pure quadrupole resonance is a potentially useful spectroscopic approach to study the coordination of quadrupolar nuclei in biological systems. We used a field-cycling NMR method to observe boron pure quadrupole resonance of two peptide boronic acid inhibitors bound to alpha-lytic protease. The method is similar to our earlier field-cycling experiment [Ivanov, D., and Redfield, A. R. (1998) Z. Naturforsch. A 53, 269-272] but uses a simple Hartmann-Hahn transfer from proton to (11)B before field cycle and direct (11)B observe after it. Pure quadrupole resonance is sensitive to the boron coordination geometry. For example, trigonal boron in neutral phenylboronic acid, which was used as a model compound, resonates at 1450 kHz, while the resonance of the tetrahedral phenylboronic acid anion appears at approximately 600 kHz. In the complex of the MeOSuc-Ala-Ala-Pro-boroVal inhibitor with the enzyme the quadrupole resonance signal was observed at 600-650 kHz, which indicates tetrahedral boron coordination in the active site. The quadrupole frequency of the MeOSuc-Ala-Ala-Pro-boroPhe enzyme-inhibitor complex, in which a boron-histidine bond is known to be formed, was found to be the same within experimental error as in the MeOSuc-Ala-Ala-Pro-boroVal enzyme-inhibitor adduct, suggesting that the boron coordination geometry in the enzyme-MeOSuc-Ala-Ala-Pro-boroPhe adduct is also close to tetrahedral.
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Affiliation(s)
- Dmitri Ivanov
- Biophysics and Structural Biology Graduate Program and Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02454, USA
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