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Sehrawat N, Nehra E, Kumar Rohilla K, Kobayashi T, Nishiyama Y, Kumar Pandey M. Determination of the relative orientation between 15N- 1H dipolar coupling and 1H chemical shift anisotropy tensors under fast MAS solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 350:107428. [PMID: 37018911 DOI: 10.1016/j.jmr.2023.107428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/10/2023]
Abstract
In this work, we have proposed a proton-detected three-dimensional (3D) 15N-1H dipolar coupling (DIP)/1H chemical shift anisotropy (CSA)/1H chemical shift (CS) correlation experiment to measure the relative orientation between the 15N-1H dipolar coupling and the 1H CSA tensors under fast magic angle spinning (MAS) solid-state NMR. In the 3D correlation experiment, the 15N-1H dipolar coupling and 1H CSA tensors are recoupled using our recently developed windowless C-symmetry-based C331-ROCSA (recoupling of chemical shift anisotropy) DIPSHIFT and C331-ROCSA pulse-based methods, respectively. The 2D 15N-1H DIP/1H CSA powder lineshapes extracted using the proposed 3D correlation method are shown to be sensitive to the sign and asymmetry of the 1H CSA tensor, a feature that allows the determination of the relative orientation between the two correlating tensors with improved accuracy. The experimental method developed in this study is demonstrated on a powdered U-15N L-Histidine.HCl·H2O sample.
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Affiliation(s)
- Neelam Sehrawat
- Indian Institute of Technology (IIT) Ropar, Rupnagar, Punjab 140001, India
| | - Ekta Nehra
- Indian Institute of Technology (IIT) Ropar, Rupnagar, Punjab 140001, India
| | | | - Takeshi Kobayashi
- U.S. DOE, Ames Laboratory, Iowa State University, Ames, IA 50011-3020, United States
| | - Yusuke Nishiyama
- RIKEN-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan; JEOL Ltd., Musashino, Akishima, Tokyo 196-8558, Japan.
| | - Manoj Kumar Pandey
- Indian Institute of Technology (IIT) Ropar, Rupnagar, Punjab 140001, India.
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2
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Greenwood AI, Clay MC, Rienstra CM. 31P-dephased, 13C-detected REDOR for NMR crystallography at natural isotopic abundance. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 278:8-17. [PMID: 28319851 PMCID: PMC5478420 DOI: 10.1016/j.jmr.2017.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/21/2017] [Accepted: 02/26/2017] [Indexed: 05/14/2023]
Abstract
Typically, the process of NMR-based structure determination relies on accurately measuring a large number of internuclear distances to serve as restraints for simulated annealing calculations. In solids, the rotational-echo double-resonance (REDOR) experiment is a widely used approach to determine heteronuclear dipolar couplings corresponding to distances usually in the range of 1.5-8Å. A challenge in the interpretation of REDOR data is the degeneracy of symmetric subunits in an oligomer or equivalent molecules in a crystal lattice, which produce REDOR trajectories that depend explicitly on two or more distances instead of one. This degeneracy cannot be overcome by either spin dilution (for molecules containing 31P, 19F and other highly abundant nuclei) or selective pulses (in the case where there is chemical shift degeneracy). For small, crystalline molecules, such as phosphoserine, we demonstrate that as many as five inter-molecular distances must be considered to model 31P-dephased REDOR data accurately. We report excellent agreement between simulation and experiment once lattice couplings, 31P chemical shift anisotropy, and radio-frequency field inhomogeneity are all taken into account. We also discuss the systematic inaccuracies that may result from approximations that consider only the initial slope of the REDOR trajectory and/or that utilize a two- or three-spin system. Furthermore, we demonstrate the applicability of 31P-dephased REDOR for validation or refinement of candidate crystal structures and show that this approach is especially informative for NMR crystallography of 31P-containing molecules.
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Affiliation(s)
- Alexander I Greenwood
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mary C Clay
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chad M Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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3
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Wilson BW, Parker AA, Gullion T. Determining the relative orientation between the chemical shift anisotropy and heteronuclear dipolar tensors in static solids by SEDOR NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2016; 79:1-5. [PMID: 27690305 DOI: 10.1016/j.ssnmr.2016.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/07/2016] [Accepted: 09/18/2016] [Indexed: 06/06/2023]
Abstract
The measurement of the dipolar interaction between two spins provides the distance between nuclei. A better structural picture emerges when the distance is combined with the orientation of the internuclear vector in the principal axis system of the chemical shift anisotropy tensor. The SEDOR experiment is used on a static sample of alanine to show that the orientation of the vector connecting the nitrogen and carboxylate carbon nuclei can be accurately determined in the CSA PAS of the 13C carboxylate spin.
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Affiliation(s)
- Brendan W Wilson
- Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Arlo A Parker
- Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Terry Gullion
- Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States.
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Wi S, Spano J. Site-specific ϕ- and ψ-torsion angle determination in a uniformly/extensively 13C- and 15N-labeled peptide. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 212:431-439. [PMID: 21889381 DOI: 10.1016/j.jmr.2011.08.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 08/04/2011] [Accepted: 08/09/2011] [Indexed: 05/31/2023]
Abstract
A solid-state rotational-echo double resonance (REDOR) NMR method was introduced to identify the ϕ- and ψ-torsion angle from a (1)H-(15)N or (1)H-(13)C' spin system of alanine-like residues in a selectively, uniformly, or extensively (15)N-/(13)C-labeled peptide. When a C(α)(i) or a (15)N peak is site-specifically obtainable in the NMR spectrum of a uniformly (15)N/(13)C-labeled sample system, the ψ- or ϕ-torsion angle specified by the conformational structure of peptide geometry involving (15)N(i)-(1)H(α)i-(15)N(i+1) or (13)C'(i-1)-(1)H(N)i-(13)C'(i) spin system can be identified based on (13)C(α)- or (15)N-detected (1)H(α)-(15)N or (1)H(N)-(13)C REDOR experiment. This method will conveniently be utilized to identify major secondary motifs, such as α-helix, β-sheet, and β-turn, from a uniformly (15)N-/(13)C-labled peptide sample system. When tested on a (13)C-/(15)N-labeled model system of a three amino acid peptide Gly-[U-(13)C, (15)N]Ala-[U-(13)C, (15)N]Leu, the ψ-angle of alanine obtained experimentally, ψ = -40 ± 30°, agreed reasonably well with the X-ray determined angle, ψ = -39°.
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Affiliation(s)
- Sungsool Wi
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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Raskar DB, Eckert H, Ewald B, Kniep R. Characterization of local environments in crystalline borophosphates using single and double resonance NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2008; 34:20-31. [PMID: 18723330 DOI: 10.1016/j.ssnmr.2008.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 07/02/2008] [Indexed: 05/26/2023]
Abstract
(11)B and (31)P magic-angle spinning as well as (11)B{(31)P} and (31)P{(11)B} rotational echo double resonance (REDOR) NMR have been applied to characterize the local environments in the crystalline borophosphates K(3)[BP(3)O(9)(OH)(3)], NH(4)[ZnBP(2)O(8)] and Rb(3)[B(2)P(3)O(11)(OH)(2)]. Dipolar second moment values extracted from the REDOR curves at short evolution times (DeltaS/S(0) < or = 0.2) are in reasonable agreement with those calculated from the internuclear distances in the corresponding crystal structures. In particular, the method is found to be useful for distinguishing between boron and phosphorus local environments with different numbers of B-O-P connectivities, making REDOR a well-suited tool for medium-range order investigations in glasses.
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Affiliation(s)
- Devidas B Raskar
- Institut für Physikalische Chemie, Westfälische Wilhems-Universität Münster, Correnstrasse 30, D48149 Münster, Germany
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Qiang W, Bodner ML, Weliky DP. Solid-state NMR spectroscopy of human immunodeficiency virus fusion peptides associated with host-cell-like membranes: 2D correlation spectra and distance measurements support a fully extended conformation and models for specific antiparallel strand registries. J Am Chem Soc 2008; 130:5459-71. [PMID: 18370385 DOI: 10.1021/ja077302m] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human immunodeficiency virus (HIV) is "enveloped" by a membrane, and infection of a host cell begins with fusion between viral and target cell membranes. Fusion is catalyzed by the HIV gp41 protein which contains a functionally critical approximately 20-residue apolar "fusion peptide" (HFP) that associates with target cell membranes. In this study, chemically synthesized HFPs were associated with host-cell-like membranes and had "scatter-uniform" labeling (SUL), that is, only one residue of each amino acid type was U-(13)C, (15)N labeled. For the first sixteen HFP residues, an unambiguous (13)C chemical shift assignment was derived from 2D (13)C/(13)C correlation spectra with short mixing times, and the shifts were consistent with continuous beta-strand conformation. (13)C-(13)C contacts between residues on adjacent strands were derived from correlation spectra with long mixing times and suggested close proximity of the following residues: Ala-6/Gly-10, Ala-6/Phe-11, and Ile-4/Gly-13. Specific antiparallel beta-strand registries were further tested using a set of HFPs that were (13)CO-labeled at Ala-14 and (15)N-labeled at either Val-2, Gly-3, Ile-4, or Gly-5. The solid-state NMR data were fit with 50-60% population of antiparallel HFP with either Ala-14/Gly-3 or Ala-14/Ile-4 registries and 40-50% population of structures not specified by the NMR experiments. The first two registries correlated with intermolecular hydrogen bonding of 15-16 apolar N-terminal residues and this hydrogen-bonding pattern would be consistent with a predominant location of these residues in the hydrophobic membrane interior. To our knowledge, these results provide the first residue-specific structural models for membrane-associated HFP in its beta-strand conformation.
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Affiliation(s)
- Wei Qiang
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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Goobes G, Raghunathan V, Louie EA, Gibson JM, Olsen GL, Drobny GP. A REDOR study of diammonium hydrogen phosphate: a model for distance measurements from adsorbed molecules to surfaces. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2006; 29:242-50. [PMID: 16257188 DOI: 10.1016/j.ssnmr.2005.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Indexed: 05/05/2023]
Abstract
Magic angle spinning NMR techniques can be used to determine the molecular structure of proteins adsorbed onto polymer and mineral surfaces, but the degree to which the orientation of proteins on surfaces can be uniquely determined by NMR is less well understood. In this manuscript, REDOR data obtained from model systems are analyzed with a view to determine the orientation of rare spins coupled to a lattice populated by strongly coupled spin 1/2 nuclei. When the surface is populated by closely spaced spins, the REDOR dephasing of a rare spin on the protein contact point to the surface is under certain circumstances complicated by contributions from homonuclear dipolar interactions between the spins of the lattice. To study multiple spin effects on the dephasing signal in rotational-echo-double-resonance experiments, we carried out a measurement on crystalline diammonium hydrogen phosphate as a model for a spin system with multiple dipolar interactions. Information about the (31)P-(31)P interactions is gathered from the reference measurement in the experiment. To fit the experimental (15)N and (31)P dephasing data well, it was necessary to account for as many as 6 and 8 spins in simulations, respectively. Using a single spin-pair interaction with an unknown distance yielded a good fit to the (31)P data with a distance of 2.7A that is nearly an Angström shorter than the shortest distance in the crystal structure. Homonuclear couplings are shown to have a significant effect on the expected dephasing.
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Affiliation(s)
- Gil Goobes
- Department of Chemistry, University of Washington, Seattle, WA 98115, USA
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Louie EA, Chirakul P, Raghunathan V, Sigurdsson ST, Drobny GP. Using solid-state 31P{19F} REDOR NMR to measure distances between a trifluoromethyl group and a phosphodiester in nucleic acids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 178:11-24. [PMID: 16213170 DOI: 10.1016/j.jmr.2005.06.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2005] [Revised: 06/25/2005] [Accepted: 06/29/2005] [Indexed: 05/04/2023]
Abstract
REDOR is a solid-state NMR technique frequently applied to biological structure problems. Through incorporation of phosphorothioate groups in the nucleic acid backbone and mono-fluorinated nucleotides, 31P{19F} REDOR has been used to study the binding of DNA to drugs and RNA to proteins through the detection of internuclear distances as large as 13-14 A. In this work, 31P{19F} REDOR is further refined for use in nucleic acids by the combined use of selective placement of phosphorothioate groups and the introduction of nucleotides containing trifluoromethyl (-CF3) groups. To ascertain the REDOR-detectable distance limit between an unique phosphorous spin and a trifluoromethyl group and to assess interference from intermolecular couplings, a series of model compounds and DNA dodecamers were synthesized each containing a unique phosphorous label and trifluoromethyl group or a single 19F nucleus. The dipolar coupling constants of the various 31P and 19F or -CF3 containing compounds were compared using experimental and theoretical dephasing curves involving several models for intermolecular interactions.
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Affiliation(s)
- Elizabeth A Louie
- University of Washington, Chemistry Department, Campus Box 351700, Seattle, WA 98195-1700, USA
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Bernard GM, Miskolzie M, Kotovych G, Wasylishen RE. A solid-state NMR investigation of orexin-B. CAN J CHEM 2004. [DOI: 10.1139/v04-131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Some key aspects of the secondary structure of solid orexin-B, a 28 amino-acid peptide, have been investigated by solid-state NMR spectroscopy. The 13C15N dipolar coupling between the carbonyl carbon of Leu11 and the nitrogen of Leu15, as determined by rotational echo double resonance (REDOR) experiments, is 35 Hz, indicating that these nuclei are separated by approximately 4.5 Å. This distance is consistent with the α-helical structure determined for this segment of orexin-B by solution NMR measurements. REDOR measurements of the dipolar coupling between the carbonyl carbon of Ala17 and the nitrogen of Ala22 support the contention in an earlier solution NMR study that a bend exists between the two α helices of orexin-B. However, in the solid state the internuclear distance (6.4 Å) is significantly greater than that observed for orexin-B in aqueous solution. In addition to the distance measurements, the principal components of the amide carbonyl carbon chemical shift (CS) tensors for Leu11 and Ala17 and of the amide nitrogen CS tensors for Leu15 and Ala22 are reported. There are only minor differences between the amide carbonyl carbon CS tensors for Leu11 and Ala17 and between the nitrogen CS tensors for Leu15 and Ala22.Key words: orexin-B, solid-state NMR, REDOR, chemical shift tensors.
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Strojek W, Kalwei M, Eckert H. Dipolar NMR Strategies for Multispin Systems Involving Quadrupolar Nuclei: 31P{23Na} Rotational Echo Double Resonance (REDOR) of Crystalline Sodium Phosphates and Phosphate Glasses. J Phys Chem B 2004. [DOI: 10.1021/jp037041c] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Wenzel Strojek
- Institut für Physikalische Chemie, Westfälische Wilhelms−Universität Münster, Corrensstrasse 30, D-48149 Münster, Germany
| | - Martin Kalwei
- Institut für Physikalische Chemie, Westfälische Wilhelms−Universität Münster, Corrensstrasse 30, D-48149 Münster, Germany
| | - Hellmut Eckert
- Institut für Physikalische Chemie, Westfälische Wilhelms−Universität Münster, Corrensstrasse 30, D-48149 Münster, Germany
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Mueller LJ, Elliott DW. Correlated tensor interactions and rotational-echo double resonance of spin clusters. J Chem Phys 2003. [DOI: 10.1063/1.1565111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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