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Yarava JR, Nishiyama Y, Raghothama S, Ramanathan KV. Conformational investigation of peptides using solid-state NMR spectroscopy-A study of polymorphism of β-turn peptides containing diprolines. Chem Biol Drug Des 2019; 95:394-407. [PMID: 31755652 DOI: 10.1111/cbdd.13649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/02/2019] [Accepted: 11/16/2019] [Indexed: 11/26/2022]
Abstract
The construction of complex protein folds relies on the precise conversion of a linear polypeptide chain into a compact 3-dimensional structure. In this context, study of isolated secondary structural modules containing short stretches of amino acids assumes significance. Additionally, peptides, both natural and synthetic, play a major role as potential drugs. With a view to understand the local conformations adopted by peptides in the solid state, we propose a multinuclear NMR approach utilizing spectra of nuclei in their natural isotopic abundance. Various solid-state NMR experiments have been utilized for assignment of the spectra. Additionally, the gauge-including projector augmented-wave (GIPAW) calculations were used to confirm the assignments. Particularly, the utility of the double-quantum-single-quantum correlation experiments is highlighted for the purpose of assignment and for inferring the conformation across the peptide bond. The methodology is illustrated for the case of designed peptides containing diproline residues occurring at the β-turns for identifying their cis-trans conformational polymorphism. The proposed method promises to be of use in the study of conformations of small- to medium-sized peptides such as antimicrobial peptides and in the study of polymorphism leading to applications in drug development protocols.
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Affiliation(s)
- Jayasubba Reddy Yarava
- NMR Research Centre, Indian Institute of Science, Bangalore, India.,Department of Physics, Indian Institute of Science, Bangalore, India
| | - Yusuke Nishiyama
- JEOL RESONANCE Inc., Musashino, Akishima, Japan.,RIKEN-JEOL Collaboration Center, Tsurumi, Yokohama, Japan
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2
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Kobayashi T, Wang Z, Pruski M. Homonuclear dipolar recoupling of arbitrary pairs in multi-spin systems under magic angle spinning: A double-frequency-selective ZQ-SEASHORE experiment. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 101:76-81. [PMID: 31129364 DOI: 10.1016/j.ssnmr.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
We describe a useful method for measuring the internuclear distances within arbitrarily selected pairs of like nuclei in dipolar-coupled multi-spin systems. The method uses a combination of the zero-quantum shift-evolution-assisted selective homonuclear recoupling (ZQ-SEASHORE) technique developed by Hu and Tycko [J. Chem. Phys. 2009, 131, 045101] and double-frequency-selective radio-frequency pulse. The double-frequency-selective pulse inverts polarizations of two spins simultaneously, and thus applications of the method presented here are only limited by the spectral resolution, and not by the number of interacting spins. Our experiments demonstrate the validity of the method and present analytical expressions for the dephasing curve.
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Affiliation(s)
- Takeshi Kobayashi
- U.S. DOE Ames Laboratory, Iowa State University, Ames, IA, 50011-3020, United States.
| | - Zhuoran Wang
- U.S. DOE Ames Laboratory, Iowa State University, Ames, IA, 50011-3020, United States; Department of Chemistry, Iowa State University, Ames, IA, 50011-3020, United States
| | - Marek Pruski
- U.S. DOE Ames Laboratory, Iowa State University, Ames, IA, 50011-3020, United States; Department of Chemistry, Iowa State University, Ames, IA, 50011-3020, United States.
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3
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Zhao L, Pinon AC, Emsley L, Rossini AJ. DNP-enhanced solid-state NMR spectroscopy of active pharmaceutical ingredients. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:583-609. [PMID: 29193278 DOI: 10.1002/mrc.4688] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 11/15/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Solid-state NMR spectroscopy has become a valuable tool for the characterization of both pure and formulated active pharmaceutical ingredients (APIs). However, NMR generally suffers from poor sensitivity that often restricts NMR experiments to nuclei with favorable properties, concentrated samples, and acquisition of one-dimensional (1D) NMR spectra. Here, we review how dynamic nuclear polarization (DNP) can be applied to routinely enhance the sensitivity of solid-state NMR experiments by one to two orders of magnitude for both pure and formulated APIs. Sample preparation protocols for relayed DNP experiments and experiments on directly doped APIs are detailed. Numerical spin diffusion models illustrate the dependence of relayed DNP enhancements on the relaxation properties and particle size of the solids and can be used for particle size determination when the other factors are known. We then describe the advanced solid-state NMR experiments that have been enabled by DNP and how they provide unique insight into the molecular and macroscopic structure of APIs. For example, with large sensitivity gains provided by DNP, natural isotopic abundance, 13 C-13 C double-quantum single-quantum homonuclear correlation NMR spectra of pure APIs can be routinely acquired. DNP also enables solid-state NMR experiments with unreceptive quadrupolar nuclei such as 2 H, 14 N, and 35 Cl that are commonly found in APIs. Applications of DNP-enhanced solid-state NMR spectroscopy for the molecular level characterization of low API load formulations such as commercial tablets and amorphous solid dispersions are described. Future perspectives for DNP-enhanced solid-state NMR experiments on APIs are briefly discussed.
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Affiliation(s)
- Li Zhao
- Department of Chemistry, Iowa State University, Ames, IA, USA
- US DOE Ames Laboratory, Ames, IA, USA
| | - Arthur C Pinon
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Aaron J Rossini
- Department of Chemistry, Iowa State University, Ames, IA, USA
- US DOE Ames Laboratory, Ames, IA, USA
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4
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Yarava JR, Sonti R, Kantharaju K, Raghothama S, Ramanathan KV. Solid-state NMR at natural isotopic abundance for the determination of conformational polymorphism - the case of designed β-turn peptides containing di-prolines. Chem Commun (Camb) 2017; 53:1317-1320. [PMID: 28074945 DOI: 10.1039/c6cc08676d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The proton double quantum-carbon single quantum correlation experiment has been applied to designed peptides in the solid state in natural isotopic abundance. Analogous to nOe studies in solution, through-space double-quantum connectivities have been exploited to obtain the cis-trans conformational polymorphism of diproline residues occurring at β-turns in the peptides.
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Affiliation(s)
- Jayasubba Reddy Yarava
- Department of Physics, Indian Institute of Science, Bangalore-560012, India and NMR Research Center, Indian Institute of Science, Bangalore-560012, India. and Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fedérale de Lausanne, Switzerland
| | - Rajesh Sonti
- NMR Research Center, Indian Institute of Science, Bangalore-560012, India. and Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India and Biozentrum, Structural Biology, Universität Basel, Basel, Switzerland
| | - K Kantharaju
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India and Department of Chemistry, Rani Channamma University, Belgavi, India
| | - S Raghothama
- NMR Research Center, Indian Institute of Science, Bangalore-560012, India.
| | - K V Ramanathan
- NMR Research Center, Indian Institute of Science, Bangalore-560012, India.
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5
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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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6
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Mou Y, Tsai TWT, Chan JCC. Constant time tensor correlation experiments by non-gamma-encoded recoupling pulse sequences. J Chem Phys 2012; 137:164201. [PMID: 23126702 DOI: 10.1063/1.4757957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Constant-time tensor correlation under magic-angle spinning conditions is an important technique in solid-state nuclear magnetic resonance spectroscopy for the measurements of backbone or side-chain torsion angles of polypeptides and proteins. We introduce a general method for the design of constant-time tensor correlation experiments under magic-angle spinning. Our method requires that the amplitude of the average Hamiltonian must depend on all the three Euler angles bringing the principal axis system to the rotor-fixed frame, which is commonly referred to as non-gamma encoding. We abbreviate this novel approach as COrrelation of Non-Gamma-Encoded Experiment (CONGEE), which exploits the orientation-dependence of non-gamma-encoded sequences with respect to the magic-angle rotation axis. By manipulating the relative orientation of the average Hamiltonians created by two non-gamma-encoded sequences, one can obtain a modulation of the detected signal, from which the structural information can be extracted when the tensor orientations relative to the molecular frame are known. CONGEE has a prominent feature that the number of rf pulses and the total pulse sequence duration can be maintained to be constant so that for torsion angle determination the effects of systematic errors owing to the experimental imperfections and/or T(2) effects could be minimized. As a proof of concept, we illustrate the utility of CONGEE in the correlation between the C' chemical shift tensor and the C(α)-H(α) dipolar tensor for the backbone psi angle determination. In addition to a detailed theoretical analysis, numerical simulations and experiments measured for [U-(13)C, (15)N]-L-alanine and N-acetyl-[U-(13)C, (15)N]-D,L-valine are used to validate our approach at a spinning frequency of 20 kHz.
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Affiliation(s)
- Yun Mou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, Taiwan
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7
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Lu X, Lafon O, Trébosc J, Tricot G, Delevoye L, Méar F, Montagne L, Amoureux JP. Observation of proximities between spin-1/2 and quadrupolar nuclei: Which heteronuclear dipolar recoupling method is preferable? J Chem Phys 2012; 137:144201. [DOI: 10.1063/1.4753987] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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8
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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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9
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Chan JCC. Solid-state NMR techniques for the structural determination of amyloid fibrils. Top Curr Chem (Cham) 2011; 306:47-88. [PMID: 21630137 DOI: 10.1007/128_2011_154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This review discusses the solid-state NMR techniques developed for the study of amyloid fibrils. Literature up to the end of 2010 has been surveyed and the materials are organized according to five categories, viz. homonuclear dipolar recoupling and polarization transfer via J-coupling, heteronuclear dipolar recoupling, correlation spectroscopy, recoupling of chemical shift anisotropy, and tensor correlation. Our emphasis is on the NMR techniques and their practical aspects. The biological implications of the results obtained for amyloid fibrils are only briefly discussed. Our main objective is to showcase the power of NMR in the study of biological unoriented solids.
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Affiliation(s)
- Jerry C C Chan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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10
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Hou G, Paramasivam S, Byeon IJL, Gronenborn AM, Polenova T. Determination of relative tensor orientations by γ-encoded chemical shift anisotropy/heteronuclear dipolar coupling 3D NMR spectroscopy in biological solids. Phys Chem Chem Phys 2010; 12:14873-83. [PMID: 20936218 PMCID: PMC3160241 DOI: 10.1039/c0cp00795a] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this paper, we present 3D chemical shift anisotropy (CSA)/dipolar coupling correlation experiments, based on γ-encoded R-type symmetry sequences. The γ-encoded correlation spectra are exquisitely sensitive to the relative orientation of the CSA and dipolar tensors and can provide important structural and dynamic information in peptides and proteins. We show that the first-order (m = ±1) and second-order (m = ±2) Hamiltonians in the R-symmetry recoupling sequences give rise to different correlation patterns due to their different dependencies on the crystallite orientation. The relative orientation between CSA and dipolar tensors can be determined by fitting the corresponding correlation patterns. The orientation of (15)N CSA tensor in the quasi-molecular frame is determined by the relative Euler angles, α(NH) and β(NH), when the combined symmetry schemes are applied for orientational studies of (1)H-(15)N dipolar and (15)N CSA tensors. The correlation experiments introduced here work at moderate magic angle spinning frequencies (10-20 kHz) and allow for simultaneous measurement of multiple sites of interest. We studied the orientational sensitivity of γ-encoded symmetry-based recoupling techniques numerically and experimentally. The results are demonstrated on [(15)N]-N-acetyl-valine (NAV) and N-formyl-Met-Leu-Phe (MLF) tripeptide.
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Affiliation(s)
- Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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11
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Mafra L, Siegel R, Fernandez C, Schneider D, Aussenac F, Rocha J. High-resolution 1H homonuclear dipolar recoupling NMR spectra of biological solids at MAS rates up to 67 kHz. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 199:111-114. [PMID: 19410491 DOI: 10.1016/j.jmr.2009.04.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Revised: 03/25/2009] [Accepted: 04/09/2009] [Indexed: 05/27/2023]
Abstract
Two-dimensional (1)H homonuclear correlation NMR spectra of solids of biological interest have been recorded at high magnetic fields (14.1 and 18.8 T) and MAS rates up to 67 kHz, using RN(n)(nu) symmetry-based homonuclear recoupling and CRAMPS decoupling; this method affords exceptional spectral resolution and is well suited to probe (1)H-(1)H proximities in powdered solids.
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Affiliation(s)
- Luis Mafra
- Department of Chemistry, University of Aveiro, CICECO, Campus de Santiago, 3810-193 Aveiro, Portugal.
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12
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Emmler T, Ayala I, Silverman D, Hafner S, Galstyan AS, Knapp EW, Buntkowsky G. Combined NMR and computational study for azide binding to human manganese superoxide dismutase. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2008; 34:6-13. [PMID: 18420387 DOI: 10.1016/j.ssnmr.2008.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2007] [Indexed: 05/26/2023]
Abstract
Human manganese superoxide dismutase (MnSOD) labeled with 3-fluorotyrosine (Tyf) was complexed with the (15)N-labeled inhibitor azide ([(15)N(3)(-)]). The sample was characterized by solid-state NMR (SSNMR) spectroscopy ((19)F-MAS and (15)N-CPMAS). Employing (19)F-(15)N-REDOR spectroscopy, we determined the distances between the fluorine label in Tyrosine-34 and the three (15)N-nuclei of the azide and the relative orientation of the azide in the binding pocket of the MnSOD. A distance of R(1)=4.85A between the (19)F-label of Tyf34 and the nearest (15)N of the azide and an azide-fluorotyrosine Tyf34 angle of 90 degrees were determined. These geometry data are employed as input for molecular modeling of the location of the inhibitor in the active site of the enzyme. In the computations, several possible binding geometries of the azide near the Mn-complex were assumed. Only when the azide replaces the water ligand at the Mn-complex we obtained a geometry of the azide-Mn-complex, which is consistent with the present NMR data. This indicates that the water molecule ligating to the Mn-complex is removed and the azide is placed at this position. As a consequence the azide forms an H bond with Gln143 instead with Tyf34, in contrast to non-(19)F-labeled MnSOD, where the azide is hydrogen bonded to the hydroxy group of Tyr34.
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Affiliation(s)
- Th Emmler
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3,6 D-14195 Berlin, Germany
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13
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Steric Zipper of the Amyloid Fibrils Formed by Residues 109–122 of the Syrian Hamster Prion Protein. J Mol Biol 2008; 378:1142-54. [DOI: 10.1016/j.jmb.2008.03.035] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 03/04/2008] [Accepted: 03/16/2008] [Indexed: 11/20/2022]
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14
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NMR-Based Strategies to Elucidate Bioactive Conformations of Weakly Binding Ligands. Top Curr Chem (Cham) 2008. [PMID: 23605457 DOI: 10.1007/128_2007_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Key processes in molecular biology are regulated by interactions between biomolecules. Protein-proteinand protein-ligand interactions, e.g., in signal transduction pathways, rely on the subtle interactionsbetween atoms at the binding interface of the involved molecules. Because biomolecules often havemany interacting partners, these interactions are not necessarily strong. The study of molecularrecognition gives insight into the complex network of signaling in life and is the basis of structure-baseddrug design.In the situation where the interaction is weak, one of the traditional methods that can be appliedto obtain structural information (internuclear distances) of the bound ligand is the so-called transferredNOE (trNOE) method. Recently, it became possible to use transferred cross-correlated relaxation (trCCR)to directly measure dihedral angles. The combined use of these two techniques significantly improvesthe precision of the structure determination of ligands weakly bound to macromolecules.The application of these techniques will be discussed in detail for a peptide derived fromIKKβ bound to the protein NEMO that plays an important rolein the NFκB pathway.
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Oyler NA, Tycko R. Conformational constraints in solid-state NMR of uniformly labeled polypeptides from double single-quantum-filtered rotational echo double resonance. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S101-S106. [PMID: 18157809 DOI: 10.1002/mrc.2110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A solid-state nuclear magnetic resonance (NMR) technique is described for obtaining constraints on the backbone conformation of a protein or peptide that is prepared with uniform (15)N,(13)C labeling of consecutive pairs of amino acids or of longer segments. The technique, called double single-quantum-filtered rotational echo double resonance (DSQ-REDOR), uses frequency-selective REDOR to prepare DSQ coherences involving directly bonded backbone (13)CO and (15)NH sites, to dephase these coherences under longer-range (15)NH-(13)CO dipole-dipole couplings in a conformationally dependent manner, and to convert the remaining DSQ coherences to detectable transverse (13)C-spin polarization. The efficacy of DSQ-REDOR is demonstrated in experiments on two isotopically labeled samples, the helical peptide MB(i + 4)EK and the amyloid-forming peptide Abeta(11-25).
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Affiliation(s)
- Nathan A Oyler
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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16
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Mou Y, Tsai TWT, Chan JCC. Determination of the backbone torsion psi angle by tensor correlation of chemical shift anisotropy and heteronuclear dipole-dipole interaction. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2007; 31:72-81. [PMID: 17329083 DOI: 10.1016/j.ssnmr.2007.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Revised: 12/25/2006] [Accepted: 01/20/2007] [Indexed: 05/14/2023]
Abstract
We demonstrate that the backbone torsion psi angle of a uniformly labeled residue can be determined accurately by correlating the chemical shift anisotropy of the carbonyl carbon and the 13C-1H heteronuclear dipole-dipole interaction of the alpha carbon. To obtain the highest sensitivity for the psi angle determination, the following conditions are desired: (i) the recoupling pulse sequences for the CSA and the heteronuclear dipolar interactions are gamma encoded, in which the spatial parts of m=2 are selected; (ii) the homonuclear polarization transfer is based on the scalar spin-spin coupling. Experimental data were obtained for [U-13C, 15N]-alanine and N-acetyl-[U-13C, 15N]-d,l-valine under magic-angle spinning at 25kHz. Only three data points are required for the measurements and the dihedral angles determined are in excellent agreement with the diffraction data.
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Affiliation(s)
- Yun Mou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, Taiwan
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17
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Tycko R. Characterization of amyloid structures at the molecular level by solid state nuclear magnetic resonance spectroscopy. Methods Enzymol 2006; 413:103-22. [PMID: 17046393 PMCID: PMC1633711 DOI: 10.1016/s0076-6879(06)13006-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Solid state nuclear magnetic resonance (NMR) spectroscopy is particularly useful in structural studies of amyloid fibrils because solid state NMR techniques have unique capabilities as site-specific, molecular-level structural probes of noncrystalline materials. These techniques provide experimental data that strongly constrain the secondary, tertiary, and quaternary structures of amyloid fibrils, permitting the development of experimentally based structural models. Examples of techniques that are applicable to amyloid samples prepared with isotopic labeling of specific sites and to samples prepared with uniform isotopic labeling of selected residues are presented, illustrating the utility of the various techniques and labeling schemes. Information regarding the preparation of amyloid samples for solid state NMR measurements is also included.
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Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 112, Bethesda, Maryland 20892-0520, e-mail: , phone: 301-402-8272, fax: 301-496-0825
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18
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Two-dimensional solid-state NMR studies of crystalline poly(ethylene oxide): Conformations and chemical shifts. POLYMER 2005. [DOI: 10.1016/j.polymer.2005.09.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Loth K, Pelupessy P, Bodenhausen G. Chemical Shift Anisotropy Tensors of Carbonyl, Nitrogen, and Amide Proton Nuclei in Proteins through Cross-Correlated Relaxation in NMR Spectroscopy. J Am Chem Soc 2005; 127:6062-8. [PMID: 15839707 DOI: 10.1021/ja042863o] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The principal components and orientations of the chemical shift anisotropy (CSA) tensors of the carbonyl (C'), nitrogen (N), and amide proton (H(N)) nuclei of 64 distinct amide bonds in human ubiquitin have been determined in isotropic solution by a set of 14 complementary auto- and cross-correlated relaxation rates involving the CSA interactions of the nuclei of interest and several dipole-dipole (DD) interactions. The CSA parameters thus obtained depend to some degree on the models used for local motions. Three cases have been considered: restricted isotropic diffusion, three-dimensional Gaussian axial fluctuations (3D-GAF), and independent out-of-plane motions of the NH(N) vectors with respect to the peptide planes.
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Affiliation(s)
- Karine Loth
- Département de Chimie, Associé au CNRS, Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris Cedex 05, France
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20
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Chan JCC, Tycko R. Solid-State NMR Spectroscopy Method for Determination of the Backbone Torsion Angle ψ in Peptides with Isolated Uniformly Labeled Residues. J Am Chem Soc 2003; 125:11828-9. [PMID: 14505399 DOI: 10.1021/ja0369820] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate a solid-state nuclear magnetic resonance technique, with the acronym ROCSA-LG, for the determination of backbone torsion angles psi in peptides with multiple, but isolated, uniformly labeled residues. The method correlates the 13C' chemical shift anisotropy and the 13Calpha-1Halpha heteronuclear dipolar tensors within a single uniformly labeled residue in a two-dimensional (2D) experiment. The technique requires the measurement of only five 2D spectra and is compatible with high-speed magic-angle spinning. Experimental results are presented for the 17-residue alpha-helical peptide MB(i+4)EK and for amyloid fibrils formed by the 15-residue peptide Abeta11-25.
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Affiliation(s)
- Jerry C C Chan
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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21
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Karlsson T, Popham JM, Long JR, Oyler N, Drobny GP. A study of homonuclear dipolar recoupling pulse sequences in solid-state nuclear magnetic resonance. J Am Chem Soc 2003; 125:7394-407. [PMID: 12797814 DOI: 10.1021/ja0294360] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dipolar recoupling pulse sequences are of great importance in magic angle spinning solid-state NMR. Recoupling sequences are used for excitation of double-quantum coherence, which, in turn, is employed in experiments to estimate internuclear distances and molecular torsion angles. Much effort is spent on the design of recoupling sequences that are able to produce double-quantum coherence with high efficiency in demanding spin systems, i.e., spin systems with small dipole-dipole couplings and large chemical-shift anisotropies (CSAs). The sequence should perform robustly under a variety of experimental conditions. This paper presents experiments and computer calculations that extend the theory of double-quantum coherence preparation from the strong coupling/small CSA limit to the weak coupling limit. The performance of several popular dipole-dipole recoupling sequences-DRAWS, POST-C7, SPC-5, R1, and R2-are compared. It is found that the optimum performance for several of these sequences, in the weak coupling/large CSA limit, varies dramatically, with respect to the sample spinning speed, the magnitude and orientation of the CSAs, and the magnitude of dipole-dipole couplings. It is found that the efficiency of double-quantum coherence preparation by gamma-encoded sequences departs from the predictions of first-order theory. The discussion is supported by density-matrix calculations.
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Affiliation(s)
- T Karlsson
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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22
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Edén M. Order-selective multiple-quantum excitation in magic-angle spinning NMR: creating triple-quantum coherences with a trilinear Hamiltonian. Chem Phys Lett 2002. [DOI: 10.1016/s0009-2614(02)01557-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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van Dam L, Ouwerkerk N, Brinkmann A, Raap J, Levitt MH. Solid-state NMR determination of sugar ring pucker in (13)C-labeled 2'-deoxynucleosides. Biophys J 2002; 83:2835-44. [PMID: 12414715 PMCID: PMC1302367 DOI: 10.1016/s0006-3495(02)75292-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The H3'-C3'-C4'-H4' torsional angles of two microcrystalline 2'-deoxynucleosides, thymidine and 2'-deoxycytidine.HCl, doubly (13)C-labeled at the C3' and C4' positions of the sugar ring, have been measured by solid-state magic-angle-spinning nuclear magnetic resonance (NMR). A double-quantum heteronuclear local field experiment with frequency-switched Lee-Goldberg homonuclear decoupling was used. The H3'-C3'-C4'-H4' torsional angles were obtained by comparing the experimental curves with numerical simulations, including the two (13)C nuclei, the directly bonded (1)H nuclei, and five remote protons. The H3'-C3'-C4'-H4' angles were converted into sugar pucker angles and compared with crystallographic data. The delta torsional angles determined by solid-state NMR and x-ray crystallography agree within experimental error. Evidence is also obtained that the proton positions may be unreliable in the x-ray structures. This work confirms that double-quantum solid-state NMR is a feasible tool for studying sugar pucker conformations in macromolecular complexes that are unsuitable for solution NMR or crystallography.
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Affiliation(s)
- Lorens van Dam
- Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden
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24
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Rienstra CM, Hohwy M, Mueller LJ, Jaroniec CP, Reif B, Griffin RG. Determination of multiple torsion-angle constraints in U-(13)C,(15)N-labeled peptides: 3D (1)H-(15)N-(13)C-(1)H dipolar chemical shift NMR spectroscopy in rotating solids. J Am Chem Soc 2002; 124:11908-22. [PMID: 12358535 DOI: 10.1021/ja020802p] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate constraint of peptide backbone and side-chain conformation with 3D (1)H-(15)N-(13)C-(1)H dipolar chemical shift, magic-angle spinning NMR experiments. In these experiments, polarization is transferred from (15)N[i] by ramped SPECIFIC cross polarization to the (13)C(alpha)[i], (13)C(beta)[i], and (13)C(alpha)[i - 1] resonances and evolves coherently under the correlated (1)H-(15)N and (1)H-(13)C dipolar couplings. The resulting set of frequency-labeled (15)N(1)H-(13)C(1)H dipolar spectra depend strongly upon the molecular torsion angles phi[i], chi1[i], and psi[i - 1]. To interpret the data with high precision, we considered the effects of weakly coupled protons and differential relaxation of proton coherences via an average Liouvillian theory formalism for multispin clusters and employed average Hamiltonian theory to describe the transfer of (15)N polarization to three coupled (13)C spins ((13)C(alpha)[i], (13)C(beta)[i], and (13)C(alpha)[i - 1]). Degeneracies in the conformational solution space were minimized by combining data from multiple (15)N(1)H-(13)C(1)H line shapes and analogous data from other 3D (1)H-(13)C(alpha)-(13)C(beta)-(1)H (chi1), (15)N-(13)C(alpha)-(13)C'-(15)N (psi), and (1)H-(15)N[i]-(15)N[i + 1]-(1)H (phi, psi) experiments. The method is demonstrated here with studies of the uniformly (13)C,(15)N-labeled solid tripeptide N-formyl-Met-Leu-Phe-OH, where the combined data constrains a total of eight torsion angles (three phi, three chi1, and two psi): phi(Met) = -146 degrees, psi(Met) = 159 degrees, chi1(Met) = -85 degrees, phi(Leu) = -90 degrees, psi(Leu) = -40 degrees, chi1(Leu) = -59 degrees, phi(Phe) = -166 degrees, and chi1(Phe) = 56 degrees. The high sensitivity and dynamic range of the 3D experiments and the data analysis methods provided here will permit immediate application to larger peptides and proteins when sufficient resolution is available in the (15)N-(13)C chemical shift correlation spectra.
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Affiliation(s)
- Chad M Rienstra
- Department of Chemistry, Center for Magnetic Resonance, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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25
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Ashida J, Ohgo K, Asakura T. Determination of the Torsion Angles of Alanine and Glycine Residues of Bombyx Mori Silk Fibroin and the Model Peptides in the Silk I and Silk II Forms Using 2D Spin Diffusion Solid-State NMR under Off Magic Angle Spinning. J Phys Chem B 2002. [DOI: 10.1021/jp020331t] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jun Ashida
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan, and Varian Technologies Japan Ltd., Minato, Tokyo 108-0023, Japan
| | - Kosuke Ohgo
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan, and Varian Technologies Japan Ltd., Minato, Tokyo 108-0023, Japan
| | - Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan, and Varian Technologies Japan Ltd., Minato, Tokyo 108-0023, Japan
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26
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Kristiansen PE, Mitchell DJ, Evans JNS. Double-quantum dipolar recoupling at high magic-angle spinning rates. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 157:253-266. [PMID: 12323144 DOI: 10.1006/jmre.2002.2594] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A full investigation of the possible homonuclear double-quantum recoupling sequences, based on the RN family of sequences with N < or = 20, is given. Several new RN sequences, R16(6)(5), R18(8)(5), and R18(10)(5), were applied at high magic-angle spinning rates and compared with theory. The R18(10)(5) technique can be used to recouple dipolar couplings at spinning rates up to 39 kHz, and the application of the sequence in an INADEQUATE experiment is shown for a spinning rate of 30 kHz.
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Affiliation(s)
- Per Eugen Kristiansen
- School of Molecular Biosciences, Washington State University, Pullman, 99164-4660, USA
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27
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Oyler NA, Tycko R. Multiple Quantum 13C NMR Spectroscopy in Solids under High-Speed Magic-Angle Spinning. J Phys Chem B 2002. [DOI: 10.1021/jp020906m] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nathan A. Oyler
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
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28
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Harris J, Bonagamba J, Schmidt-Rohr K. NMR Characterization of Sodium Poly(α-l-glutamate)/Poly(ethylene oxide) Blends. Macromolecules 2002. [DOI: 10.1021/ma010545t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. Harris
- Polymer Science and Engineering Department, University of Massachusetts, Amherst, Massachusetts 01003; Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil, Caixa Postal 369, 13560-970; and Chemistry Department and Ames Laboratory, Iowa State University, Ames, Iowa 50011
| | - J. Bonagamba
- Polymer Science and Engineering Department, University of Massachusetts, Amherst, Massachusetts 01003; Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil, Caixa Postal 369, 13560-970; and Chemistry Department and Ames Laboratory, Iowa State University, Ames, Iowa 50011
| | - K. Schmidt-Rohr
- Polymer Science and Engineering Department, University of Massachusetts, Amherst, Massachusetts 01003; Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil, Caixa Postal 369, 13560-970; and Chemistry Department and Ames Laboratory, Iowa State University, Ames, Iowa 50011
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29
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Goobes G, Vega S. Improved narrowband dipolar recoupling for homonuclear distance measurements in rotating solids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 154:236-251. [PMID: 11846581 DOI: 10.1006/jmre.2001.2463] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Recovery of the magnetic dipolar interaction between nuclei bearing the same gyromagnetic ratio in rotating solids can be promoted by synchronous rf irradiation. Determination of the dipolar interaction strength can serve as a tool for structural elucidation in polycrystalline powders. Spinning frequency dependent narrow-band (nb) RFDR and SEDRA experiments are utilized as simple techniques for the determination of dipolar interactions between the nuclei in coupled homonuclear spin pairs. The magnetization exchange and coherence dephasing due to a fixed number of rotor-synchronously applied pi-pulses is monitored at spinning frequencies in the vicinity of the rotational resonance (R(2)) conditions. The powder nbRFDR and nbSEDRA decay curves of spin magnetizations and coherences, respectively, as a function of the spinning frequency can be measured and analyzed using simple rate equations providing a quantitative measure of the dipolar coupling. The effects of the phenomenological relaxation parameters in these rate equations are discussed and an improved methodology is suggested for analyzing nbRFDR data for small dipolar couplings. The distance between the labeled nuclei in the 1,3-(13)C(2)-hydroxybutyric acid molecule is rederived using existing nbRFDR results and the new simulation procedure. A nbSEDRA experiment has been performed successfully on a powder sample of singly labeled 1-(13)C-L-leucine measuring the dipolar interaction between the labeled carboxyl carbon and the natural abundant beta-carbon. Both narrowband techniques are employed for the determination of the nuclear distances between the side-chain carbons of leucine and its carbonyl carbon in a tripeptide Leu-Gly-Phe that is singly (13)C-labeled at the leucine carbonyl carbon position.
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Affiliation(s)
- G Goobes
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
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30
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Ladizhansky V, Veshtort M, Griffin RG. NMR determination of the torsion angle psi in alpha-helical peptides and proteins: the HCCN dipolar correlation experiment. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 154:317-324. [PMID: 11846590 DOI: 10.1006/jmre.2001.2488] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Several existing methods permit measurement of the torsion angles phi, psi and chi in peptides and proteins with solid-state MAS NMR experiments. Currently, however, there is not an approach that is applicable to measurement of psi in the angular range -20 degree to -70 degree, commonly found in alpha-helical structures. Accordingly, we have developed a HCCN dipolar correlation MAS experiment that is sensitive and accurate in this regime. An initial REDOR driven (13)C'--(15)N dipolar evolution period is followed by the C' to C(alpha) polarization transfer and by Lee--Goldburg cross polarization recoupling of the (13)C(alpha)(1)H dipolar interaction. The difference between the effective (13)C(1)H and (13)C(15)N dipolar interaction strengths is balanced out by incrementing the (13)C--(15)N dipolar evolution period in steps that are a factor of R(R approximately omega(CH)/omega(CN)) larger than the (13)C--(1)H steps. The resulting dephasing curves are sensitive to variations in psi in the angular region associated with alpha-helical secondary structure. To demonstrate the validity of the technique, we apply it to N-formyl-[U-(13)C,(15)N] Met-Leu-Phe-OH (MLF). The value of psi extracted is consistent with the previous NMR measurements and close to that reported in diffraction studies for the methyl ester of MLF, N-formyl-[U-(13)C,(15)N]Met-Leu-Phe-OMe.
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Affiliation(s)
- Vladimir Ladizhansky
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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31
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Schwalbe H, Carlomagno T, Hennig M, Junker J, Reif B, Richter C, Griesinger C. Cross-correlated relaxation for measurement of angles between tensorial interactions. Methods Enzymol 2002; 338:35-81. [PMID: 11460558 DOI: 10.1016/s0076-6879(02)38215-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- H Schwalbe
- Center for Magnetic Resonance, Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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32
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Lipid-peptide interaction investigated by NMR. CURRENT TOPICS IN MEMBRANES 2002. [DOI: 10.1016/s1063-5823(02)52008-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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33
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Tycko R. Biomolecular solid state NMR: advances in structural methodology and applications to peptide and protein fibrils. Annu Rev Phys Chem 2001; 52:575-606. [PMID: 11326075 DOI: 10.1146/annurev.physchem.52.1.575] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Solid state nuclear magnetic resonance (NMR) methods can provide atomic-level structural constraints on peptides and proteins in forms that are not amenable to characterization by other high-resolution structural techniques, owing to insolubility, high molecular weight, noncrystallinity, or other characteristics. Important examples include peptide and protein fibrils and membrane-bound peptides and proteins. Recent advances in solid state NMR methodology aimed at structural problems in biological systems are reviewed. The power of these methods is illustrated by experimental results on amyloid fibrils and other protein fibrils.
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Affiliation(s)
- R Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
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34
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Brinkmann A, Levitt MH. Symmetry principles in the nuclear magnetic resonance of spinning solids: Heteronuclear recoupling by generalized Hartmann–Hahn sequences. J Chem Phys 2001. [DOI: 10.1063/1.1377031] [Citation(s) in RCA: 187] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Ravindranathan S, Karlsson T, Lycknert K, Widmalm G, Levitt MH. Conformation of the glycosidic linkage in a disaccharide investigated by double-quantum solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 151:136-141. [PMID: 11444948 DOI: 10.1006/jmre.2001.2357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Double-quantum heteronuclear local field NMR is performed on a sample of a 13C2-labeled disaccharide, in which the two 13C spins are located on opposite sides of the glycosidic linkage. The evolution of the double-quantum coherences is found to be consistent with the solid-state conformation of the molecule, as previously determined by X-ray diffraction. The dependence of the double-quantum evolution on the glycosidic torsional angles is examined by using a graphical molecular manipulation program interfaced to a numerical spin simulation module.
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Affiliation(s)
- S Ravindranathan
- Physical Chemistry Division, Stockholm University, Stockholm, S-10691, Sweden
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36
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37
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38
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Ishii Y. 13C–13C dipolar recoupling under very fast magic angle spinning in solid-state nuclear magnetic resonance: Applications to distance measurements, spectral assignments, and high-throughput secondary-structure determination. J Chem Phys 2001. [DOI: 10.1063/1.1359445] [Citation(s) in RCA: 247] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Towards selective recoupling and mutual decoupling of dipolar-coupled spin pairs in double-quantum magic-angle spinning NMR experiments on multiply labelled solid-state samples. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)00027-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Karlsson T, Hughes CE, Schmedt auf der Günne J, Levitt MH. Double-quantum excitation in the NMR of spinning solids by pulse-assisted rotational resonance. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 148:238-247. [PMID: 11237629 DOI: 10.1006/jmre.2000.2243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We describe a new technique for double-quantum excitation in magic-angle-spinning NMR of powdered solids. The technique is designed to efficiently excite double-quantum coherence in the vicinity of a rotational resonance condition. The offset from rotational resonance allows the double-quantum filtered signals to be observed with high resolution and sensitivity. The method uses rotational excitation of zero-quantum coherence, assisted by radiofrequency pulse cycles. The zero-quantum coherence is converted into double-quantum coherence by a frequency-selective inversion sequence. Experiments on [(13)C(2), (15)N]-glycine demonstrate a double-quantum filtering efficiency of approximately 41% at a sample rotation frequency of 8.300 kHz, which is 1.600 kHz away from the n = 1 rotational resonance. We achieve 32% double-quantum filtering efficiency at a spinning frequency of 9.250 kHz, which is 2.550 kHz away from rotational resonance.
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Affiliation(s)
- T Karlsson
- Division of Physical Chemistry, Stockholm University, S-106 91 Stockhom, Sweden
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41
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Metzler DE, Metzler CM, Sauke DJ. Determining Structures and Analyzing Cells. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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42
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Huster D, Yamaguchi S, Hong M. Efficient β-Sheet Identification in Proteins by Solid-State NMR Spectroscopy. J Am Chem Soc 2000. [DOI: 10.1021/ja001674c] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Huster
- Contribution from the Department of Chemistry, Gilman Hall 0108, Iowa State University, Ames, Iowa 50011
| | - Satoru Yamaguchi
- Contribution from the Department of Chemistry, Gilman Hall 0108, Iowa State University, Ames, Iowa 50011
| | - Mei Hong
- Contribution from the Department of Chemistry, Gilman Hall 0108, Iowa State University, Ames, Iowa 50011
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43
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Deuterium-carbon NMR correlation spectroscopy: a tool for structural characterization of solids. Chem Phys Lett 2000. [DOI: 10.1016/s0009-2614(00)00878-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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44
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Reif B, Hohwy M, Jaroniec CP, Rienstra CM, Griffin RG. NH-NH vector correlation in peptides by solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 145:132-141. [PMID: 10873504 DOI: 10.1006/jmre.2000.2067] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present a novel solid-state magic angle-spinning NMR method for measuring the NH(i)-NH(i+1) projection angle θ(i,i+1) in peptides. The experiment is applicable to uniformly (15)N-labeled peptides and is demonstrated on the chemotactic tripeptide N-formyl-l-Met-l-Leu-l-Phe. The projection angle θ(i,i+1) is directly related to the peptide backbone torsion angles φ(i) and psi(i). The method utilizes the T-MREV recoupling scheme to restore (15)N-(1)H interactions, and proton-mediated spin diffusion to establish (15)N-(15)N correlations. T-MREV has recently been shown to increase the dynamic range of the (15)N-(1)H recoupling by gamma-encoding, and permits an accurate determination of the recoupled NH dipolar interaction. The results are interpreted in a quasi-analytical fashion that permits efficient extraction of the structural parameters.
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Affiliation(s)
- B Reif
- Department of Chemistry and MIT/Harvard Center for Magnetic Resonance, Cambridge, Massachusetts, 02139, USA
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45
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Karlsson T, Edén M, Luthman H, Levitt MH. Efficient double-quantum excitation in rotational resonance NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 145:95-107. [PMID: 10873500 DOI: 10.1006/jmre.2000.2080] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present a new technique for double-quantum excitation in magic-angle-spinning solid-state NMR. The method involves (i) preparation of nonequilibrium longitudinal magnetization; (ii) mechanical excitation of zero-quantum coherence by spinning the sample at rotational resonance, and (iii) phase-coherent conversion of the zero-quantum coherence into double-quantum coherence by frequency-selective spin inversion. The double-quantum coherence is converted into observable magnetization by reversing the excitation process, followed by a pi/2 pulse. The method is technically simple, does not require strong RF fields, and is feasible at high spinning frequencies. In [(13)C(2),(15)N]-glycine, with an internuclear (13)C-(13)C distance of 0.153 nm, we achieve a double-quantum filtering efficiency of approximately 56%. In [11, 20-(13)C(2)]-all-E-retinal, with an internuclear (13)C-(13)C distance of 0.296 nm, we obtain approximately 45% double-quantum filtering efficiency.
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Affiliation(s)
- T Karlsson
- Division of Physical Chemistry, Stockholm University, Stockholm, S-106 91, Sweden
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46
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Kaji H, Schmidt-Rohr K. Conformation and Dynamics of Atactic Poly(acrylonitrile). 1. Trans/Gauche Ratio from Double-Quantum Solid-State 13C NMR of the Methylene Groups. Macromolecules 2000. [DOI: 10.1021/ma0002592] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hironori Kaji
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003
| | - Klaus Schmidt-Rohr
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003
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Edén M, Brinkmann A, Luthman H, Eriksson L, Levitt MH. Determination of molecular geometry by high-order multiple-quantum evolution in solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 144:266-279. [PMID: 10828194 DOI: 10.1006/jmre.2000.2042] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The principles of molecular geometry determination by high-quantum heteronuclear local field spectroscopy in solid-state NMR are discussed. The extreme multiple-quantum coherences in a cluster of nuclear spins are allowed to evolve in the presence of heteronuclear through-space couplings to two spins of a different type. The multiple-quantum dephasing curve is independent of the homonuclear spin-spin couplings and may be described in terms of geometric parameters. The triple-quantum version of the experiment is demonstrated by determining the psi torsion angle in a [(15)N(2), (13)C(3)]-labeled sample of the peptide ala-ala-gly. Two regions of torsion angle space fit the experimental data, one in the neighborhood of -152 degrees and one in the neighborhood of +161 degrees. The latter determination is in excellent agreement with the X-ray estimate of +160.5 degrees.
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Affiliation(s)
- M Edén
- Physical Chemistry Division, Stockholm University, Stockholm, S-106 91, Sweden.
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Pauli J, van Rossum B, Förster H, de Groot HJ, Oschkinat H. Sample optimization and identification of signal patterns of amino acid side chains in 2D RFDR spectra of the alpha-spectrin SH3 domain. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 143:411-6. [PMID: 10729269 DOI: 10.1006/jmre.2000.2029] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Future structural investigations of proteins by solid-state CPMAS NMR will rely on uniformly labeled protein samples showing spectra with an excellent resolution. NMR samples of the solid alpha-spectrin SH3 domain were generated in four different ways, and their (13)C CPMAS spectra were compared. The spectrum of a [u-(13)C, (15)N]-labeled sample generated by precipitation shows very narrow (13)C signals and resolved scalar carbon-carbon couplings. Linewidths of 16-19 Hz were found for the three alanine C(beta )signals of a selectively labeled [70% 3-(13)C]alanine-enriched SH3 sample. The signal pattern of the isoleucine, of all prolines, valines, alanines, and serines, and of three of the four threonines were identified in 2D (13)C-(13)C RFDR spectra of the [u-(13)C, (15)N]-labeled SH3 sample. A comparison of the (13)C chemical shifts of the found signal patterns with the (13)C assignment obtained in solution shows an intriguing match.
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Affiliation(s)
- J Pauli
- Forschungsinstitut für Molekulare Pharmakologie, Alfred-Kowalke-Strasse 4, Berlin, D-10315, Germany
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Harris DJ, Bonagamba TJ, Hong M, Schmidt-Rohr K. Conformation of Poly(ethylene oxide)−Hydroxybenzene Molecular Complexes Studied by Solid-State NMR. Macromolecules 2000. [DOI: 10.1021/ma992087i] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. J. Harris
- Polymer Science and Engineering Department, University of Massachusetts, Amherst, Massachusetts 01003, Universidade de São Paulo, Instituto de Física de São Carlos, PO Box 369, 13560-970, São Carlos, São Paulo, Brazil, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - T. J. Bonagamba
- Polymer Science and Engineering Department, University of Massachusetts, Amherst, Massachusetts 01003, Universidade de São Paulo, Instituto de Física de São Carlos, PO Box 369, 13560-970, São Carlos, São Paulo, Brazil, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - M. Hong
- Polymer Science and Engineering Department, University of Massachusetts, Amherst, Massachusetts 01003, Universidade de São Paulo, Instituto de Física de São Carlos, PO Box 369, 13560-970, São Carlos, São Paulo, Brazil, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - K. Schmidt-Rohr
- Polymer Science and Engineering Department, University of Massachusetts, Amherst, Massachusetts 01003, Universidade de São Paulo, Instituto de Física de São Carlos, PO Box 369, 13560-970, São Carlos, São Paulo, Brazil, and Department of Chemistry, Iowa State University, Ames, Iowa 50011
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Reif B, Diener A, Hennig M, Maurer M, Griesinger C. Cross-correlated relaxation for the measurement of angles between tensorial interactions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 143:45-68. [PMID: 10698646 DOI: 10.1006/jmre.1999.1980] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Theory,experimental aspects, and use in structure calculation of cross-correlated relaxation rates measured on zero- and double-quantum coherences in liquid state NMR are presented. The relative size of the interaction depends on the projection angle between the two tensorial interactions. The tensorial interaction can be either a dipolar interaction or a chemical shift anisotropy relaxation mechanism (CSA). Effects of additional sources of relaxation on the cross-correlated relaxation rates are analyzed. Also, an easy-to-use formalism is given to manipulate different cross-correlated relaxation interactions. The application addresses measurement of the backbone angle psi in a protein by measuring dipole((15)N-(1)H)-dipole((13)C(alpha)-(1)H(alpha)) and CSA((15)N)-dipole((13)C(alpha)-(1)H(alpha)) cross-correlated relaxation rates. It is shown that ambiguities due to the 3 cos(2)θ-1 dependence of one cross-correlated relaxation rate can be overcome by measuring additional cross-correlated relaxation rates. The use of cross-correlated relaxation rates is demonstrated in structure calculations.
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Affiliation(s)
- B Reif
- Institut für Organische Chemie, Universität Frankfurt, Marie-Curie-Strasse 11, Frankfurt, D-60439, Germany
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