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McCoy KM, Fritzsching KJ, McDermott AE. GTP-Bound Escherichia coli FtsZ Filaments Are Composed of Tense Monomers: a Dynamic Nuclear Polarization-Nuclear Magnetic Resonance Study Using Interface Detection. mBio 2022; 13:e0235822. [PMID: 36214571 PMCID: PMC9765660 DOI: 10.1128/mbio.02358-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
FtsZ filaments are the major structural component of the bacterial Z ring and are drivers of bacterial division. Crystal structures for FtsZ from some Gram-positive bacteria in the presence of GTP analogs suggest the possibility of a high-energy, "tense" conformation. It remains important to elucidate whether this tense form is the dominant form in filaments. Using dynamic nuclear polarization (DNP) solid-state nuclear magnetic resonance (NMR) and differential isotopic labeling, we directly detected residues located at the intermonomer interface of GTP-bound wild-type (WT) Escherichia coli FtsZ filaments. We combined chemical shift prediction, homology modeling, and heteronuclear dipolar recoupling techniques to characterize the E. coli FtsZ filament interface and demonstrated that the monomers in active filaments assume a tense conformation. IMPORTANCE Bacterial replication is dependent on the cytoskeletal protein FtsZ, which forms filaments that scaffold and recruit other essential division proteins. While the FtsZ monomer is well studied across organisms, many questions remain about how the filaments form and function. Recently, a second monomer form was identified in Staphylococcus aureus that has far-reaching implications for FtsZ structure and function. However, to date, this form has not been directly observed outside S. aureus. In this study, we used solid-state NMR and dynamic nuclear polarization (DNP) to directly study the filaments of E. coli FtsZ to demonstrate that E. coli FtsZ filaments are primarily composed of this second, "tense" form of the monomer. This work is the first time GTP-bound, wild-type FtsZ filaments have been studied directly at atomic resolution and is an important step forward for the study of FtsZ filaments.
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Affiliation(s)
- Kelsey M. McCoy
- Department of Chemistry, Columbia University, New York, New York, USA
| | | | - Ann E. McDermott
- Department of Chemistry, Columbia University, New York, New York, USA
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2
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Liang L, Ji Y, Zhao Z, Quinn CM, Han X, Bao X, Polenova T, Hou G. Accurate heteronuclear distance measurements at all magic-angle spinning frequencies in solid-state NMR spectroscopy. Chem Sci 2021; 12:11554-11564. [PMID: 34567504 PMCID: PMC8409495 DOI: 10.1039/d1sc03194e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 07/20/2021] [Indexed: 11/21/2022] Open
Abstract
Heteronuclear dipolar coupling is indispensable in revealing vital information related to the molecular structure and dynamics, as well as intermolecular interactions in various solid materials. Although numerous approaches have been developed to selectively reintroduce heteronuclear dipolar coupling under MAS, most of them lack universality and can only be applied to limited spin systems. Herein, we introduce a new and robust technique dubbed phase modulated rotary resonance (PMRR) for reintroducing heteronuclear dipolar couplings while suppressing all other interactions under a broad range of MAS conditions. The standard PMRR requires the radiofrequency (RF) field strength of only twice the MAS frequency, can efficiently recouple the dipolar couplings with a large scaling factor of 0.50, and is robust to experimental imperfections. Moreover, the adjustable window modification of PMRR, dubbed wPMRR, can improve its performance remarkably, making it well suited for the accurate determination of dipolar couplings in various spin systems. The robust performance of such pulse sequences has been verified theoretically and experimentally via model compounds, at different MAS frequencies. The application of the PMRR technique was demonstrated on the H-ZSM-5 zeolite, where the interaction between the Brønsted acidic hydroxyl groups of H-ZSM-5 and the absorbed trimethylphosphine oxide (TMPO) were probed, revealing the detailed configuration of super acid sites.
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Affiliation(s)
- Lixin Liang
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Zhongshan Road 457 Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Yi Ji
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Zhongshan Road 457 Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhenchao Zhao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Zhongshan Road 457 Dalian 116023 China
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware Newark Delaware 19716 USA
| | - Xiuwen Han
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Zhongshan Road 457 Dalian 116023 China
| | - Xinhe Bao
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Zhongshan Road 457 Dalian 116023 China
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware Newark Delaware 19716 USA
| | - Guangjin Hou
- State Key Laboratory of Catalysis, National Laboratory for Clean Energy, 2011-Collaborative Innovation Center of Chemistry for Energy Materials, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Zhongshan Road 457 Dalian 116023 China
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3
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Shaw WJ, Tarasevich BJ, Buchko GW, Arachchige RMJ, Burton SD. Controls of nature: Secondary, tertiary, and quaternary structure of the enamel protein amelogenin in solution and on hydroxyapatite. J Struct Biol 2020; 212:107630. [PMID: 32979496 PMCID: PMC7744360 DOI: 10.1016/j.jsb.2020.107630] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/12/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
Abstract
Amelogenin, a protein critical to enamel formation, is presented as a model for understanding how the structure of biomineralization proteins orchestrate biomineral formation. Amelogenin is the predominant biomineralization protein in the early stages of enamel formation and contributes to the controlled formation of hydroxyapatite (HAP) enamel crystals. The resulting enamel mineral is one of the hardest tissues in the human body and one of the hardest biominerals in nature. Structural studies have been hindered by the lack of techniques to evaluate surface adsorbed proteins and by amelogenin's disposition to self-assemble. Recent advancements in solution and solid state nuclear magnetic resonance (NMR) spectroscopy, atomic force microscopy (AFM), and recombinant isotope labeling strategies are now enabling detailed structural studies. These recent studies, coupled with insights from techniques such as CD and IR spectroscopy and computational methodologies, are contributing to important advancements in our structural understanding of amelogenesis. In this review we focus on recent advances in solution and solid state NMR spectroscopy and in situ AFM that reveal new insights into the secondary, tertiary, and quaternary structure of amelogenin by itself and in contact with HAP. These studies have increased our understanding of the interface between amelogenin and HAP and how amelogenin controls enamel formation.
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Affiliation(s)
- Wendy J Shaw
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
| | - Barbara J Tarasevich
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Garry W Buchko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA; School of Molecular Bioscience, Washington State University, Pullman, WA 99164, USA
| | - Rajith M J Arachchige
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sarah D Burton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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4
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Xie L, Ghosh U, Schmick SD, Weliky DP. Residue-specific membrane location of peptides and proteins using specifically and extensively deuterated lipids and ¹³C-²H rotational-echo double-resonance solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2013; 55:11-7. [PMID: 23225071 PMCID: PMC3557618 DOI: 10.1007/s10858-012-9692-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/28/2012] [Indexed: 05/12/2023]
Abstract
Residue-specific location of peptides in the hydrophobic core of membranes was examined using (13)C-(2)H REDOR and samples in which the lipids were selectively deuterated. The transmembrane topology of the KALP peptide was validated with this approach with substantial dephasing observed for deuteration in the bilayer center and reduced or no dephasing for deuteration closer to the headgroups. Insertion of β sheet HIV and helical and β sheet influenza virus fusion peptides into the hydrophobic core of the membrane was validated in samples with extensively deuterated lipids.
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Affiliation(s)
- Li Xie
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Ujjayini Ghosh
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - Scott D. Schmick
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
| | - David P. Weliky
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA
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5
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Magic angle spinning NMR study of interaction of N-terminal sequence of dermorphin (Tyr-d-Ala-Phe-Gly) with phospholipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2579-87. [DOI: 10.1016/j.bbamem.2012.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 06/05/2012] [Accepted: 06/18/2012] [Indexed: 01/02/2023]
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6
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Nieuwkoop AJ, Wylie BJ, Franks WT, Shah GJ, Rienstra CM. Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy. J Chem Phys 2010; 131:095101. [PMID: 19739873 DOI: 10.1063/1.3211103] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We show that quantitative internuclear (15)N-(13)C distances can be obtained in sufficient quantity to determine a complete, high-resolution structure of a moderately sized protein by magic-angle spinning solid-state NMR spectroscopy. The three-dimensional ZF-TEDOR pulse sequence is employed in combination with sparse labeling of (13)C sites in the beta1 domain of the immunoglobulin binding protein G (GB1), as obtained by bacterial expression with 1,3-(13)C or 2-(13)C-glycerol as the (13)C source. Quantitative dipolar trajectories are extracted from two-dimensional (15)N-(13)C planes, in which approximately 750 cross peaks are resolved. The experimental data are fit to exact theoretical trajectories for spin clusters (consisting of one (13)C and several (15)N each), yielding quantitative precision as good as 0.1 A for approximately 350 sites, better than 0.3 A for another 150, and approximately 1.0 A for 150 distances in the range of 5-8 A. Along with isotropic chemical shift-based (TALOS) dihedral angle restraints, the distance restraints are incorporated into simulated annealing calculations to yield a highly precise structure (backbone RMSD of 0.25+/-0.09 A), which also demonstrates excellent agreement with the most closely related crystal structure of GB1 (2QMT, bbRMSD 0.79+/-0.03 A). Moreover, side chain heavy atoms are well restrained (0.76+/-0.06 A total heavy atom RMSD). These results demonstrate for the first time that quantitative internuclear distances can be measured throughout an entire solid protein to yield an atomic-resolution structure.
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Affiliation(s)
- Andrew J Nieuwkoop
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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7
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Matsuoka S, Inoue M. Application of REDOR NMR in natural product chemistry. Chem Commun (Camb) 2009:5664-75. [DOI: 10.1039/b910230b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Wickramasinghe NP, Shaibat MA, Jones CR, Casabianca LB, de Dios AC, Harwood JS, Ishii Y. Progress in C13 and H1 solid-state nuclear magnetic resonance for paramagnetic systems under very fast magic angle spinning. J Chem Phys 2008; 128:052210. [DOI: 10.1063/1.2833574] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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9
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Graesser DT, Wylie BJ, Nieuwkoop AJ, Franks WT, Rienstra CM. Long-range 19F-15N distance measurements in highly-13C, 15N-enriched solid proteins with 19F-dephased REDOR shift (FRESH) spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S129-S134. [PMID: 18157807 DOI: 10.1002/mrc.2126] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We present a novel rotational-echo double resonance (REDOR) method for detection of multiple (19)F-(15)N distances in solid proteins. The method is applicable to protein samples containing a single (19)F label, in addition to high levels of (13)C and (15)N enrichment. REDOR dephasing pulses are applied on the (19)F channel during an indirect constant time chemical shift evolution period on (15)N, and polarization is then transferred to (13)C for detection, with high-power (1)H decoupling throughout the sequence. This four-channel experiment reports site-specifically on (19)F-(15)N distances, with highly accurate determinations of approximately 5 A distances and detection of correlations arising from internuclear distances of at least 8 A. We demonstrate the method on the well-characterized 56-residue model protein GB1, where the sole tryptophan residue (Trp-43) has been labeled with 5-(19)F-Trp, in a bacterial growth medium also including (13)C-glucose and (15)N ammonium chloride. In GB1, 11 distances are determined, all agreeing within 20% of the X-ray structure distances. We envision the experiment will be utilized to measure quantitative long-range distances for protein structure determination.
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Affiliation(s)
- Daniel T Graesser
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 68101, USA
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10
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Gibson JM, Popham JM, Raghunathan V, Stayton PS, Drobny GP. A solid-state NMR study of the dynamics and interactions of phenylalanine rings in a statherin fragment bound to hydroxyapatite crystals. J Am Chem Soc 2007; 128:5364-70. [PMID: 16620107 DOI: 10.1021/ja056731m] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extracellular matrix proteins regulate hard tissue growth by acting as adhesion sites for cells, by triggering cell signaling pathways, and by directly regulating the primary and/or secondary crystallization of hydroxyapatite, the mineral component of bone and teeth. Despite the key role that these proteins play in the regulation of hard tissue growth in humans, the exact mechanism used by these proteins to recognize mineral surfaces is poorly understood. Interactions between mineral surfaces and proteins very likely involve specific contacts between the lattice and the protein side chains, so elucidation of the nature of interactions between protein side chains and their corresponding inorganic mineral surfaces will provide insight into the recognition and regulation of hard tissue growth. Isotropic chemical shifts, chemical shift anisotropies (CSAs), NMR line-width information, (13)C rotating frame relaxation measurements, as well as direct detection of correlations between (13)C spins on protein side chains and (31)P spins in the crystal surface with REDOR NMR show that, in the peptide fragment derived from the N-terminal 15 amino acids of salivary statherin (i.e., SN-15), the side chain of the phenylalanine nearest the C-terminus of the peptide (F14) is dynamically constrained and oriented near the surface, whereas the side chain of the phenylalanine located nearest to the peptide's N-terminus (F7) is more mobile and is oriented away from the hydroxyapatite surface. The relative dynamics and proximities of F7 and F14 to the surface together with prior data obtained for the side chain of SN-15's unique lysine (i.e., K6) were used to construct a new picture for the structure of the surface-bound peptide and its orientation to the crystal surface.
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Affiliation(s)
- James M Gibson
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
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11
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Matsuoka S, Ikeuchi H, Umegawa Y, Matsumori N, Murata M. Membrane interaction of amphotericin B as single-length assembly examined by solid state NMR for uniformly 13C-enriched agent. Bioorg Med Chem 2006; 14:6608-14. [PMID: 16782343 DOI: 10.1016/j.bmc.2006.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 05/31/2006] [Accepted: 06/01/2006] [Indexed: 11/29/2022]
Abstract
The membrane interaction of amphotericin B (AmB), one of the most important anti-fungal drugs, was investigated by solid state NMR measurements of uniformly 13C-enriched AmB, which was prepared by the culture of the drug-producing microorganism in the presence of [u-13C6]glucose. All the 13C NMR signals of AmB upon binding to DLPC membrane were successfully assigned on the basis of the 13C-13C correlation spectrum. 13C-31P RDX (Rotational-Echo Double Resonance for X-clusters) experiments clearly revealed the REDOR dephasing effects for carbon atoms residing in the both terminal parts, whereas no dephasing was observed for the middle parts including polyolefinic C20-C33 and hydroxyl-bearing C8/C9 parts. These observations suggest that AmB binds to DLPC membrane with a high affinity to the phospholipid and spans the membrane with a single molecular length.
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Affiliation(s)
- Shigeru Matsuoka
- Department of Chemistry, Graduate School of Science, Osaka University, 1-16 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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12
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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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13
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Gibson JM, Raghunathan V, Popham JM, Stayton PS, Drobny GP. A REDOR NMR study of a phosphorylated statherin fragment bound to hydroxyapatite crystals. J Am Chem Soc 2005; 127:9350-1. [PMID: 15984845 DOI: 10.1021/ja050910m] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydroxyapatite (HAP) is the main mineral component of teeth. It is well-known that several salivary proteins and peptides bind strongly to HAP to regulate crystal growth. Interactions between a peptide derived from the N-terminal fragment of the salivary protein statherin and HAP were measured utilizing rotational-echo double-resonance (REDOR) nuclear magnetic resonance (NMR). The REDOR measurement from the side chain of the salivary peptide to the HAP surface is complicated by two effects: a possible additional dipolar coupling to a phosphorylated side chain and the potential proximity of phosphorus atoms to each other, resulting in a homonuclear dipolar interaction. Both of these effects were addressed, and the smallest model applicable to our system includes the nitrogen-15 (15N) spin in the lysine side chain and two phosphorus-31 (31P) spins, at least one of which must be from the surface phosphates of the HAP.
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Affiliation(s)
- James M Gibson
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
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14
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McDermott AE. Structural and dynamic studies of proteins by solid-state NMR spectroscopy: rapid movement forward. Curr Opin Struct Biol 2005; 14:554-61. [PMID: 15465315 DOI: 10.1016/j.sbi.2004.09.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Revised: 08/24/2004] [Accepted: 09/03/2004] [Indexed: 10/26/2022]
Abstract
Starting only a few years ago, many solid-state NMR spectroscopy laboratories have become engaged in solving the complete structures of biological macromolecules using high-resolution methods based on magic angle spinning. These efforts typically involve structurally homogeneous samples, and utilize recently developed pulse sequences for the sequential correlation of resonances, the detection of tertiary contacts and the characterization of torsion angles. Thereby, systems have been studied that evaded other, more established, structure determination methods.
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Affiliation(s)
- Ann E McDermott
- Columbia University, Department of Chemistry, MC 3113, 3000 Broadway, New York, New York 10027, USA.
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15
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Bechinger B, Aisenbrey C, Bertani P. The alignment, structure and dynamics of membrane-associated polypeptides by solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2005; 1666:190-204. [PMID: 15519315 DOI: 10.1016/j.bbamem.2004.08.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 08/06/2004] [Indexed: 10/26/2022]
Abstract
Solid-state NMR spectroscopy is being developed at a fast pace for the structural investigation of immobilized and non-crystalline biomolecules. These include proteins and peptides associated with phospholipid bilayers. In contrast to solution NMR spectroscopy, where complete or almost complete averaging leads to isotropic values, the anisotropic character of nuclear interactions is apparent in solid-state NMR spectra. In static samples the orientation dependence of chemical shift, dipolar or quadrupolar interactions, therefore, provides angular constraints when the polypeptides have been reconstituted into oriented membranes. Furthermore, solid-state NMR spectroscopy of aligned samples offers distinct advantages in allowing access to dynamic processes such as topological equilibria or rotational diffusion in membrane environments. Alternatively, magic angle sample spinning (MAS) results in highly resolved NMR spectra, provided that the sample is sufficiently homogenous. MAS spinning solid-state NMR spectra allow to measure distances and dihedral angles with high accuracy. The technique has recently been developed to selectively establish through-space and through-bond correlations between nuclei, similar to the approaches well-established in solution-NMR spectroscopy.
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Affiliation(s)
- Burkhard Bechinger
- Faculté de chimie, Institut le Bel, 4, rue Blaise Pascal, 67000 Strasbourg, France.
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16
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Straus SK. Recent developments in solid-state magic-angle spinning, nuclear magnetic resonance of fully and significantly isotopically labelled peptides and proteins. Philos Trans R Soc Lond B Biol Sci 2004; 359:997-1008. [PMID: 15306412 PMCID: PMC1693383 DOI: 10.1098/rstb.2003.1398] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In recent years, a large number of solid-state nuclear magnetic resonance (NMR) techniques have been developed and applied to the study of fully or significantly isotopically labelled ((13)C, (15)N or (13)C/(15)N) biomolecules. In the past few years, the first structures of (13)C/(15)N-labelled peptides, Gly-Ile and Met-Leu-Phe, and a protein, Src-homology 3 domain, were solved using magic-angle spinning NMR, without recourse to any structural information obtained from other methods. This progress has been made possible by the development of NMR experiments to assign solid-state spectra and experiments to extract distance and orientational information. Another key aspect to the success of solid-state NMR is the advances made in sample preparation. These improvements will be reviewed in this contribution. Future prospects for the application of solid-state NMR to interesting biological questions will also briefly be discussed.
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Affiliation(s)
- Suzana K Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada.
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17
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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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18
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Yang J, Parkanzky PD, Bodner ML, Duskin CA, Weliky DP. Application of REDOR subtraction for filtered MAS observation of labeled backbone carbons of membrane-bound fusion peptides. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 159:101-110. [PMID: 12482688 DOI: 10.1016/s1090-7807(02)00033-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Clean MAS observation of 13C-labeled carbons in membrane-bound HIV-1 and influenza fusion peptides was made by using a rotational-echo double-resonance spectroscopy (REDOR) filter of directly bonded 13C-15N pairs. The clean filtering achieved with the REDOR approach is superior to filtering done with sample difference spectroscopy. In one labeling approach, the peptide had labels at a single 13C carbonyl and its directly bonded 15N. The resulting chemical shift distribution of the filtered signal is used to assess the distribution of local secondary structures at the labeled carbonyl. For the influenza peptide, the Leu-2 carbonyl chemical shift distribution is shown to vary markedly with lipid and detergent composition, as well as peptide:lipid ratio, suggesting that the local peptide structure also has a strong dependence on these factors. Because most carboxylic- and amino-labeled amino acids are commercially available, this REDOR approach should have broad applicability to chemically synthesized peptides as well as bacterially synthesized proteins. In a second labeling approach, the HIV-1 fusion peptide had U-13C, 15N labeling over three sequential residues. When a 1.6 ms REDOR dephasing time is used, only backbone 13C signals are observed. The resulting spectra are used to determine spectral linewidths and to assess feasibility of assignment of uniformly labeled peptide.
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Affiliation(s)
- Jun Yang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
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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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Jaroniec CP, Filip C, Griffin RG. 3D TEDOR NMR experiments for the simultaneous measurement of multiple carbon-nitrogen distances in uniformly (13)C,(15)N-labeled solids. J Am Chem Soc 2002; 124:10728-42. [PMID: 12207528 DOI: 10.1021/ja026385y] [Citation(s) in RCA: 222] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe three-dimensional magic-angle-spinning NMR experiments for the simultaneous measurement of multiple carbon-nitrogen distances in uniformly (13)C,(15)N-labeled solids. The approaches employ transferred echo double resonance (TEDOR) for (13)C-(15)N coherence transfer and (15)N and (13)C frequency labeling for site-specific resolution, and build on several previous 3D TEDOR techniques. The novel feature of the 3D TEDOR pulse sequences presented here is that they are specifically designed to circumvent the detrimental effects of homonuclear (13)C-(13)C J-couplings on the measurement of weak (13)C-(15)N dipolar couplings. In particular, homonuclear J-couplings lead to two undesirable effects: (i) they generate anti-phase and multiple-quantum (MQ) spin coherences, which lead to spurious cross-peaks and phase-twisted lines in the 2D (15)N-(13)C correlation spectra, and thus degrade the spectral resolution and prohibit the extraction of reliable cross-peak intensities, and (ii) they significantly reduce cross-peak intensities for strongly J-coupled (13)C sites (e.g., CO and C(alpha)). The first experiment employs z-filter periods to suppress the anti-phase and MQ coherences and generates 2D spectra with purely absorptive peaks for all TEDOR mixing times. The second approach uses band-selective (13)C pulses to refocus J-couplings between (13)C spins within the selective pulse bandwidth and (13)C spins outside the bandwidth. The internuclear distances are extracted by using a simple analytical model, which accounts explicitly for multiple spin-spin couplings contributing to cross-peak buildup. The experiments are demonstrated in two U-(13)C,(15)N-labeled peptides, N-acetyl-L-Val-L-Leu (N-ac-VL) and N-formyl-L-Met-L-Leu-L-Phe (N-f-MLF), where 20 and 26 (13)C-(15)N distances up to approximately 5-6 A were measured, respectively. Of the measured distances, 10 in N-ac-VL and 13 in N-f-MLF are greater than 3 A and provide valuable structural constraints.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry, Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Nishimura K, Ebisawa K, Suzuki E, Saitô H, Naito A. Natural abundance 13C REDOR coupled to a singly 15N-labeled nucleus: simultaneous determination of interatomic distances in crystalline ammonium [15N] l-glutamate monohydrate. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(00)00761-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Sack I, Balazs YS, Rahimipour S, Vega S. Peptide torsion angle measurements: effects of nondilute spin pairs on carbon-observed, deuterium-dephased PM5-REDOR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2001; 148:104-114. [PMID: 11133282 DOI: 10.1006/jmre.2000.2214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Reintroducing dipolar coupling between spin-1/2 nuclei (e.g., (13)C, (15)N) and spin-1 (2)H, using phase-modulated deuterium dephasing pulses, provides a simple and efficient basis for obtaining peptide backbone torsion angles (phi, psi) in specific stable-isotope enriched samples. Multiple homonuclear spin-1/2 interactions due to isotopic enrichment can arise between neighboring molecules or within a multiply labeled protein after folding. The consequences of (13)C homonuclear interactions present during (13)C-observed, (2)H-dephased REDOR measurements are explored and the theoretical basis of the experimentally observed effects is investigated. Two tripeptides are taken to represent both the general case of (2)H(alpha)-alanine (in the tripeptide LAF) and the special case of (2)H(alpha)(2)-glycine (in the tripeptide LGF). The lyophilized tripeptides exhibit narrowed spectral linewidths over time due to reduced conformational dispersion. This is due to a hydration process whereby a small fraction of peptides is reorienting and the bulk peptide fraction undergoes a conformational change. The new molecular packing arrangement lacks homonuclear (13)C spin interactions, allowing determination of (phi, psi) backbone torsion angles.
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Affiliation(s)
- I Sack
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
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Jaroniec CP, Tounge BA, Rienstra CM, Herzfeld J, Griffin RG. Recoupling of heteronuclear dipolar interactions with rotational-echo double-resonance at high magic-angle spinning frequencies. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 146:132-139. [PMID: 10968966 DOI: 10.1006/jmre.2000.2128] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Heteronuclear dipolar recoupling with rotational-echo double-resonance (REDOR) is investigated in the rapid magic-angle spinning regime, where radiofrequency irradiation occupies a significant fraction of the rotor period (10-60%). We demonstrate, in two model (13)C-(15)N spin systems, [1-(13)C, (15)N] and [2-(13)C, (15)N]glycine, that REDOR DeltaS/S(0) curves acquired at high MAS rates and relatively low recoupling fields are nearly identical to the DeltaS/S(0) curve expected for REDOR with ideal delta-function pulses. The only noticeable effect of the finite pi pulse length on the recoupling is a minor scaling of the dipolar oscillation frequency. Experimental results are explained using both numerical calculations and average Hamiltonian theory, which is used to derive analytical expressions for evolution under REDOR recoupling sequences with different pi pulse phasing schemes. For xy-4 and extensions thereof, finite pulses scale only the dipolar oscillation frequency by a well-defined factor. For other phasing schemes (e.g., xx-4 and xx-4) both the frequency and amplitude of the oscillation are expected to change.
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Affiliation(s)
- C P Jaroniec
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
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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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Sack I, Vega S. Efficient deuterium-carbon REDOR NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 145:52-61. [PMID: 10873496 DOI: 10.1006/jmre.2000.2072] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Phase modulated pulses for deuterium recoupling in (2)H-(13)C REDOR NMR spectroscopy have been introduced to improve dephasing of the detected (13)C nuclei. The deuterium inversion properties of phase modulated recoupling pulses have been studied experimentally on l-alanine-2-d(1) and theoretically using average Hamiltonian theory and exact simulations of the equation of motion of the density matrix. The best (13)C dephasing was observed when XYXYX (PM5) deuterium recoupling pulses were applied. A comparison to the 90 degrees -180 degrees -90 degrees (CPL) composite pulse scheme revealed an improvement of recoupling on the order of 2.5. Simple CW recoupling pulses of the same length of PM5 and CPL pulses showed the weakest (13)C dephasing. Simulations have shown that the (2)H recoupling efficiency of PM5 REDOR experiments approach the very efficient REAPDOR results. However, in our case a REAPDOR study of l-alanine-2-d(1) resulted in a significant decrease of the (13)C signal intensity due to pulse imperfections of (13)C pi-pulses. The new PM5-REDOR technique has been employed to study the torsion angle between C1/2 and C5 in ethylmalonic acid-4-d(2).
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Affiliation(s)
- I Sack
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
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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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Jaroniec CP, Tounge BA, Rienstra CM, Herzfeld J, Griffin RG. Measurement of13C−15N Distances in Uniformly13C Labeled Biomolecules: J-Decoupled REDOR. J Am Chem Soc 1999. [DOI: 10.1021/ja9921569] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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