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Nishiyama Y, Hou G, Agarwal V, Su Y, Ramamoorthy A. Ultrafast Magic Angle Spinning Solid-State NMR Spectroscopy: Advances in Methodology and Applications. Chem Rev 2023; 123:918-988. [PMID: 36542732 PMCID: PMC10319395 DOI: 10.1021/acs.chemrev.2c00197] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solid-state NMR spectroscopy is one of the most commonly used techniques to study the atomic-resolution structure and dynamics of various chemical, biological, material, and pharmaceutical systems spanning multiple forms, including crystalline, liquid crystalline, fibrous, and amorphous states. Despite the unique advantages of solid-state NMR spectroscopy, its poor spectral resolution and sensitivity have severely limited the scope of this technique. Fortunately, the recent developments in probe technology that mechanically rotate the sample fast (100 kHz and above) to obtain "solution-like" NMR spectra of solids with higher resolution and sensitivity have opened numerous avenues for the development of novel NMR techniques and their applications to study a plethora of solids including globular and membrane-associated proteins, self-assembled protein aggregates such as amyloid fibers, RNA, viral assemblies, polymorphic pharmaceuticals, metal-organic framework, bone materials, and inorganic materials. While the ultrafast-MAS continues to be developed, the minute sample quantity and radio frequency requirements, shorter recycle delays enabling fast data acquisition, the feasibility of employing proton detection, enhancement in proton spectral resolution and polarization transfer efficiency, and high sensitivity per unit sample are some of the remarkable benefits of the ultrafast-MAS technology as demonstrated by the reported studies in the literature. Although the very low sample volume and very high RF power could be limitations for some of the systems, the advantages have spurred solid-state NMR investigation into increasingly complex biological and material systems. As ultrafast-MAS NMR techniques are increasingly used in multidisciplinary research areas, further development of instrumentation, probes, and advanced methods are pursued in parallel to overcome the limitations and challenges for widespread applications. This review article is focused on providing timely comprehensive coverage of the major developments on instrumentation, theory, techniques, applications, limitations, and future scope of ultrafast-MAS technology.
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Affiliation(s)
- Yusuke Nishiyama
- JEOL Ltd., Akishima, Tokyo196-8558, Japan
- RIKEN-JEOL Collaboration Center, Yokohama, Kanagawa230-0045, Japan
| | - Guangjin Hou
- State Key Laboratory of Catalysis, Dalian 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, Dalian116023, China
| | - Vipin Agarwal
- Tata Institute of Fundamental Research, Sy. No. 36/P, Gopanpally, Hyderabad500 046, India
| | - Yongchao Su
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey07065, United States
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan41809-1055, United States
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Kumar S, Borish K, Dey S, Nagesh J, Das A. Sequence dependent folding motifs of the secondary structures of Gly-Pro and Pro-Gly containing oligopeptides. Phys Chem Chem Phys 2022; 24:18408-18418. [PMID: 35880873 DOI: 10.1039/d2cp01306a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Folding motifs of the secondary structures of peptides and proteins are primarily based on the hydrogen bonding interactions in the backbone as well as the sequence of the amino acid residues present. For instance, the β-turn structure directed by the Pro-Gly sequence is the key to the β-hairpin structure of peptides/proteins as well as a selective site for the enzymatic hydroxylation of pro-collagen. Herein, we have investigated the sequence dependent folding motifs of end-protected Gly-Pro and Pro-Gly dipeptides using a combination of gas phase laser spectroscopy, quantum chemistry calculations, solution phase IR and NMR spectroscopy and single crystal X-Ray diffraction (XRD). All three observed conformers of the Gly-Pro peptide in the gas phase have been found to have extended β-strand or polyproline-II (PP-II) structures with C5-C7 hydrogen bonding interactions, which correlates well with the structure obtained from solution phase spectroscopy and XRD. On the other hand, we have found that the Pro-Gly peptide has a C10/β-turn structure in the solution phase in contrast to the C7-C7 (i.e. 27-ribbon) structure observed in the gas phase. Although the lowest energy structure in the gas phase is not C10, we find that C7-C7 is an abundantly found structural motif of Pro-Gly containing peptides in the Cambridge Structural Database, indicating that the gas phase conformers are not sampling any unusual forms. We surmise that the role of the solvent could be crucial in dictating the preferential stabilization of the C10 structure in the solution phase. The present investigation provides a comprehensive picture of the folding motifs of the Gly-Pro and Pro-Gly peptides observed in the gas phase and condensed phase weaving a fine interplay of the intrinsic conformational properties, solvation, and crystal packing of the peptides.
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Affiliation(s)
- Satish Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
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Ji Y, Liang L, Bao X, Hou G. Recent progress in dipolar recoupling techniques under fast MAS in solid-state NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2021; 112:101711. [PMID: 33508579 DOI: 10.1016/j.ssnmr.2020.101711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/04/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
With the recent advances in NMR hardware and probe design technology, magic-angle spinning (MAS) rates over 100 kHz are accessible now, even on commercial solid NMR probes. Under such fast MAS conditions, excellent spectral resolution has been achieved by efficient suppression of anisotropic interactions, which also opens an avenue to the proton-detected NMR experiments in solids. Numerous methods have been developed to take full advantage of fast MAS during the last decades. Among them, dipolar recoupling techniques under fast MAS play vital roles in the determination of the molecular structure and dynamics, and are also key elements in multi-dimensional correlation NMR experiments. Herein, we review the dipolar recoupling techniques, especially those developed in the past two decades for fast-to-ultrafast MAS conditions. A major focus for our discussion is the ratio of RF field strength (in frequency) to MAS frequency, ν1/νr, in different pulse sequences, which determines whether these dipolar recoupling techniques are suitable for NMR experiments under fast MAS conditions. Systematic comparisons are made among both heteronuclear and homonuclear dipolar recoupling schemes. In addition, the schemes developed specially for proton-detection NMR experiments under ultrafast MAS conditions are highlighted as well.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - 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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Asakura T, Aoki A, Komatsu K, Ito C, Suzuki I, Naito A, Kaji H. Lamellar Structure in Alanine-Glycine Copolypeptides Studied by Solid-State NMR Spectroscopy: A Model for the Crystalline Domain of Bombyx mori Silk Fibroin in Silk II Form. Biomacromolecules 2020; 21:3102-3111. [PMID: 32603138 DOI: 10.1021/acs.biomac.0c00486] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Bombyx mori silk fibroin (SF) fibers with excellent mechanical properties have attracted widespread attention as new biomaterials. However, the structural details are still not conclusive. Here, we propose a lamellar structure for the crystalline domain of the SF fiber based on structural analyses of the Ala Cβ peaks in the 13C cross-polarization/magic angle spinning NMR spectra of (Ala-Gly)m (m = 9, 12, 15, and 25) and 13C selectively labeled (Ala-Gly)15 model peptides. Namely, three Ala Cβ peaks with relative intensities of 1:2:1 obtained by deconvolution were assigned to two kinds of β-sheet and a β-turn, which are interpreted as a lamellar structure formed by repetitive folding using β-turns every eighth amino acid, for which the basic structure is (Ala-Gly)4 in an antipolar arrangement. The dynamics and intermolecular arrangement were further studied using 13C solid-state spin-lattice relaxation time observations and the rotational echo double resonance experiments, respectively.
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Affiliation(s)
- Tetsuo Asakura
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Akihiro Aoki
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kohei Komatsu
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Chie Ito
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Ikue Suzuki
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Akira Naito
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Hironori Kaji
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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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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Naito A, Okushita K, Nishimura K, Boutis GS, Aoki A, Asakura T. Quantitative Analysis of Solid-State Homonuclear Correlation Spectra of Antiparallel β-Sheet Alanine Tetramers. J Phys Chem B 2018; 122:2715-2724. [PMID: 29420030 DOI: 10.1021/acs.jpcb.7b11126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Poly-l-alanine (PLA) sequences are a key element in the structure of the crystalline domains of spider dragline silks, wild silkworm silks, antifreeze proteins, and amyloids. To date, no atomic-level structures of antiparallel (AP)-PLA longer than Ala4 have been reported using the single-crystal X-ray diffraction analysis. In this work, dipolar-assisted rotational resonance solid-state NMR spectra were observed to determine the effective internuclear distances of 13C uniformly labeled alanine tetramer with antiparallel (AP) β-sheet structure whose atomic coordinates are determined from the X-ray crystallographic analysis. Initial build-up rates, R j, k, were obtained from the build-up curves of the cross peaks by considering the internuclear distances arising in the master equation. Subsequently, experimentally obtained effective internuclear distances, reffj, k(obs), were compared with the calculated reffj, k(calc) values obtained from the X-ray crystallographic data. Fairly good correlation between reffj, k(obs) and reffj, k(calc) was obtained in the range of 1.0-6.0 Å, with the standard deviation of 0.244 Å, without considering the zero-quantum line-shape functions. It was further noted that the internuclear distances of intermolecular contributions provide details relating to the molecular packing in solid-state samples. Thus, the present data agree well with AP-β-sheet packing but do not agree with P-β-sheet packing.
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Affiliation(s)
- Akira Naito
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei , Tokyo 184-8588 , Japan
| | - Keiko Okushita
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei , Tokyo 184-8588 , Japan.,Institute for Molecular Science , 38 Nishigo-Naka , Myodaiji, Okazaki 444-8585 , Japan
| | - Katsuyuki Nishimura
- Institute for Molecular Science , 38 Nishigo-Naka , Myodaiji, Okazaki 444-8585 , Japan
| | - Gregory S Boutis
- Department of Physics , Brooklyn College of The City University of New York , 2900 Bedford Avenue , Brooklyn , New York 11210 , United States.,Department of Physics , The Graduate Center of The City University of New York , 365 5th Avenue , New York , New York 10016 , United States
| | - Akihiro Aoki
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei , Tokyo 184-8588 , Japan
| | - Tetsuo Asakura
- Department of Biotechnology , Tokyo University of Agriculture and Technology , Koganei , Tokyo 184-8588 , Japan
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Naito A, Matsumori N, Ramamoorthy A. Dynamic membrane interactions of antibacterial and antifungal biomolecules, and amyloid peptides, revealed by solid-state NMR spectroscopy. Biochim Biophys Acta Gen Subj 2018; 1862:307-323. [PMID: 28599848 PMCID: PMC6384124 DOI: 10.1016/j.bbagen.2017.06.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 05/28/2017] [Accepted: 06/02/2017] [Indexed: 12/12/2022]
Abstract
A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules. This review article focuses on the applications of solid-state NMR techniques to study a few selected antibacterial and amyloid peptides. Solid-state NMR studies revealing the membrane inserted bent α-helical structure associated with the hemolytic activity of bee venom melittin and the chemical shift oscillation analysis used to determine the transmembrane structure (with α-helix and 310-helix in the N- and C-termini, respectively) of antibiotic peptide alamethicin are discussed in detail. Oligomerization of an amyloidogenic islet amyloid polypeptide (IAPP, or also known as amylin) resulting from its aggregation in a membrane environment, molecular interactions of the antifungal natural product amphotericin B with ergosterol in lipid bilayers, and the mechanism of lipid raft formation by sphingomyelin studied using solid state NMR methods are also discussed in this review article. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Akira Naito
- Graduate School of Engineering, Yokohama National University, Yokohama 240-8501, Japan.
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, Fukuoka 819-0395, Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109-1055, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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8
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Greenwood AI, Clay MC, Rienstra CM. 31P-dephased, 13C-detected REDOR for NMR crystallography at natural isotopic abundance. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 278:8-17. [PMID: 28319851 PMCID: PMC5478420 DOI: 10.1016/j.jmr.2017.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/21/2017] [Accepted: 02/26/2017] [Indexed: 05/14/2023]
Abstract
Typically, the process of NMR-based structure determination relies on accurately measuring a large number of internuclear distances to serve as restraints for simulated annealing calculations. In solids, the rotational-echo double-resonance (REDOR) experiment is a widely used approach to determine heteronuclear dipolar couplings corresponding to distances usually in the range of 1.5-8Å. A challenge in the interpretation of REDOR data is the degeneracy of symmetric subunits in an oligomer or equivalent molecules in a crystal lattice, which produce REDOR trajectories that depend explicitly on two or more distances instead of one. This degeneracy cannot be overcome by either spin dilution (for molecules containing 31P, 19F and other highly abundant nuclei) or selective pulses (in the case where there is chemical shift degeneracy). For small, crystalline molecules, such as phosphoserine, we demonstrate that as many as five inter-molecular distances must be considered to model 31P-dephased REDOR data accurately. We report excellent agreement between simulation and experiment once lattice couplings, 31P chemical shift anisotropy, and radio-frequency field inhomogeneity are all taken into account. We also discuss the systematic inaccuracies that may result from approximations that consider only the initial slope of the REDOR trajectory and/or that utilize a two- or three-spin system. Furthermore, we demonstrate the applicability of 31P-dephased REDOR for validation or refinement of candidate crystal structures and show that this approach is especially informative for NMR crystallography of 31P-containing molecules.
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Affiliation(s)
- Alexander I Greenwood
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mary C Clay
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chad M Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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9
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Siskos MG, Choudhary MI, Gerothanassis IP. Hydrogen Atomic Positions of O-H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with ¹H-NMR Chemical Shifts and X-ray Diffraction Methods. Molecules 2017; 22:E415. [PMID: 28272366 PMCID: PMC6155303 DOI: 10.3390/molecules22030415] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 02/27/2017] [Accepted: 03/03/2017] [Indexed: 12/21/2022] Open
Abstract
The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.
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Affiliation(s)
- Michael G Siskos
- Section of Organic Chemistry & Biochemistry, Department of Chemistry, University of Ioannina, Ioannina GR-45110, Greece.
| | - M Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Biological and Chemical Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Ioannis P Gerothanassis
- Section of Organic Chemistry & Biochemistry, Department of Chemistry, University of Ioannina, Ioannina GR-45110, Greece.
- H.E.J. Research Institute of Chemistry, International Center for Biological and Chemical Sciences, University of Karachi, Karachi 75270, Pakistan.
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Nagao T, Mishima D, Javkhlantugs N, Wang J, Ishioka D, Yokota K, Norisada K, Kawamura I, Ueda K, Naito A. Structure and orientation of antibiotic peptide alamethicin in phospholipid bilayers as revealed by chemical shift oscillation analysis of solid state nuclear magnetic resonance and molecular dynamics simulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2789-98. [PMID: 26248014 DOI: 10.1016/j.bbamem.2015.07.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/01/2015] [Accepted: 07/31/2015] [Indexed: 11/26/2022]
Abstract
The structure, topology and orientation of membrane-bound antibiotic alamethicin were studied using solid state nuclear magnetic resonance (NMR) spectroscopy. (13)C chemical shift interaction was observed in [1-(13)C]-labeled alamethicin. The isotropic chemical shift values indicated that alamethicin forms a helical structure in the entire region. The chemical shift anisotropy of the carbonyl carbon of isotopically labeled alamethicin was also analyzed with the assumption that alamethicin molecules rotate rapidly about the bilayer normal of the phospholipid bilayers. It is considered that the adjacent peptide planes form an angle of 100° or 120° when it forms α-helix or 310-helix, respectively. These properties lead to an oscillation of the chemical shift anisotropy with respect to the phase angle of the peptide plane. Anisotropic data were acquired for the 4 and 7 sites of the N- and C-termini, respectively. The results indicated that the helical axes for the N- and C-termini were tilted 17° and 32° to the bilayer normal, respectively. The chemical shift oscillation curves indicate that the N- and C-termini form the α-helix and 310-helix, respectively. The C-terminal 310-helix of alamethicin in the bilayer was experimentally observed and the unique bending structure of alamethicin was further confirmed by measuring the internuclear distances of [1-(13)C] and [(15)N] doubly-labeled alamethicin. Molecular dynamics simulation of alamethicin embedded into dimyristoyl phophatidylcholine (DMPC) bilayers indicates that the helical axes for α-helical N- and 310-helical C-termini are tilted 12° and 32° to the bilayer normal, respectively, which is in good agreement with the solid state NMR results.
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Affiliation(s)
- Takashi Nagao
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Daisuke Mishima
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Namsrai Javkhlantugs
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan; Center for Nanoscience and Nanotechnology, School of Engineering and Applied Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia
| | - Jun Wang
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Daisuke Ishioka
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kiyonobu Yokota
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kazushi Norisada
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Kazuyoshi Ueda
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5 Hodogaya-ku, Yokohama 240-8501, Japan.
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11
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Siskos MG, Tzakos AG, Gerothanassis IP. Accurate ab initio calculations of O-HO and O-H(-)O proton chemical shifts: towards elucidation of the nature of the hydrogen bond and prediction of hydrogen bond distances. Org Biomol Chem 2015. [PMID: 26196256 DOI: 10.1039/c5ob00920k] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The inability to determine precisely the location of labile protons in X-ray molecular structures has been a key barrier to progress in many areas of molecular sciences. We report an approach for predicting hydrogen bond distances beyond the limits of X-ray crystallography based on accurate ab initio calculations of O-HO proton chemical shifts, using a combination of DFT and contactor-like polarizable continuum model (PCM). Very good linear correlation between experimental and computed (at the GIAO/B3LYP/6-311++G(2d,p) level of theory) chemical shifts were obtained with a large set of 43 compounds in CHCl3 exhibiting intramolecular O-HO and intermolecular and intramolecular ionic O-H(-)O hydrogen bonds. The calculated OH chemical shifts exhibit a strong linear dependence on the computed (O)HO hydrogen bond length, in the region of 1.24 to 1.85 Å, of -19.8 ppm Å(-1) and -20.49 ppm Å(-1) with optimization of the structures at the M06-2X/6-31+G(d) and B3LYP/6-31+G(d) level of theory, respectively. A Natural Bond Orbitals (NBO) analysis demonstrates a very good linear correlation between the calculated (1)H chemical shifts and (i) the second-order perturbation stabilization energies, corresponding to charge transfer between the oxygen lone pairs and σ antibonding orbital and (ii) Wiberg bond order of the O-HO and O-H(-)O hydrogen bond. Accurate ab initio calculations of O-HO and O-H(-)O (1)H chemical shifts can provide improved structural and electronic description of hydrogen bonding and a highly accurate measure of distances of short and strong hydrogen bonds.
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Affiliation(s)
- Michael G Siskos
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, GR 45110, Greece.
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12
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Matsuoka S. [Structural study on small molecules in biological solid samples by using solid state NMR]. YAKUGAKU ZASSHI 2012; 132:969-78. [PMID: 23023412 DOI: 10.1248/yakushi.132.969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many small molecule drugs have molecular targets that are non-crystalline and insoluble biological matrices, such as proteins embedded in lipid membrane, cell membranes, and cell walls. To understand the action mechanisms, it is essential to determine the binding structure with atomic-level resolution. Although solution nuclear magnetic resonance (NMR) and X-ray crystallography have been used to determine molecular structures of cell membrane and membrane proteins, these methods are unable to reproduce the complexity of biological systems because either solubilization or crystallization of target molecules is requisite. For structural studies of insoluble non-crystalline biological samples, so-called "biological solids", high resolution distance measurements using solid-state NMR are indispensable techniques, of which rotational-echo double-resonance (REDOR) is one of the most widely used methods. In this paper, a brief introduction to REDOR NMR and its applications to structural studies on the antifungal amphotericin B-membrane phospholipid complex and a structural elucidation of photorespiration metabolites in plant cells without extraction or isolation is provided.
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Affiliation(s)
- Shigeru Matsuoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
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13
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Uekusa Y, Kamihira-Ishijima M, Sugimoto O, Ishii T, Kumazawa S, Nakamura K, Tanji KI, Naito A, Nakayama T. Interaction of epicatechin gallate with phospholipid membranes as revealed by solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1654-60. [DOI: 10.1016/j.bbamem.2011.02.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 01/27/2011] [Accepted: 02/17/2011] [Indexed: 11/24/2022]
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14
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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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15
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Kawamura I, Ohmine M, Tanabe J, Tuzi S, Saitô H, Naito A. Dynamic aspects of extracellular loop region as a proton release pathway of bacteriorhodopsin studied by relaxation time measurements by solid state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3090-7. [DOI: 10.1016/j.bbamem.2007.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2007] [Revised: 11/02/2007] [Accepted: 11/05/2007] [Indexed: 11/30/2022]
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16
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Karp ES, Tiburu EK, Abu-Baker S, Lorigan GA. The structural properties of the transmembrane segment of the integral membrane protein phospholamban utilizing 13C CPMAS, 2H, and REDOR solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1758:772-80. [PMID: 16839519 DOI: 10.1016/j.bbamem.2006.04.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 03/22/2006] [Accepted: 04/04/2006] [Indexed: 11/18/2022]
Abstract
Solid-state NMR spectroscopic techniques were used to investigate the secondary structure of the transmembrane peptide phospholamban (TM-PLB), a sarcoplasmic Ca(2+) regulator. (13)C cross-polarization magic angle spinning spectra of (13)C carbonyl-labeled Leu39 of TM-PLB exhibited two peaks in a pure 1-palmitoyl-2-oleoyl-phosphocholine (POPC) bilayer, each due to a different structural conformation of phospholamban as characterized by the corresponding (13)C chemical shift. The addition of a negatively charged phospholipid (1-palmitoyl-2-oleoylphosphatidylglycerol (POPG)) to the POPC bilayer stabilized TM-PLB to an alpha-helical conformation as monitored by an enhancement of the alpha-helical carbonyl (13)C resonance in the corresponding NMR spectrum. (13)C-(15)N REDOR solid-state NMR spectroscopic experiments revealed the distance between the (13)C carbonyl carbon of Leu39 and the (15)N amide nitrogen of Leu42 to be 4.2+/-0.2A indicating an alpha-helical conformation of TM-PLB with a slight deviation from an ideal 3.6 amino acid per turn helix. Finally, the quadrupolar splittings of three (2)H labeled leucines (Leu28, Leu39, and Leu51) incorporated in mechanically aligned DOPE/DOPC bilayers yielded an 11 degrees +/-5 degrees tilt of TM-PLB with respect to the bilayer normal. In addition to elucidating valuable TM-PLB secondary structure information, the solid-state NMR spectroscopic data indicates that the type of phospholipids and the water content play a crucial role in the secondary structure and folding of TM-PLB in a phospholipid bilayer.
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Affiliation(s)
- Ethan S Karp
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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17
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Riedel K, Leppert J, Ohlenschläger O, Görlach M, Ramachandran R. TEDOR with adiabatic inversion pulses: Resonance assignments of 13C/15N labelled RNAs. JOURNAL OF BIOMOLECULAR NMR 2005; 31:49-57. [PMID: 15692738 DOI: 10.1007/s10858-004-6066-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/22/2004] [Indexed: 05/24/2023]
Abstract
We have examined via numerical simulations the performance characteristics of different 15N RF pulse schemes employed in the transferred echo double resonance (TEDOR) experimental protocol for generating 13C-15N dipolar chemical shift correlation spectra of isotopically labelled biological systems at moderate MAS frequencies (omega(r) approximately 10 kHz). With an 15N field strength of approximately 30-35 kHz that is typically available in 5 mm triple resonance MAS NMR probes, it is shown that a robust TEDOR sequence with significant tolerance to experimental imperfections sa as H1 inhomogeneity and resonance offsets can be effectively implemented using adiabatic heteronuclear dipolar recoupling pulse schemes. TEDOR-based 15N-13C and 15N-13C-13C chemical shift correlation experiments were carried out for obtaining 13C and 15N resonance assignments of an RNA composed of 97 (CUG) repeats which has been implicated in the neuromuscular disease myotonic dystrophy.
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Affiliation(s)
- Kerstin Riedel
- Abteilung Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie, 07745 Jena, Germany
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18
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Toraya S, Nishimura K, Naito A. Dynamic structure of vesicle-bound melittin in a variety of lipid chain lengths by solid-state NMR. Biophys J 2004; 87:3323-35. [PMID: 15339796 PMCID: PMC1304800 DOI: 10.1529/biophysj.104.046102] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Accepted: 08/20/2004] [Indexed: 11/18/2022] Open
Abstract
Solid-state 31P- and 13C-NMR spectra were recorded in melittin-lecithin vesicles composed of 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) or 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). Highly ordered magnetic alignments were achieved with the membrane surface parallel to the magnetic field above the gel-to-liquid crystalline phase transition temperature (Tc). Using these magnetically oriented vesicle systems, dynamic structures of melittin bound to the vesicles were investigated by analyzing the 13C anisotropic and isotropic chemical shifts of selectively 13C-labeled carbonyl carbons of melittin under the static and magic-angle spinning conditions. These results indicate that melittin molecules adopt an alpha-helical structure and laterally diffuse to rotate rapidly around the membrane normal with tilt angles of the N-terminal helix being -33 degrees and -36 degrees and those of the C-terminal helix being 21 degrees and 25 degrees for DLPC and DPPC vesicles, respectively. The rotational-echo double-resonance method was used to measure the interatomic distance between [1-13C]Val8 and [15N]Leu13 to further identify the bending alpha-helical structure of melittin to possess the interhelical angles of 126 degrees and 119 degrees in DLPC and DPPC membranes, respectively. These analyses further lead to the conclusion that the alpha-helices of melittin molecules penetrate the hydrophobic cores of the bilayers incompletely as a pseudo-trans-membrane structure and induce fusion and disruption of vesicles.
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Affiliation(s)
- Shuichi Toraya
- Faculty of Engineering, Yokohama National University, Yokohama, Japan
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19
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19F/29Si distance determination and heteronuclear spin counting under fast magic-angle spinning in fluoride-containing octadecasil. CR CHIM 2004. [DOI: 10.1016/j.crci.2003.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Kameda T, Zhao C, Ashida J, Asakura T. Determination of distance of intra-molecular hydrogen bonding in (Ala-Gly)15 with silk I form after removal of the effect of MAS frequency in REDOR experiment. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 160:91-96. [PMID: 12615148 DOI: 10.1016/s1090-7807(02)00131-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
It is important to know the structure of silk I (Bombyx mori silk structure before spinning in the solid state) in order to understand the mechanism of fiber formation at the atomic level. In this study, 15N-dephased, 13C-observe REDOR has been carried out to determine the atomic distance of intra-molecular hydrogen bond between the 13C=O carbon of the 14th Gly residue and the 15N nitrogen of the 17th Ala residue of (AG)(6)A[1-13C]GAG[15N]AG(AG)(6) with silk I form after removal of the effect of MAS frequency on the re-coupling. The distance was determined to be 4.3A, which confirmed the intra-molecular hydrogen bonding formation between these two atomic sites.
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Affiliation(s)
- Tsunenori Kameda
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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21
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Vogt FG, Gibson JM, Mattingly SM, Mueller KT. Determination of Molecular Geometry in Solid-State NMR: Rotational-Echo Double Resonance of Three-Spin Systems. J Phys Chem B 2003. [DOI: 10.1021/jp021686f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Frederick G. Vogt
- Department of Chemistry, The Pennsylvania State University, 152 Davey Laboratory, University Park, Pennsylvania 16802
| | - James M. Gibson
- Department of Chemistry, The Pennsylvania State University, 152 Davey Laboratory, University Park, Pennsylvania 16802
| | - Sue M. Mattingly
- Department of Chemistry, The Pennsylvania State University, 152 Davey Laboratory, University Park, Pennsylvania 16802
| | - Karl T. Mueller
- Department of Chemistry, The Pennsylvania State University, 152 Davey Laboratory, University Park, Pennsylvania 16802
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22
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Nishimura K, Kim S, Zhang L, Cross TA. The closed state of a H+ channel helical bundle combining precise orientational and distance restraints from solid state NMR. Biochemistry 2002; 41:13170-7. [PMID: 12403618 DOI: 10.1021/bi0262799] [Citation(s) in RCA: 185] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An interhelical distance has been precisely measured by REDOR solid-state NMR spectroscopy in the transmembrane tetrameric bundle of M2-TMP, from the M2 proton channel of the influenza A viral coat. The high-resolution structure of the helical backbone has been determined using orientational restraints from uniformly aligned peptide preparations in hydrated dimyristoylphosphatidylcholine bilayers. Here, the distance between (15)N(pi) labeled His37 and (13)C(gamma) labeled Trp41 is determined to be less than 3.9 A. Such a short distance, in combination with the known tilt and rotational orientation of the individual helices, permits not only a determination of which specific side chain pairings give rise to the interaction, but also the side chain torsion angles and restraints for the tetrameric bundle can also be characterized. The resulting proton channel structure is validated in a variety of ways. Both histidine and tryptophan side chains are oriented in toward the pore where they can play a significant functional role. The channel appears to be closed by the proximity of the four indoles consistent with electrophysiology and mutagenesis studies of the intact protein at pH 7.0 and above. The pore maintains its integrity to the N terminal side of the membrane, and at the same time, a cavity is generated that appears adequate for binding amantadine. Finally, the observation of a 2 kHz coupling in the PISEMA spectrum of (15)N(pi)His37 validates the orientation of the His37 side chain based on the observed REDOR distance.
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Affiliation(s)
- Katsuyuki Nishimura
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, USA
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23
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Alberti E, Gilbert SM, Tatham AS, Shewry PR, Gil AM. Study of high molecular weight wheat glutenin subunit 1Dx5 by 13C and 1H solid-state NMR spectroscopy. I. Role of covalent crosslinking. Biopolymers 2002; 67:487-98. [PMID: 12209455 DOI: 10.1002/bip.10168] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This work describes a carbon and proton solid-state NMR study of the hydration of a high molecular weight wheat glutenin subunit, 1Dx5. The effect of the presence of disulfide bonds on the hydration behavior of the subunit is investigated by a comparison of the unalkylated and alkylated forms of the protein. Hydration induces partial plasticization of the protein so that some segments become more mobile than others. The 13C cross-polarization and magic-angle spinning (MAS) spectra of the samples in the dry state and at two hydration levels (approximately 40 and approximately 65% D2O) were used to monitor the protein fraction resisting plasticization (trains). Conversely, 13C single pulse excitation and 1H-MAS experiments were used to gain information on the more plasticized segments (loops). The molecular motion of the two protein dynamic populations was further characterized by 13C T1 and 1H T(1rho), T2, and T1 relaxation times. The results suggest that hydration leads to the formation of a network held by a cooperative action of hydrogen bonded glutamines and some hydrophobic interactions. The looser protein segments are suggested to be glycine- and glutamine-rich segments. The primary structure is therefore expected to significantly determine the proportion of trains and loops in the network. The presence of disulfide bonds was observed to promote easier plasticization of the protein and the formation of a more mobile network, probably involving a higher number of loops and/or larger loops.
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Affiliation(s)
- Enrica Alberti
- Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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24
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Bertani P, Raya J, Hirschinger J. 19F/29Si rotational-echo double-resonance and heteronuclear spin counting under fast magic-angle spinning in fluoride-containing octadecasil. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2002; 22:188-203. [PMID: 12469810 DOI: 10.1006/snmr.2002.0081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
19F/29Si rotational-echo double-resonance (REDOR) and theta-REDOR NMR techniques have been applied under fast magic-angle spinning to a powder sample of fluoride-containing octadecasil. Efficient dipolar recoupling was observed and the effect of finite pulse lengths was found to be negligible using standard radiofrequency field strengths. Moreover, the determined internuclear distance of the 19F-29Si spin pairs formed by the silicons in the D4R units (T-1 site) and the fluoride anions is in very good agreement with previous REDOR and Hartmann-Hahn cross-polarization measurements. Numerical simulation of the REDOR dephasing curves at both the T-1 and T-2 sites considering all fluoride anions in the infinite solid lattice clearly confirm the X-ray crystal structure of octadecasil. Heteronuclear spin-counting theta-REDOR experiments are found to be very useful to obtain direct insight into the local network of dipolar interactions. Indeed, while 19F-29Si pair-like behavior is confirmed at the T-1 site, multiple dipolar interactions are clearly evidenced at the T-2 site.
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Affiliation(s)
- Philippe Bertani
- Institut de Chimie, FRE 2446 CNRS, Université Louis Pasteur, BP 296, 67008 Strasbourg Cedex, France
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25
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Kameda T, Nakazawa Y, Kazuhara J, Yamane T, Asakura T. Determination of intermolecular distance for a model peptide of Bombyx mori silk fibroin, GAGAG, with rotational echo double resonance. Biopolymers 2002; 64:80-5. [PMID: 11979518 DOI: 10.1002/bip.10132] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Rotational echo double resonance NMR spectroscopy is applied for the determination of the distance of intermolecular chains of pentapeptide, GAGAG (G: Gly, A: Ala), a model typical of the crystalline domain in Bombyx mori silk fibroin. 1:4 mixture of G[1-(13)C]AGAG and GAG[(15)N]AG with antiparallel beta-sheet structure was used to determine the distance of intermolecular hydrogen bonding between adjacent molecules within pleated sheet and the (13)C-(15)N interatomic distance was determined to be 4.3 A. On the other hand, 1:4 mixture of GAG[1-(13)C]AG and GAG[(15)N]AG gave information on the interpleated sheet arrangement. When we assumed the same distances between two interpleated sheets, the distance was calculated to be 5.3 A and the angle (15)N-(13)C-(15)N was 180 degrees.
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Affiliation(s)
- Tsunenori Kameda
- Department of Biotechnology, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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26
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Tekely P, Gardiennet C, Potrzebowski MJ, Sebald A, Reichert D, Luz Z. Probing molecular geometry of solids by nuclear magnetic resonance spin exchange at the n=0 rotational-resonance condition. J Chem Phys 2002. [DOI: 10.1063/1.1465416] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Kimura S, Naito A, Tuzi S, Saitô H. Dynamic structure of transmembrane α-helical fragments of bacteriorhodopsin in lipid bilayer characterized by 13C chemical shift tensor and hydrogen bond distance by REDOR NMR. J Mol Struct 2002. [DOI: 10.1016/s0022-2860(01)00720-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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Fukutani A, Naito A, Tuzi S, Saitô H. Determination of principal components and their directions of 15N chemical shift tensor and N–H bond lengths in simple peptides as parameters for characterization of N–H⋯OC hydrogen bonds. J Mol Struct 2002. [DOI: 10.1016/s0022-2860(01)00730-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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29
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Kimura S, Naito A, Saitô H, Ogawa K, Shoji A. Characterization of α-helix structures in polypeptides, revealed by 13CO⋯H–15N hydrogen bond lengths determined by 13C REDOR NMR. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(00)00959-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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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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31
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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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32
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Heise B, Leppert J, Ramachandran R. REDOR with adiabatic dephasing pulses. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 146:181-187. [PMID: 10968971 DOI: 10.1006/jmre.2000.2129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The response of a spin (1/2) ensemble, at thermal equilibrium and experiencing chemical shift anisotropy (CSA), to the application of adiabatic inversion pulses has been studied under magic-angle spinning (MAS). Numerical simulations and experimental studies on such systems, carried out under slow spinning conditions, show that the response to adiabatic inversion pulses has much more favorable characteristics than the response to conventional rectangular pulses. We have also explored the possibilities of employing adiabatic 180 degrees pulses as dephasing pulses in rotational-echo double-resonance (REDOR) experiments. Our results show that it is indeed possible to employ such adiabatic inversion pulses conveniently in REDOR experiments to eliminate resonance offset and H(1) inhomogeneity effects which may arise from the usage of conventional rectangular 180 degrees pulses. Copyright 2000 Academic Press.
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Affiliation(s)
- B Heise
- Abteilung Molekulare Biophysik/NMR Spektroskopie, Institut fur Molekulare Biotechnologie, Jena, 07745, Germany
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33
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Kamihira M, Naito A, Tuzi S, Nosaka AY, Saitô H. Conformational transitions and fibrillation mechanism of human calcitonin as studied by high-resolution solid-state 13C NMR. Protein Sci 2000; 9:867-77. [PMID: 10850796 PMCID: PMC2144639 DOI: 10.1110/ps.9.5.867] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Conformational transitions of human calcitonin (hCT) during fibril formation in the acidic and neutral conditions were investigated by high-resolution solid-state 13C NMR spectroscopy. In aqueous acetic acid solution (pH 3.3), a local alpha-helical form is present around Gly10 whereas a random coil form is dominant as viewed from Phe22, Ala26, and Ala31 in the monomer form on the basis of the 13C chemical shifts. On the other hand, a local beta-sheet form as viewed from Gly10 and Phe22, and both beta-sheet and random coil as viewed from Ala26 and Ala31 were detected in the fibril at pH 3.3. The results indicate that conformational transitions from alpha-helix to beta-sheet, and from random coil to beta-sheet forms occurred in the central and C-terminus regions, respectively, during the fibril formation. The increased 13C resonance intensities of fibrils after a certain delay time suggests that the fibrillation can be explained by a two-step reaction mechanism in which the first step is a homogeneous association to form a nucleus, and the second step is an autocatalytic heterogeneous fibrillation. In contrast to the fibril at pH 3.3, the fibril at pH 7.5 formed a local beta-sheet conformation at the central region and exhibited a random coil at the C-terminus region. Not only a hydrophobic interaction among the amphiphilic alpha-helices, but also an electrostatic interaction between charged side chains can play an important role for the fibril formation at pH 7.5 and 3.3 acting as electrostatically favorable and unfavorable interactions, respectively. These results suggest that hCT fibrils are formed by stacking antiparallel beta-sheets at pH 7.5 and a mixture of antiparallel and parallel beta-sheets at pH 3.3.
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Affiliation(s)
- M Kamihira
- Department of Life Science, Himeji Institute of Technology, Harime Science Garden City, Kamigori, Hyogo, Japan
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34
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Kao HM, Liu H, Jiang JC, Lin SH, Grey CP. Determining the Structure of Trimethylphosphine Bound to the Brønsted Acid Site in Zeolite HY: Double-Resonance NMR and ab Initio Studies. J Phys Chem B 2000. [DOI: 10.1021/jp994199h] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hsien-Ming Kao
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, and Institute of Atomic and Molecular Sciences, Academic Sinica, Taipei, Taiwan, Republic of China
| | - Haiming Liu
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, and Institute of Atomic and Molecular Sciences, Academic Sinica, Taipei, Taiwan, Republic of China
| | - Jyh-Chiang Jiang
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, and Institute of Atomic and Molecular Sciences, Academic Sinica, Taipei, Taiwan, Republic of China
| | - Sheng-Hsien Lin
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, and Institute of Atomic and Molecular Sciences, Academic Sinica, Taipei, Taiwan, Republic of China
| | - Clare P. Grey
- Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, and Institute of Atomic and Molecular Sciences, Academic Sinica, Taipei, Taiwan, Republic of China
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35
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Fyfe CA, Lewis AR, Chézeau JM. A comparison of NMR distance determinations in the solid state by cross polarization, REDOR, and TEDOR techniques. CAN J CHEM 1999. [DOI: 10.1139/v99-199] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Solid-state NMR distance determinations using Hartmann-Hahn cross polarization between spin-1/2 nuclei (19F/29Si) are reported. 19F –> 29Si polarization transfer for the T-1 silicon site in the clathrasil octadecasil shows an oscillatory behaviour as a function of the contact time. These oscillations were observed for non-spinning powder samples and also for different spinning speeds at the various MAS sideband matching conditions. Three analytical functions that allow efficient nonlinear least-square regression analyses of the experimental data to determine the internuclear distances for non-spinning powder samples as well as at the ±1 and ±2 MAS sideband matching conditions are reported. Using these functions, a 19F-29Si distance of 2.53 ± 0.04 Å was determined for the T-1 silicon in octadecasil from fitting of the oscillatory behaviour. This distance is in good agreement with that known from the X-ray structure and the previous 19F/29Si REDOR and TEDOR distance measurements. The advantages and limits of the different dipolar-based NMR techniques for heteronuclear distance determinations are examined and discussed.Key words: cross polarization (CP), NMR distance measurements, octadecasil, 19F-29Si distances, REDOR, TEDOR.
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Nishimura K, Naito A, Tuzi S, Saitô H. Analysis of Dipolar Dephasing Pattern in I−Sn Multispin System for Obtaining the Information of Molecular Packing and Its Application to Crystalline N-Acetyl-Pro-Gly-Phe by REDOR Solid State NMR. J Phys Chem B 1999. [DOI: 10.1021/jp9917502] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katsuyuki Nishimura
- Department of Life Science, Faculty of Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, 678-1297, Japan
| | - Akira Naito
- Department of Life Science, Faculty of Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, 678-1297, Japan
| | - Satoru Tuzi
- Department of Life Science, Faculty of Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, 678-1297, Japan
| | - Hazime Saitô
- Department of Life Science, Faculty of Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, 678-1297, Japan
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Fu R, Cross TA. Solid-state nuclear magnetic resonance investigation of protein and polypeptide structure. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1999; 28:235-68. [PMID: 10410802 DOI: 10.1146/annurev.biophys.28.1.235] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) is rapidly emerging as a successful and important technique for protein and peptide structural elucidation from samples in anisotropic environments. Because of the diversity of nuclei and nuclear spin interactions that can be observed, and because of the broad range of sample conditions that can be studied by solid-state NMR, the potential for gaining structural constraints is great. Structural constraints in the form of orientational, distance, and torsional constraints can be obtained on proteins in crystalline, liquid-crystalline, or amorphous preparations. Great progress in the past few years has been made in developing techniques for obtaining these constraints, and now it has also been clearly demonstrated that these constraints can be assembled into uniquely defined three-dimensional structures at high resolution. Although much progress toward the development of solid-state NMR as a routine structural tool has been documented, the future is even brighter with the continued development of the experiments, of NMR hardware, and of the molecular biological methods for the preparation of labeled samples.
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Affiliation(s)
- R Fu
- Center for Interdisciplinary Magnetic Resonance, Florida State University, Tallahassee 32310, USA.
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Arshava B, Breslav M, Antohi O, Stark RE, Garbow JR, Becker JM, Naider F. Long-distance rotational echo double resonance measurements for the determination of secondary structure and conformational heterogeneity in peptides. SOLID STATE NUCLEAR MAGNETIC RESONANCE 1999; 14:117-136. [PMID: 10437665 DOI: 10.1016/s0926-2040(99)00018-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The utility of rotational echo double resonance (REDOR) NMR spectroscopy for determining the conformations of linear peptides has been examined critically using a series of crystalline and amorphous samples. The focus of the present work was the evaluation of long-distance (> 5 A) interactions using 13C-15N dephasing. Detailed studies of specifically labeled melanostatin and synthetic analogs of the alpha-factor yeast mating hormone show that nitrogen-dephased, carbon-observe REDOR measurements are reliable for distances up to 6.0 A, and that dipolar interactions can be detected for distances up to 7 A. By contrast, nitrogen-observe REDOR gives reliable results only for distances shorter than 5.0 A. To measure distances accurately, REDOR data must be corrected for the effects of natural-abundance spins. These corrections are particularly important for measuring long distances, which are of the greatest value for determining peptide secondary structure. We have developed a spherical shell model for calculating the effect of these background spins. The REDOR studies also indicate that in a lyophilized powder, the tridecapeptide alpha-factor mating pheromone from Saccharomyces cerevisiae (WHWLQLKPGQPMY) probably exists as a distribution of different turn structures around the KPGQ region. This finding revises previous solid-state NMR studies on this peptide, which concluded alpha-factor assumes a distorted type-I beta-turn in the Pro-Gly central region of the molecule [J.R. Garbow, M. Breslav, O. Antohi, F. Naider, Biochemistry, 33 (1994) 10094].
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Affiliation(s)
- B Arshava
- Department of Chemistry, College of Staten Island and the Graduate School of the City University of New York, 10314, USA
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Nishimura K, Naito A, Tuzi S, Saitô H, Hashimoto C, Aida M. Determination of the Three-Dimensional Structure of Crystalline Leu-Enkephalin Dihydrate Based on Six Sets of Accurately Determined Interatomic Distances from 13C-REDOR NMR and the Conformation-Dependent 13C Chemical Shifts. J Phys Chem B 1998. [DOI: 10.1021/jp981683w] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Katsuyuki Nishimura
- Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| | - Akira Naito
- Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| | - Satoru Tuzi
- Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| | - Hazime Saitô
- Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| | - Chikao Hashimoto
- Department of Chemistry, The Jikei University School of Medicine, Kokuryo-cho, Chofu-shi, Tokyo 182-0022, Japan
| | - Misako Aida
- Biophysics Division, National Cancer Center Research Institute, Tukiji 5-chome, Chuo-ku, Tokyo 104-0045, Japan
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Fretigny C. Analysis of the REDOR signal and inversion. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1998; 133:273-280. [PMID: 9716468 DOI: 10.1006/jmre.1998.1462] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
An inversion of the REDOR signal to recover the dipolar couplings has been recently proposed [K. T. Mueller et al., Chem. Phys. Lett. 242, 535 (1995)]: The corresponding integral transform was performed by tabulation of the kernel followed by numerical integration. After explicit determination of the inverse REDOR kernel by the Mellin transform method, we propose an alternative inversion method based on Fourier transforms. Representation of the inverse REDOR kernel by its asymptotic expansion reveals that the inverse REDOR operator is essentially a weighted sum of a cosine transform and of its derivative. Consequently, known properties of Fourier transforms can easily be transposed to the REDOR inversion, allowing for a precise discussion of the value of the method. Moreover, the first term of the asymptotic expansion leading to a derivative of a cosine transform, the REDOR inversion is found to be extremely sensitive to noise, thus considerably reducing the useful part of the theoretical dipolar window. Copyright 1998 Academic Press.
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Kamihira M, Naito A, Nishimura K, Tuzi S, Saitô H. High-Resolution Solid-State 13C and 15N NMR Study on Crystalline Leu- and Met-enkephalins: Distinction of Polymorphs, Backbone Dynamics, and Local Conformational Rearrangements Induced by Dehydration or Freezing of Motions of Bound Solvent Molecules. J Phys Chem B 1998. [DOI: 10.1021/jp970106p] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miya Kamihira
- Laboratory of Molecular Biophysics II, Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, Japan 678-1297
| | - Akira Naito
- Laboratory of Molecular Biophysics II, Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, Japan 678-1297
| | - Katsuyuki Nishimura
- Laboratory of Molecular Biophysics II, Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, Japan 678-1297
| | - Satoru Tuzi
- Laboratory of Molecular Biophysics II, Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, Japan 678-1297
| | - Hazime Saitô
- Laboratory of Molecular Biophysics II, Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, Japan 678-1297
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Saitô H, Tuzi S, Yamaguchi S, Kimura S, Tanio M, Kamihira M, Nishimura K, Naito A. Conformation and dynamics of membrane proteins and biologically active peptides as studied by high-resolution solid-state 13C NMR. J Mol Struct 1998. [DOI: 10.1016/s0022-2860(97)00295-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Polysaccharides and biological systems. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0167-6881(98)80032-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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44
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Quist PO, Förster H, Johnels D. A 6Li−13C REDOR Study of the TMEDA Complex of Solid Fluorenyllithium. J Am Chem Soc 1997. [DOI: 10.1021/ja963726x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Per-Ola Quist
- Contribution from the Departments of Physical Chemistry and Organic Chemistry, Umeå University, S-901 87 Umeå, Sweden, and Bruker Analytische Messtechnik, D-76287 Rheinstetten, Germany
| | - Hans Förster
- Contribution from the Departments of Physical Chemistry and Organic Chemistry, Umeå University, S-901 87 Umeå, Sweden, and Bruker Analytische Messtechnik, D-76287 Rheinstetten, Germany
| | - Dan Johnels
- Contribution from the Departments of Physical Chemistry and Organic Chemistry, Umeå University, S-901 87 Umeå, Sweden, and Bruker Analytische Messtechnik, D-76287 Rheinstetten, Germany
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Gil AM, Masui K, Naito A, Tatham AS, Belton PS, Saitô H. A13C-NMR study on the conformational and dynamical properties of a cereal seed storage protein, C-hordein, and its model peptides. Biopolymers 1997. [DOI: 10.1002/(sici)1097-0282(199703)41:3<289::aid-bip4>3.0.co;2-o] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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46
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Aida M, Naito A, Saitô H. Molecular dynamics simulations of a simple tripeptide, N-acetyl-Pro-Gly-Phe in the crystalline states: distinction of the β-turn Type I from the Type II form. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s0166-1280(96)80032-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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