1
|
Arunachalam V, Sharma K, Mote KR, Madhu PK. Asynchronising five-fold symmetry sequence for better homonuclear polarisation transfer in magic-angle-spinning solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2023; 124:101858. [PMID: 36796278 DOI: 10.1016/j.ssnmr.2023.101858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Recoupling, decoupling, and multidimensional correlation experiments in magic-angle-spinning (MAS) solid-state NMR can be designed by exploiting the symmetry of internal spin interactions. One such scheme, namely, C521, and its supercycled version SPC521, notated as a five-fold symmetry sequence, is widely used for double-quantum dipole-dipole recoupling. Such schemes are generally rotor synchronised by design. We demonstrate an asynchronous implementation of the SPC521 sequence leading to higher double-quantum homonuclear polarisation transfer efficiency compared to the normal synchronous implementation. Rotor-synchronisation is broken in two different ways: lengthening the duration of one of the pulses, denoted as pulse-width variation (PWV), and mismatching the MAS frequency denoted as MAS variation (MASV). The application of this asynchronous sequence is shown on three different samples, namely, U-13C-alanine and 1,4-13C-labelled ammonium phthalate which include 13Cα-13Cβ, 13Cα-13Co, and 13Co-13Co spin systems, and adenosine 5'- triphosphate disodium salt trihydrate (ATP⋅3H2O). We show that the asynchronous version performs better for spin pairs with small dipole-dipole couplings and large chemical-shift anisotropies, for example, 13Co-13Co. Simulations and experiments are shown to corroborate the results.
Collapse
Affiliation(s)
- Vaishali Arunachalam
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| | - Kshama Sharma
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| | - P K Madhu
- Tata Institute of Fundamental Research Hyderabad, 36/P Gopanpally Village, Ranga Reddy District, Hyderabad, 500046, India.
| |
Collapse
|
2
|
Fritzsching KJ, Keeler EG, He C, McDermott AE. Scaled recoupling of chemical shift anisotropies at high magnetic fields under MAS with interspersed C-elements. J Chem Phys 2021; 153:104201. [PMID: 32933302 DOI: 10.1063/5.0020682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The power of chemical shift anisotropy (CSA) measurements for probing structure and dynamics of molecules has been long recognized. NMR pulse sequences that allow measurement of CSA values in an indirect dimension of a protein correlation spectrum have been employed for aliphatic groups, but for practical reasons, carbonyl functional groups have been little studied, despite the fact that carbonyls are expected to give particularly varied and informative CSA values. Specifically, the wide spectral widths of carbonyl tensors make their measurements difficult with typically attainable spectrometer settings. We present here an extended family of experiments that enable the recovery of static CSA lineshapes in an indirect dimension of magic angle spinning (MAS) solid-state NMR experiments, except for various real valued scaling factors. The experiment is suitable for uniformly labeled material, at moderate MAS rates (10 kHz-30 kHz) and at higher magnetic fields (ν0H > 600 MHz). Specifically, the experiments are based on pulse sequence elements from a previous commonly used pulse sequence for CSA measurement, recoupling of chemical shift anisotropy (ROCSA), while modification of scaling factors is achieved by interspersing different blocks of C-elements of the same Cnn 1 cycle. Using experimental conditions similar to the parent ROCSA sequence, a CSA scaling factor between 0 and 0.272 can be obtained, thus allowing a useful practical range of possibilities in experimental conditions for measurement of larger CSA values. Using these blocks, it is also possible to make a constant-time CSA recoupling sequence. The effectiveness of this approach, fROCSA, is shown on model compounds 1-13C-Gly, U-13C,15N-l-His, and microcrystalline U-13C,15N-Ubiquitin.
Collapse
Affiliation(s)
| | - Eric G Keeler
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Chengming He
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Ann E McDermott
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| |
Collapse
|
3
|
Martial B, Raîche-Marcoux G, Lefèvre T, Audet P, Voyer N, Auger M. Structure of a Parkinson’s Disease-Involved α-Synuclein Peptide Is Modulated by Membrane Composition and Physical State. J Phys Chem B 2020; 124:3469-3481. [DOI: 10.1021/acs.jpcb.0c00945] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Benjamin Martial
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Gabrielle Raîche-Marcoux
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Thierry Lefèvre
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Pierre Audet
- Department of Chemistry, Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Normand Voyer
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Michèle Auger
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| |
Collapse
|
4
|
Kobayashi T, Wang Z, Pruski M. Homonuclear dipolar recoupling of arbitrary pairs in multi-spin systems under magic angle spinning: A double-frequency-selective ZQ-SEASHORE experiment. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2019; 101:76-81. [PMID: 31129364 DOI: 10.1016/j.ssnmr.2019.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
We describe a useful method for measuring the internuclear distances within arbitrarily selected pairs of like nuclei in dipolar-coupled multi-spin systems. The method uses a combination of the zero-quantum shift-evolution-assisted selective homonuclear recoupling (ZQ-SEASHORE) technique developed by Hu and Tycko [J. Chem. Phys. 2009, 131, 045101] and double-frequency-selective radio-frequency pulse. The double-frequency-selective pulse inverts polarizations of two spins simultaneously, and thus applications of the method presented here are only limited by the spectral resolution, and not by the number of interacting spins. Our experiments demonstrate the validity of the method and present analytical expressions for the dephasing curve.
Collapse
Affiliation(s)
- Takeshi Kobayashi
- U.S. DOE Ames Laboratory, Iowa State University, Ames, IA, 50011-3020, United States.
| | - Zhuoran Wang
- U.S. DOE Ames Laboratory, Iowa State University, Ames, IA, 50011-3020, United States; Department of Chemistry, Iowa State University, Ames, IA, 50011-3020, United States
| | - Marek Pruski
- U.S. DOE Ames Laboratory, Iowa State University, Ames, IA, 50011-3020, United States; Department of Chemistry, Iowa State University, Ames, IA, 50011-3020, United States.
| |
Collapse
|
5
|
Wilson BW, Parker AA, Gullion T. Determining the relative orientation between the chemical shift anisotropy and heteronuclear dipolar tensors in static solids by SEDOR NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2016; 79:1-5. [PMID: 27690305 DOI: 10.1016/j.ssnmr.2016.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/07/2016] [Accepted: 09/18/2016] [Indexed: 06/06/2023]
Abstract
The measurement of the dipolar interaction between two spins provides the distance between nuclei. A better structural picture emerges when the distance is combined with the orientation of the internuclear vector in the principal axis system of the chemical shift anisotropy tensor. The SEDOR experiment is used on a static sample of alanine to show that the orientation of the vector connecting the nitrogen and carboxylate carbon nuclei can be accurately determined in the CSA PAS of the 13C carboxylate spin.
Collapse
Affiliation(s)
- Brendan W Wilson
- Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Arlo A Parker
- Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Terry Gullion
- Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States.
| |
Collapse
|
6
|
Ren J, Eckert H. Measurement of homonuclear magnetic dipole-dipole interactions in multiple 1/2-spin systems using constant-time DQ-DRENAR NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 260:46-53. [PMID: 26397219 DOI: 10.1016/j.jmr.2015.08.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/22/2015] [Accepted: 08/28/2015] [Indexed: 06/05/2023]
Abstract
A new pulse sequence entitled DQ-DRENAR (Double-Quantum based Dipolar Recoupling Effects Nuclear Alignment Reduction) was recently described for the quantitative measurement of magnetic dipole-dipole interactions in homonuclear spin-1/2 systems involving multiple nuclei. As described in the present manuscript, the efficiency and performance of this sequence can be significantly improved, if the measurement is done in the constant-time mode. We describe both the theoretical analysis of this method and its experimental validation of a number of crystalline model compounds, considering both symmetry-based and back-to-back (BABA) DQ-coherence excitation schemes. Based on the combination of theoretical analysis and experimental results we discuss the effect of experimental parameters such as the chemical shift anisotropy (CSA), the spinning rate, and the radio frequency field inhomogeneity upon its performance. Our results indicate that constant-time (CT-) DRENAR is a method of high efficiency and accuracy for compounds with multiple homonuclear spin systems with particular promise for the analysis of stronger-coupled and short T2 spin systems.
Collapse
Affiliation(s)
- Jinjun Ren
- Key Laboratory of Materials for High-Power Laser, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800, China.
| | - Hellmut Eckert
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstr. 30, D-48149 Münster, Germany; Instituto de Física de São Carlos, Universidade de São Paulo (USP), C.P. 369, CEP 13560-970, São Carlos, SP, Brazil.
| |
Collapse
|
7
|
Ren J, Eckert H. DQ-DRENAR with back-to-back (BABA) excitation: Measuring homonuclear dipole-dipole interactions in multiple spin-1/2 systems. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2015; 71:11-18. [PMID: 26483328 DOI: 10.1016/j.ssnmr.2015.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A new pulse sequence entitled DQ-DRENAR, (Double-Quantum based Dipolar Recoupling Effects Nuclear Alignment Reduction) was recently described for the quantitative measurement of magnetic dipole-dipole interactions in homonuclear spin-1/2 systems involving multiple nuclei. The double quantum coherences were created via a windowless symmetry-based pulse sequence (POST-C7). The present contribution evaluates the performance of the "Back-to-Back" excitation pulse scheme BABA-xy16 in such DRENAR experiments. Using SIMPSON simulations, special attention is given to finite pulse length effects, dipolar truncation, and chemical shift anisotropy interference. Experimental results on model compounds demonstrate good stability up to long mixing times (>10 ms) as well as high accuracy. As its dipolar coupling efficiency is relatively high (the dipolar coupling scaling factor is 4.24 times as high as that of POST-C7), DQ-DRENAR-BABA-xy16 is most appropriate for the measurement of relatively weak dipolar coupling strengths (<400 Hz). Different from POST-C7, for which the spinning rate is limited to 1/7 of the nutation frequency, DQ-DRENAR-BABA-xy16 experiments can take full advantage of ultrafast MAS experiments.
Collapse
Affiliation(s)
- Jinjun Ren
- Key Laboratory of Materials for High-Power Laser, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800, China.
| | - Hellmut Eckert
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, Corrensstr. 30, D-48149 Münster, Germany; Instituto de Física de São Carlos, Universidade de São Paulo (USP), C.P. 369, CEP 13560-970, São Carlos, SP, Brazil.
| |
Collapse
|
8
|
Liang C, Ni R, Smith JE, Childers WS, Mehta AK, Lynn DG. Kinetic Intermediates in Amyloid Assembly. J Am Chem Soc 2014; 136:15146-9. [DOI: 10.1021/ja508621b] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Chen Liang
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Rong Ni
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Jillian E. Smith
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - W. Seth Childers
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - Anil K. Mehta
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| | - David G. Lynn
- Departments of Chemistry
and Biology, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
9
|
Goobes G. Past and Future Solid-State NMR Spectroscopy Studies at the Convergence Point between Biology and Materials Research. Isr J Chem 2014. [DOI: 10.1002/ijch.201300113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
10
|
Mehta AK, Rosen RF, Childers WS, Gehman JD, Walker LC, Lynn DG. Context dependence of protein misfolding and structural strains in neurodegenerative diseases. Biopolymers 2013; 100:722-30. [PMID: 23893572 PMCID: PMC3979318 DOI: 10.1002/bip.22283] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 04/19/2013] [Accepted: 05/07/2013] [Indexed: 01/28/2023]
Abstract
Vast arrays of structural forms are accessible to simple amyloid peptides and environmental conditions can direct assembly into single phases. These insights are now being applied to the aggregation of the Aβ peptide of Alzheimer's disease and the identification of causative phases. We extend use of the imaging agent Pittsburgh compound B to discriminate among Aβ phases and begin to define conditions of relevance to the disease state. Also, we specifically highlight the development of methods for defining the structures of these more complex phases.
Collapse
Affiliation(s)
- Anil K. Mehta
- Departments of Chemistry and Biology, Alzheimer’s Disease Research Center, Emory University, Atlanta, Georgia 30322, USA
| | - Rebecca F. Rosen
- Yerkes National Primate Research Center, Center for Neurodegenerative Disease, Emory University, Atlanta, Georgia 30322, USA
| | - W. Seth Childers
- Departments of Chemistry and Biology, Alzheimer’s Disease Research Center, Emory University, Atlanta, Georgia 30322, USA
| | - John D. Gehman
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, Vic. 3010, Australia
| | - Lary C. Walker
- Yerkes National Primate Research Center, Center for Neurodegenerative Disease, Emory University, Atlanta, Georgia 30322, USA
- Department of Neurology, Emory University, Atlanta, Georgia 30322, USA
| | - David G. Lynn
- Departments of Chemistry and Biology, Alzheimer’s Disease Research Center, Emory University, Atlanta, Georgia 30322, USA
| |
Collapse
|
11
|
Morgan DM, Lynn DG, Lakdawala AS, Snyder JP, Liotta DC. Amyloid Structure: Models and Theoretical Considerations in Fibrous Aggregates. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200200072] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
12
|
Ren J, Eckert H. DQ-DRENAR: A new NMR technique to measure site-resolved magnetic dipole-dipole interactions in multispin-1/2 systems: Theory and validation on crystalline phosphates. J Chem Phys 2013; 138:164201. [DOI: 10.1063/1.4801634] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
13
|
Ananthanarayanan A, van Wüllen L. Achieving high resolution dipolar NMR information without fast sample spinning: combining magic angle turning with dipolar based NMR methods. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2013; 49-50:42-46. [PMID: 23290723 DOI: 10.1016/j.ssnmr.2012.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 11/22/2012] [Accepted: 11/23/2012] [Indexed: 06/01/2023]
Abstract
In this article we present a new approach to high resolution NMR combining the concepts of magic angle hopping (MAH)/magic angle turning (MAT) and dipolar based NMR methods such as SEDOR, REDOR or cross polarization (CP). Employing aluminophosphates as model systems we demonstrate that No MAS needed (NOMAS) is capable of supplying high resolution dipolar information without the need of fast MAS.
Collapse
Affiliation(s)
- A Ananthanarayanan
- Institute of Physics, Augsburg University, Universitätsstr. 1, D-86159 Augsburg, Germany
| | | |
Collapse
|
14
|
Mou Y, Tsai TWT, Chan JCC. Constant time tensor correlation experiments by non-gamma-encoded recoupling pulse sequences. J Chem Phys 2012; 137:164201. [PMID: 23126702 DOI: 10.1063/1.4757957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Constant-time tensor correlation under magic-angle spinning conditions is an important technique in solid-state nuclear magnetic resonance spectroscopy for the measurements of backbone or side-chain torsion angles of polypeptides and proteins. We introduce a general method for the design of constant-time tensor correlation experiments under magic-angle spinning. Our method requires that the amplitude of the average Hamiltonian must depend on all the three Euler angles bringing the principal axis system to the rotor-fixed frame, which is commonly referred to as non-gamma encoding. We abbreviate this novel approach as COrrelation of Non-Gamma-Encoded Experiment (CONGEE), which exploits the orientation-dependence of non-gamma-encoded sequences with respect to the magic-angle rotation axis. By manipulating the relative orientation of the average Hamiltonians created by two non-gamma-encoded sequences, one can obtain a modulation of the detected signal, from which the structural information can be extracted when the tensor orientations relative to the molecular frame are known. CONGEE has a prominent feature that the number of rf pulses and the total pulse sequence duration can be maintained to be constant so that for torsion angle determination the effects of systematic errors owing to the experimental imperfections and/or T(2) effects could be minimized. As a proof of concept, we illustrate the utility of CONGEE in the correlation between the C' chemical shift tensor and the C(α)-H(α) dipolar tensor for the backbone psi angle determination. In addition to a detailed theoretical analysis, numerical simulations and experiments measured for [U-(13)C, (15)N]-L-alanine and N-acetyl-[U-(13)C, (15)N]-D,L-valine are used to validate our approach at a spinning frequency of 20 kHz.
Collapse
Affiliation(s)
- Yun Mou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, Taiwan
| | | | | |
Collapse
|
15
|
Mananga ES, Charpentier T. Introduction of the Floquet-Magnus expansion in solid-state nuclear magnetic resonance spectroscopy. J Chem Phys 2011; 135:044109. [DOI: 10.1063/1.3610943] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
16
|
Chan JCC. Solid-state NMR techniques for the structural determination of amyloid fibrils. Top Curr Chem (Cham) 2011; 306:47-88. [PMID: 21630137 DOI: 10.1007/128_2011_154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This review discusses the solid-state NMR techniques developed for the study of amyloid fibrils. Literature up to the end of 2010 has been surveyed and the materials are organized according to five categories, viz. homonuclear dipolar recoupling and polarization transfer via J-coupling, heteronuclear dipolar recoupling, correlation spectroscopy, recoupling of chemical shift anisotropy, and tensor correlation. Our emphasis is on the NMR techniques and their practical aspects. The biological implications of the results obtained for amyloid fibrils are only briefly discussed. Our main objective is to showcase the power of NMR in the study of biological unoriented solids.
Collapse
Affiliation(s)
- Jerry C C Chan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
17
|
Leskes M, Madhu PK, Vega S. Floquet theory in solid-state nuclear magnetic resonance. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:345-380. [PMID: 20920756 DOI: 10.1016/j.pnmrs.2010.06.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 06/11/2010] [Indexed: 05/29/2023]
Affiliation(s)
- Michal Leskes
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel.
| | | | | |
Collapse
|
18
|
Caporini MA, Bajaj VS, Veshtort M, Fitzpatrick A, MacPhee CE, Vendruscolo M, Dobson CM, Griffin RG. Accurate determination of interstrand distances and alignment in amyloid fibrils by magic angle spinning NMR. J Phys Chem B 2010; 114:13555-61. [PMID: 20925357 PMCID: PMC2959142 DOI: 10.1021/jp106675h] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid fibrils are structurally ordered aggregates of proteins whose formation is associated with many neurodegenerative and other diseases. For that reason, their high-resolution structures are of considerable interest and have been studied using a wide range of techniques, notably electron microscopy, X-ray diffraction, and magic angle spinning (MAS) NMR. Because of the excellent resolution in the spectra, MAS NMR is uniquely capable of delivering site-specific, atomic resolution information about all levels of amyloid structure: (1) the monomer, which packs into several (2) protofilaments that in turn associate to form a (3) fibril. Building upon our high-resolution structure of the monomer of an amyloid-forming peptide from transthyretin (TTR(105-115)), we introduce single 1-(13)C labeled amino acids at seven different sites in the peptide and measure intermolecular carbonyl-carbonyl distances with an accuracy of ~0.11 A. Our results conclusively establish a parallel, in register, topology for the packing of this peptide into a β-sheet and provide constraints essential for the determination of an atomic resolution structure of the fibril. Furthermore, the approach we employ, based on a combination of a double-quantum filtered variant of the DRAWS recoupling sequence and multispin numerical simulations in SPINEVOLUTION, is general and should be applicable to a wide range of systems.
Collapse
Affiliation(s)
- Marc A Caporini
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Childers W, Mehta A, Ni R, Taylor J, Lynn D. Peptides Organized as Bilayer Membranes. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000212] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
20
|
Childers W, Mehta A, Ni R, Taylor J, Lynn D. Peptides Organized as Bilayer Membranes. Angew Chem Int Ed Engl 2010; 49:4104-7. [DOI: 10.1002/anie.201000212] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
21
|
McNeill SA, Gor’kov PL, Shetty K, Brey WW, Long JR. A low-E magic angle spinning probe for biological solid state NMR at 750 MHz. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 197:135-44. [PMID: 19138870 PMCID: PMC2659328 DOI: 10.1016/j.jmr.2008.12.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2008] [Revised: 12/02/2008] [Accepted: 12/05/2008] [Indexed: 05/02/2023]
Abstract
Crossed-coil NMR probes are a useful tool for reducing sample heating for biological solid state NMR. In a crossed-coil probe, the higher frequency (1)H field, which is the primary source of sample heating in conventional probes, is produced by a separate low-inductance resonator. Because a smaller driving voltage is required, the electric field across the sample and the resultant heating is reduced. In this work we describe the development of a magic angle spinning (MAS) solid state NMR probe utilizing a dual resonator. This dual resonator approach, referred to as "low-E," was originally developed to reduce heating in samples of mechanically aligned membranes. The study of inherently dilute systems, such as proteins in lipid bilayers, via MAS techniques requires large sample volumes at high field to obtain spectra with adequate signal-to-noise ratio under physiologically relevant conditions. With the low-E approach, we are able to obtain homogeneous and sufficiently strong radiofrequency fields for both (1)H and (13)C frequencies in a 4mm probe with a (1)H frequency of 750 MHz. The performance of the probe using windowless dipolar recoupling sequences is demonstrated on model compounds as well as membrane-embedded peptides.
Collapse
Affiliation(s)
- Seth A. McNeill
- Department of Electrical and Computer Engineering, University of Florida, 32611
| | | | - Kiran Shetty
- National High Magnetic Field Laboratory, Tallahassee, FL 32310
| | - William W. Brey
- National High Magnetic Field Laboratory, Tallahassee, FL 32310
| | - Joanna R. Long
- Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
- Correspondence: telephone :(352)846-1506 fax :(352)392-3422
| |
Collapse
|
22
|
Liu P, Ni R, Mehta AK, Childers WS, Lakdawala A, Pingali SV, Thiyagarajan P, Lynn DG. Nucleobase-directed amyloid nanotube assembly. J Am Chem Soc 2009; 130:16867-9. [PMID: 19053426 DOI: 10.1021/ja807425h] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytosine nucleobases were successfully incorporated into the side chain of the self-assembling amyloid peptide fragment HHQALVFFA to give ccAQLVFFA. At a pH range of 3-4, where cytosine is expected to be partially protonated, small-angle X-ray scattering analyses revealed the nucleobase peptide assembles to be well-defined nanotubes with an outer diameter of 24.8 nm and wall thicknesses of 3.3 nm. FT-IR and X-ray diffraction confirmed beta-sheet-rich assembly with the characteristic cross-beta architecture of amyloid. The beta-sheet registry, determined by measuring (13)CO-(13)CO backbone distances with solid-state NMR and linear dichroism, placed the cytosine bases roughly perpendicular to the nanotube axis, resulting in a model where the complementary interactions between the cytosine bases increases beta-sheet stacking to give the nanotube architecture. These scaffolds then extend the templates used to encode biological information beyond the nucleic acid duplexes and into covalent networks whose self-assembly is still defined by a precise complementarity of the side-chain registry.
Collapse
Affiliation(s)
- Peng Liu
- Center for Fundamental and Applied Molecular Evolution, Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Mills FD, Antharam VC, Ganesh OK, Elliott DW, McNeill SA, Long JR. The helical structure of surfactant peptide KL4 when bound to POPC: POPG lipid vesicles. Biochemistry 2008; 47:8292-300. [PMID: 18636713 PMCID: PMC2629594 DOI: 10.1021/bi702551c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
KL 4 is a 21-residue peptide employed as a functional mimic of lung surfactant protein B, which successfully lowers surface tension in the alveoli. A mechanistic understanding of how KL 4 affects lipid properties has proven elusive as the secondary structure of KL 4 in lipid preparations has not been determined at high resolution. The sequence of KL 4 is based on the C-terminus of SP-B, a naturally occurring helical protein that binds to lipid interfaces. The spacing of the lysine residues in KL 4 precludes the formation of a canonical amphipathic alpha-helix; qualitative measurements using Raman, CD, and FTIR spectroscopies have given conflicting results as to the secondary structure of the peptide as well as its orientation in the lipid environment. Here, we present a structural model of KL 4 bound to lipid bilayers based on solid state NMR data. Double-quantum correlation experiments employing (13)C-enriched peptides were used to quantitatively determine the backbone torsion angles in KL 4 at several positions. These measurements, coupled with CD experiments, verify the helical nature of KL 4 when bound to lipids, with (phi, psi) angles that differ substantially from common values for alpha-helices of (-60, -45). The average torsion angles found for KL 4 bound to POPC:POPG lipid vesicles are (-105, -30); this deviation from ideal alpha-helical structure allows KL 4 to form an amphipathic helix at the lipid interface.
Collapse
Affiliation(s)
- Frank D Mills
- Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Box 100245, Gainesville, Florida 32610-0245, USA
| | | | | | | | | | | |
Collapse
|
24
|
Ash JT, Trease NM, Grandinetti PJ. Separating Chemical Shift and Quadrupolar Anisotropies via Multiple-Quantum NMR Spectroscopy. J Am Chem Soc 2008; 130:10858-9. [PMID: 18652455 DOI: 10.1021/ja802865x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jason T. Ash
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210-1173
| | - Nicole M. Trease
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210-1173
| | - Philip J. Grandinetti
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210-1173
| |
Collapse
|
25
|
Mehta MA, Eddy MT, McNeill SA, Mills FD, Long JR. Determination of Peptide Backbone Torsion Angles Using Double-Quantum Dipolar Recoupling Solid-State NMR Spectroscopy. J Am Chem Soc 2008; 130:2202-12. [DOI: 10.1021/ja074244w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Manish A. Mehta
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Matthew T. Eddy
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Seth A. McNeill
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Frank D. Mills
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| | - Joanna R. Long
- Department of Chemistry and Biochemistry, 119 Woodland Street, Oberlin College, Oberlin, Ohio 44074, and Department of Biochemistry and Molecular Biology and McKnight Brain Institute, University of Florida, Gainesville, Florida 32610
| |
Collapse
|
26
|
A high resolution structure of the putative hinge region in M2 channel-lining segments of the nicotinic acetylcholine receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2961-70. [DOI: 10.1016/j.bbamem.2007.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Revised: 10/12/2007] [Accepted: 10/15/2007] [Indexed: 02/07/2023]
|
27
|
McNeill SA, Gor'kov PL, Struppe J, Brey WW, Long JR. Optimizing ssNMR experiments for dilute proteins in heterogeneous mixtures at high magnetic fields. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S209-20. [PMID: 18157844 DOI: 10.1002/mrc.2146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Solid-state NMR spectroscopy at high magnetic fields is proving to be an effective technique in structural biology, particularly for proteins which are not amenable to traditional X-ray and solution NMR approaches. Several parameters can be selected to provide optimal sensitivity, improve sample stability, and ensure biological relevance for ssNMR measurements on protein samples. These include selection of sample conditions, NMR probe design, and design of pulse experiments. Here, we demonstrate and evaluate several engineering and experimental approaches for pursuing measurements on dilute proteins in heterogeneous mixtures.
Collapse
Affiliation(s)
- Seth A McNeill
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA
| | | | | | | | | |
Collapse
|
28
|
Zheng Z, Qiang W, Weliky DP. Investigation of finite-pulse radiofrequency-driven recoupling methods for measurement of intercarbonyl distances in polycrystalline and membrane-associated HIV fusion peptide samples. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2007; 45 Suppl 1:S247-S260. [PMID: 18157840 DOI: 10.1002/mrc.2160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Two finite-pulse radiofrequency-driven recoupling (RFDR) methods were compared and applied to the measurement of 3-6 Å (13)CO-(13)CO distances in polycrystalline and membrane-associated HIV fusion peptide (HFP) samples. The RFDR methods were based on π pulses and were relatively straightforward to implement and insensitive to pulse imperfections. The two tested methods were: (i) constant-time double-quantum buildup with finite pulses (fpCTDQBU) for which the pulse sequence maintained a constant transverse relaxation period while allowing a variable period of dipolar dephasing; and (ii) constant-time finite-pulse rf-driven recoupling (fpRFDR-CT) for which the duration of transverse relaxation increased with increasing dephasing period. The fpRFDR-CT method yielded higher signal-to-noise and an accurate determination of a ~5 Å intercarbonyl distance was made in a crystalline peptide which had T(2) ≈ 55 ms. In some contrast, the HFP samples had T(2) ≈ 15 ms and the fpRFDR-CT data were dominated by transverse relaxation. Examination of the fpCTDQBU sequence showed: (i) the most rapid signal buildup was obtained with application of one (13) C π pulse per rotor period rather than one (13)C π pulse per multiple rotor periods and (ii) the data were insensitive to ~15 ppm transmitter offset and to ~5° variation of π pulse nutation angle. For HFP samples which were (13)CO labeled at a single residue, analyses of the fpCTDQBU data were interpreted with a model of mixed parallel and antiparallel β-strand arrangements in the N-terminal region of HFP and loss of parallel β-sheet structure in the C-terminal region of HFP.
Collapse
Affiliation(s)
- Zhaoxiong Zheng
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | | | | |
Collapse
|
29
|
Ying J, Grishaev A, Bryce DL, Bax A. Chemical shift tensors of protonated base carbons in helical RNA and DNA from NMR relaxation and liquid crystal measurements. J Am Chem Soc 2007; 128:11443-54. [PMID: 16939267 DOI: 10.1021/ja061984g] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Knowledge of (13)C chemical shift anisotropy (CSA) tensors in nucleotide bases is important for interpretation of NMR relaxation data in terms of local dynamic properties of nucleic acids and for analysis of residual chemical shift anisotropy (RCSA) resulting from weak alignment. CSA tensors for protonated nucleic acid base carbons have been derived from measurements on a uniformly (13)C-enriched helical A-form RNA segment and a helical B-form DNA dodecamer at natural (13)C abundance. The magnitudes of the derived CSA principal values are tightly restricted by the magnetic field dependencies of the (13)C transverse relaxation rates, whereas the tensor orientation and asymmetry follow from quantitative measurements of interference between (13)C-{(1)H} dipolar and (13)C CSA relaxation mechanisms. Changes in the chemical shift between the isotropic and aligned states, Deltadelta, complement these measurements and permit cross-validation. The CSA tensors are determined from the experimental Deltadelta values and relaxation rates, under the assumption that the CSA tensor of any specific carbon in a given type of base is independent of the base position in either the RNA or DNA helix. However, the experimental data indicate that for pyrimidine C(6) carbons in A-form RNA the CSA magnitude is considerably larger than in B-form DNA. This result is supported by quantum chemical calculations and is attributed in part to the close proximity between intranucleotide C(6)H and O(5)' atoms in RNA. The magnitudes of the measured CSA tensors, on average, agree better with previous solid-state NMR results obtained on powdered nucleosides than with prior results from quantum chemical calculations on isolated bases, which depend rather strongly on the level of theory at which the calculations are carried out. In contrast, previously computed orientations of the chemical shift tensors agree well with the present experimental results and exhibit less dependence on the level of theory at which the computations are performed.
Collapse
Affiliation(s)
- Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | |
Collapse
|
30
|
Czinki E, Császár AG, Magyarfalvi G, Schreiner PR, Allen WD. Secondary Structures of Peptides and Proteins via NMR Chemical-Shielding Anisotropy (CSA) Parameters. J Am Chem Soc 2007; 129:1568-77. [PMID: 17284001 DOI: 10.1021/ja065461k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Complete nuclear magnetic resonance (NMR) chemical-shielding tensors, sigma, have been computed at different levels of density-functional theory (DFT), within the gauge-including atomic orbital (GIAO) formalism, for the atoms of the peptide model For-L-Ala-NH2 as a function of the backbone dihedral angles phi and psi by employing a dense grid of 10 degrees. A complete set of rigorously orthogonal symmetric tensor invariants, {sigma iso, rho, tau}, is introduced, where sigma iso is the usual isotropic chemical shielding, while the newly introduced rho and tau parameters describe the magnitude and the orientation/shape of the chemical-shielding anisotropy (CSA), respectively. The set {sigma iso, rho, tau} is unaffected by unitary transformations of the symmetric part of the shielding tensor. The mathematically and physically motivated {rho, tau} anisotropy pair is easily connected to more traditional shielding anisotropy measures, like span (Omega) and skew (kappa). The effectiveness of the different partitions of the CSA information in predicting conformations of peptides and proteins has been tested throughout the Ramachandran space by generating theoretical NMR anisotropy surfaces for our For-L-Ala-NH2 model. The CSA surfaces, including Omega(phi, psi), kappa(phi, psi), rho(phi, psi), and tau(phi, psi) are highly structured. Individually, none of these surfaces is able to distinguish unequivocally between the alpha-helix and beta-strand secondary structural types of proteins. However, two- and three-dimensional correlated plots, including Omega versus kappa, rho versus tau, and sigma iso versus rho versus tau, especially for 13Calpha, have considerable promise in distinguishing among all four of the major secondary structural elements.
Collapse
Affiliation(s)
- Eszter Czinki
- Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, H-1518 Budapest 112, P.O. Box 32, Hungary
| | | | | | | | | |
Collapse
|
31
|
Kristiansen PE, Carravetta M, van Beek JD, Lai WC, Levitt MH. Theory and applications of supercycled symmetry-based recoupling sequences in solid-state nuclear magnetic resonance. J Chem Phys 2006; 124:234510. [PMID: 16821932 DOI: 10.1063/1.2205857] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present the theoretical principles of supercycled symmetry-based recoupling sequences in solid-state magic-angle-spinning NMR. We discuss the construction procedure of the SR26 pulse sequence, which is a particularly robust sequence for double-quantum homonuclear dipole-dipole recoupling. The supercycle removes destructive higher-order average Hamiltonian terms and renders the sequence robust over long time intervals. We demonstrate applications of the SR26 sequence to double-quantum spectroscopy, homonuclear spin counting, and determination of the relative orientations of chemical shift anisotropy tensors.
Collapse
Affiliation(s)
- Per Eugen Kristiansen
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041-Blindern, 0316 Oslo, Norway
| | | | | | | | | |
Collapse
|
32
|
Riedel K, Herbst C, Leppert J, Ohlenschläger O, Görlach M, Ramachandran R. Broadband homonuclear double-quantum NMR/filtering via zero-quantum dipolar recoupling in rotating solids. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.04.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
33
|
Raghunathan V, Gibson JM, Goobes G, Popham JM, Louie EA, Stayton PS, Drobny GP. Homonuclear and Heteronuclear NMR Studies of a Statherin Fragment Bound to Hydroxyapatite Crystals. J Phys Chem B 2006; 110:9324-32. [PMID: 16671751 DOI: 10.1021/jp056644g] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acidic proteins found in mineralized tissues act as nature's crystal engineers, where they play a key role in promoting or inhibiting the growth of minerals such as hydroxyapatite (HAP), Ca10(PO4)6(OH)2, the main mineral component of bone and teeth. Key to understanding the structural basis of protein-crystal recognition and protein control of hard tissue growth is the nature of interactions between the protein side chains and the crystal surface. In an earlier work we have measured the proximity of the lysine (K6) side chain in an SN-15 peptide fragment of the salivary protein statherin adsorbed to the Phosphorus-rich surface of HAP using solid-state NMR recoupling experiments. 15N{31P} rotational echo double resonance (REDOR) NMR data on the side-chain nitrogen in K6 gave rise to three different models of protein-surface interaction to explain the experimental data acquired. In this work we extend the analysis of the REDOR data by examining the contribution of interactions between surface phosphorus atoms to the observed 15N REDOR decay. We performed 31P-31P recoupling experiments in HAP and (NH4)2HPO4 (DHP) to explore the nature of dipolar coupled 31P spin networks. These studies indicate that extensive networks of dipolar coupled 31P spins can be represented as stronger effective dipolar couplings, the existence of which must be included in the analysis of REDOR data. We carried out 15N{31P} REDOR in the case of DHP to determine how the size of the dephasing spin network influences the interpretation of the REDOR data. Although use of an extended 31P coupled spin network simulates the REDOR data well, a simplified 31P dephasing system composed of two spins with a larger dipolar coupling also simulates the REDOR data and only perturbs the heteronuclear couplings very slightly. The 31P-31P dipolar couplings between phosphorus nuclei in HAP can be replaced by an effective dipolar interaction of 600 Hz between two 31P spins. We incorporated this coupling and applied the above approach to reanalyze the 15N{31P} REDOR of the lysine side chain approaching the HAP surface and have refined the binding models proposed earlier. We obtain 15N-31P distances between 3.3 and 5 A from these models that are indicative of the possibility of a lysine-phosphate hydrogen bond.
Collapse
Affiliation(s)
- Vinodhkumar Raghunathan
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | | | | | | | | | | | | |
Collapse
|
34
|
Bower PV, Louie EA, Long JR, Stayton PS, Drobny GP. Solid-state NMR structural studies of peptides immobilized on gold nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:3002-3007. [PMID: 15779977 DOI: 10.1021/la040092w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In this paper we describe solid-state NMR experiments that provide information on the structures of surface-immobilized peptides. The peptides are covalently bound to alkanethiolates that are self-assembled as monolayers on colloidal gold nanoparticles. The secondary structure of the immobilized peptides was characterized by quantifying the Ramachandran angles phi and psi. These angles were determined in turn from distances between backbone carbonyl 13C spins, measured with the double-quantum filtered dipolar recoupling with a windowless sequence experiment, and by determination of the mutual orientation of chemical shift anisotropy tensors of 13C carbonyl spins on adjacent peptide planes, obtained from the double-quantum cross-polarization magic-angle spinning spectrum. It was found that peptides composed of periodic sequences of leucines and lysines were bound along the length of the peptide sequence and displayed a tight alpha-helical secondary structure on the gold nanoparticles. These results are compared to similar studies of peptides immobilized on hydrophobic surfaces.
Collapse
Affiliation(s)
- P V Bower
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | | | | | | | | |
Collapse
|
35
|
Kristiansen PE, Carravetta M, Lai WC, Levitt MH. A robust pulse sequence for the determination of small homonuclear dipolar couplings in magic-angle spinning NMR. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.03.075] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
36
|
Karlsson T, Popham JM, Long JR, Oyler N, Drobny GP. A study of homonuclear dipolar recoupling pulse sequences in solid-state nuclear magnetic resonance. J Am Chem Soc 2003; 125:7394-407. [PMID: 12797814 DOI: 10.1021/ja0294360] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dipolar recoupling pulse sequences are of great importance in magic angle spinning solid-state NMR. Recoupling sequences are used for excitation of double-quantum coherence, which, in turn, is employed in experiments to estimate internuclear distances and molecular torsion angles. Much effort is spent on the design of recoupling sequences that are able to produce double-quantum coherence with high efficiency in demanding spin systems, i.e., spin systems with small dipole-dipole couplings and large chemical-shift anisotropies (CSAs). The sequence should perform robustly under a variety of experimental conditions. This paper presents experiments and computer calculations that extend the theory of double-quantum coherence preparation from the strong coupling/small CSA limit to the weak coupling limit. The performance of several popular dipole-dipole recoupling sequences-DRAWS, POST-C7, SPC-5, R1, and R2-are compared. It is found that the optimum performance for several of these sequences, in the weak coupling/large CSA limit, varies dramatically, with respect to the sample spinning speed, the magnitude and orientation of the CSAs, and the magnitude of dipole-dipole couplings. It is found that the efficiency of double-quantum coherence preparation by gamma-encoded sequences departs from the predictions of first-order theory. The discussion is supported by density-matrix calculations.
Collapse
Affiliation(s)
- T Karlsson
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | | | | | | | | |
Collapse
|
37
|
Carravetta M, Schmedt auf der Günne J, Levitt MH. Enhanced triple-quantum excitation in 13C magic-angle spinning NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 162:443-453. [PMID: 12810030 DOI: 10.1016/s1090-7807(03)00059-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We describe a new method for exciting triple-quantum coherences in 13C-labelled powder samples under MAS. The proposed method combines selective double-quantum excitation with rotational resonance and frequency-selective composite pulses. The spin dynamics of this new method are described theoretically. Numerical calculations of the spin dynamics are compared to experimental results on fully 13C-labelled L-alanine. The observed triple-quantum filtering efficiency is around 10% for the most intense spectral peak. The method is also demonstrated on other fully 13C-labelled compounds, including a uniformly 13C-labelled amino acid.
Collapse
|
38
|
Tishmack PA, Bugay DE, Byrn SR. Solid-state nuclear magnetic resonance spectroscopy--pharmaceutical applications. J Pharm Sci 2003; 92:441-74. [PMID: 12587108 DOI: 10.1002/jps.10307] [Citation(s) in RCA: 168] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy has become an integral technique in the field of pharmaceutical sciences. This review focuses on the use of solid-state NMR techniques for the characterization of pharmaceutical solids (drug substance and dosage form). These techniques include methods for (1) studying structure and conformation, (2) analyzing molecular motions (relaxation and exchange spectroscopy), (3) assigning resonances (spectral editing and two-dimensional correlation spectroscopy), and (4) measuring internuclear distances.
Collapse
|
39
|
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
| |
Collapse
|
40
|
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.
Collapse
Affiliation(s)
- Jun Yang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | | | | | | | | |
Collapse
|
41
|
van Dam L, Ouwerkerk N, Brinkmann A, Raap J, Levitt MH. Solid-state NMR determination of sugar ring pucker in (13)C-labeled 2'-deoxynucleosides. Biophys J 2002; 83:2835-44. [PMID: 12414715 PMCID: PMC1302367 DOI: 10.1016/s0006-3495(02)75292-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The H3'-C3'-C4'-H4' torsional angles of two microcrystalline 2'-deoxynucleosides, thymidine and 2'-deoxycytidine.HCl, doubly (13)C-labeled at the C3' and C4' positions of the sugar ring, have been measured by solid-state magic-angle-spinning nuclear magnetic resonance (NMR). A double-quantum heteronuclear local field experiment with frequency-switched Lee-Goldberg homonuclear decoupling was used. The H3'-C3'-C4'-H4' torsional angles were obtained by comparing the experimental curves with numerical simulations, including the two (13)C nuclei, the directly bonded (1)H nuclei, and five remote protons. The H3'-C3'-C4'-H4' angles were converted into sugar pucker angles and compared with crystallographic data. The delta torsional angles determined by solid-state NMR and x-ray crystallography agree within experimental error. Evidence is also obtained that the proton positions may be unreliable in the x-ray structures. This work confirms that double-quantum solid-state NMR is a feasible tool for studying sugar pucker conformations in macromolecular complexes that are unsuitable for solution NMR or crystallography.
Collapse
Affiliation(s)
- Lorens van Dam
- Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden
| | | | | | | | | |
Collapse
|
42
|
Hohwy M, Rienstra CM, Griffin RG. Band-selective homonuclear dipolar recoupling in rotating solids. J Chem Phys 2002. [DOI: 10.1063/1.1488136] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
43
|
Oyler NA, Tycko R. Multiple Quantum 13C NMR Spectroscopy in Solids under High-Speed Magic-Angle Spinning. J Phys Chem B 2002. [DOI: 10.1021/jp020906m] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nathan A. Oyler
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
| | - Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520
| |
Collapse
|
44
|
Long JR, Oyler N, Drobny GP, Stayton PS. Assembly of alpha-helical peptide coatings on hydrophobic surfaces. J Am Chem Soc 2002; 124:6297-303. [PMID: 12033857 DOI: 10.1021/ja011624n] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The adsorption or covalent attachment of biological macromolecules onto polymer materials to improve their biocompatibility has been pursued using a variety of approaches, but key to understanding their efficacy is the verification of the structure and dynamics of the immobilized biomolecules. Here we present data on peptides designed to adsorb from aqueous solutions onto highly porous hydrophobic surfaces with specific helical secondary structures. Small linear peptides composed of alternating leucine and lysine residues were synthesized, and their adsorption onto porous polystyrene surfaces was studied using a combination of solid-state NMR techniques. Using conventional solid-state NMR experiments and newly developed double-quantum techniques, their helical structure was verified. Large-amplitude dynamics on the NMR time scale were not observed, suggesting irreversible adsorption of the peptides. Their association, adsorption, and structure were examined as a function of helix length and sequence periodicity, and it was found that, at higher solution concentrations, peptides as short as seven amino acids adsorb with defined secondary structures. Two-dimensional double-quantum experiments using (13)C-enriched peptide sequences allow high-resolution determination of secondary structure in heterogeneous environments where the peptides are a minor component of the material. These results shed light on how polymeric surfaces may be surface-modified by structured peptides and demonstrate the level of molecular structural and dynamic information solid-state NMR can provide.
Collapse
Affiliation(s)
- Joanna R Long
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
| | | | | | | |
Collapse
|
45
|
Lupulescu A, Brown SP, Spiess HW. Rotor-encoded heteronuclear MQ MAS NMR spectroscopy of half-integer quadrupolar and spin I=1/2 nuclei. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 154:101-129. [PMID: 11820831 DOI: 10.1006/jmre.2001.2464] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A new two-dimensional heteronuclear multiple-quantum magic-angle spinning (MQ MAS) experiment is presented which combines high resolution for the half-integer quadrupolar nucleus with information about the dipolar coupling between the quadrupolar nucleus and a spin I=1/2 nucleus. Homonuclear MQ coherence is initially created for the half-integer quadrupolar nucleus by a single pulse as in a standard MQ MAS experiment. REDOR recoupling of the heteronuclear dipolar coupling then allows the creation of a heteronuclear multiple-quantum coherence comprising multiple- and single-quantum coherence of the quadrupolar and spin I=1/2 nucleus, respectively, which evolves during t1. Provided that the t1 increment is not rotor synchronized, rotor-encoded spinning-sideband patterns are observed in the indirect dimension. Simulated spectra for an isolated IS spin pair show that these patterns depend on the recoupling time, the magnitude of the dipolar coupling, the quadrupolar parameters, as well as the relative orientation of the quadrupolar and dipolar principal axes systems. Spectra are presented for Na2HPO4, with the heteronuclear 23Na-1HMQ MAS experiments beginning with the excitation of 23Na (spin I=3/2) three-quantum coherence. Coherence counting experiments demonstrate that four- and two-quantum coherences evolve during t1. The heteronuclear spinning-sideband patterns observed for the three-spin H-Na-H system associated with the Na(2) site are analyzed. For an IS2 system, simulated spectra show that, considering the free parameters, the spinning-sideband patterns are particularly sensitive to only, first, the angle between the two IS internuclear vectors and, second, the two heteronuclear dipolar couplings. It is demonstrated that the proton localization around the Na(2) site according to the literature crystal structure of Na2HPO4 is erroneous. Instead, the experimental data is consistent with two alternative different structural arrangements, whereby either there is a deviation of 10 degrees from linearity for the case of two identical Na-H distances, or there is a linear arrangement, but the two Na-H distances are different. Furthermore, the question of the origin of spinning-sidebands in the (homonuclear) MQ MAS experiment is revisited. It is shown that the asymmetric experimental MQ sideband pattern observed for the low-C(Q) Na(2) site in Na(2)HPO4 can only be explained by considering the 23Na chemical shift anisotropy.
Collapse
Affiliation(s)
- Adonis Lupulescu
- Max-Planck-Institut für Polymerforschung, D-55021 Mainz, Germany
| | | | | |
Collapse
|
46
|
Brown SP, Spiess HW. Advanced solid-state NMR methods for the elucidation of structure and dynamics of molecular, macromolecular, and supramolecular systems. Chem Rev 2001; 101:4125-56. [PMID: 11740929 DOI: 10.1021/cr990132e] [Citation(s) in RCA: 320] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S P Brown
- Max-Planck-Institut für Polymerforschung, Postfach 3148, D-55021 Mainz, Germany
| | | |
Collapse
|
47
|
Carravetta M, Edén M, Johannessen OG, Luthman H, Verdegem PJ, Lugtenburg J, Sebald A, Levitt MH. Estimation of carbon-carbon bond lengths and medium-range internuclear distances by solid-state nuclear magnetic resonance. J Am Chem Soc 2001; 123:10628-38. [PMID: 11673994 DOI: 10.1021/ja016027f] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe magic-angle-spinning NMR methods for the accurate determination of internuclear dipole-dipole couplings between homonuclear spins-(1/2) in the solid state. The new sequences use symmetry principles to treat the effect of magic-angle sample-rotation and resonant radio frequency fields. The pulse-sequence symmetries generate selection rules which reduce the interference of undesirable interactions and improve the robustness of the pulse sequences with respect to chemical shift anisotropies. We show that the pulse sequences may be used to estimate distances between 13C spins in organic solids, including bond lengths in systems with large chemical shift anisotropies, such as conjugated systems. For bond-length measurements, the precision of the method is +/-2 pm with a systematic overestimate of the internuclear distance by 3 +/- 1 pm. The method is expected to be a useful tool for investigating structural changes in macromolecules.
Collapse
Affiliation(s)
- M Carravetta
- Physical Chemistry Division, Stockholm University, S-106 91 Stockholm, Sweden
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Abstract
Determination of the conformational flexibility of the furanose ring is of vital importance in understanding the structure of DNA. In this work we have applied a model of furanose ring motion to the analysis of deuterium line shape data obtained from sugar rings in solid hydrated DNA. The model describes the angular trajectories of the atoms in the furanose ring in terms of pseudorotation puckering amplitude (q) and the pseudorotation puckering phase phi. Fixing q, the motion is thus treated as Brownian diffusion through an angular-dependent potential U(phi). We have simulated numerous line shapes varying the adjustable parameters, including the diffusion coefficient D, pseudorotation puckering amplitude q, and the form of the potential U(phi). We have used several forms of the potential, including equal double-well potentials, unequal double-well potentials, and a potential truncated to "second order" in the Fourier series. To date, we have obtained best simulations for both equilibrium and nonequilibrium (partially relaxed) solid-state deuterium NMR line shapes for the sample [2' '-2H]-2'-deoxycytidine at the position C3 (underlined) in the DNA sequence [d(CGCGAATTCGCG)]2, using a double-well potential with an equal barrier height of U(0) = 5.5k(B)T ( approximately 3.3 kcal/mol), a puckering amplitude of q = 0.4 A, and a diffusion coefficient characterizing the underlying stochastic jump rate D = 9.9 x 10(8) Hz. Then the rate of flux for the C-D bond over the barrier, i.e., the escape velocity or the overall rate of puckering between modes, was found to be 0.7 x 10(7) Hz.
Collapse
Affiliation(s)
- G A Meints
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | | | | |
Collapse
|
49
|
FILIP CLAUDIU, BERTMER MARKO, DEMCO DANE, BLÜMICH BERNHARD. Application of the Floquet theory to multiple quantum NMR of dipolar-coupled multi-spin systems under magic angle spinning. Mol Phys 2001. [DOI: 10.1080/00268970110060118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
50
|
Tycko R. Biomolecular solid state NMR: advances in structural methodology and applications to peptide and protein fibrils. Annu Rev Phys Chem 2001; 52:575-606. [PMID: 11326075 DOI: 10.1146/annurev.physchem.52.1.575] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Solid state nuclear magnetic resonance (NMR) methods can provide atomic-level structural constraints on peptides and proteins in forms that are not amenable to characterization by other high-resolution structural techniques, owing to insolubility, high molecular weight, noncrystallinity, or other characteristics. Important examples include peptide and protein fibrils and membrane-bound peptides and proteins. Recent advances in solid state NMR methodology aimed at structural problems in biological systems are reviewed. The power of these methods is illustrated by experimental results on amyloid fibrils and other protein fibrils.
Collapse
Affiliation(s)
- R Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
| |
Collapse
|