1
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Kehl A, Hiller M, Hecker F, Tkach I, Dechert S, Bennati M, Meyer A. Resolution of chemical shift anisotropy in 19F ENDOR spectroscopy at 263 GHz/9.4 T. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 333:107091. [PMID: 34749036 DOI: 10.1016/j.jmr.2021.107091] [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: 09/03/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
Pulsed 19F ENDOR spectroscopy provides a selective method for measuring angstrom to nanometer distances in structural biology. Here, the performance of 19F ENDOR at fields of 3.4 T and 9.4 T is compared using model compounds containing one to three 19F atoms. CF3 groups are included in two compounds, for which the possible occurrence of uniaxial rotation might affect the distance distribution. At 9.4 T, pronounced asymmetric features are observed in many of the presented 19F ENDOR spectra. Data analysis by spectral simulations shows that these features arise from the chemical shift anisotropy (CSA) of the 19F nuclei. This asymmetry is also observed at 3.4 T, albeit to a much smaller extent, confirming the physical origin of the effect. The CSA parameters are well consistent with DFT predicted values and can be extracted from simulation of the experimental data in favourable cases, thereby providing additional information about the geometrical and electronic structure of the spin system. The feasibility of resolving the CSA at 9.4 T provides important information for the interpretation of line broadening in ENDOR spectra also at lower fields, which is relevant for developing methods to extract distance distributions from 19F ENDOR spectra.
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Affiliation(s)
- Annemarie Kehl
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Markus Hiller
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Fabian Hecker
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Igor Tkach
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sebastian Dechert
- Department of Chemistry, Georg August University of Göttingen, Tammannstr. 4, Göttingen, Germany
| | - Marina Bennati
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Department of Chemistry, Georg August University of Göttingen, Tammannstr. 4, Göttingen, Germany.
| | - Andreas Meyer
- Research Group EPR Spectroscopy, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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2
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Guo C, Fritz MP, Struppe J, Wegner S, Stringer J, Sergeyev IV, Quinn CM, Gronenborn AM, Polenova T. Fast 19F Magic Angle Spinning NMR Crystallography for Structural Characterization of Fluorine-Containing Pharmaceutical Compounds. Anal Chem 2021; 93:8210-8218. [PMID: 34080855 DOI: 10.1021/acs.analchem.1c00784] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Fluorine-containing compounds comprise 20 to 30 percent of all commercial drugs, and the proportion of fluorinated pharmaceuticals is rapidly growing. While magic angle spinning (MAS) NMR spectroscopy is a popular technique for analysis of solid pharmaceutical compounds, fluorine has been underutilized as a structural probe so far. Here, we report a fast (40-60 kHz) MAS 19F NMR approach for structural characterization of fluorine-containing crystalline pharmaceutical compounds at natural abundance, using the antimalarial fluorine-containing drug mefloquine as an example. We demonstrate the utility of 2D 19F-13C and 19F-19F dipolar-coupling-based correlation experiments for 19F and 13C resonance frequency assignment, which permit identification of crystallographically inequivalent sites. The efficiency of 19F-13C cross-polarization and the effect of 1H and 19F decoupling on spectral resolution and sensitivity were evaluated in a broad range of experimental conditions. We further demonstrate a protocol for measuring accurate interfluorine distances based on 1D DANTE-RFDR experiments combined with multispin numerical simulations.
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Affiliation(s)
- Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Matthew P Fritz
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Jochem Struppe
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | | | - John Stringer
- PhoenixNMR, 510 E. 5th Street, Loveland, Colorado 80537, United States
| | - Ivan V Sergeyev
- Bruker Biospin Corporation, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Angela M Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States.,Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States.,Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
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3
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Takahashi M, Shirasaki J, Komura N, Sasaki K, Tanaka HN, Imamura A, Ishida H, Hanashima S, Murata M, Ando H. Efficient diversification of GM3 gangliosides via late-stage sialylation and dynamic glycan structural studies with 19F solid-state NMR. Org Biomol Chem 2020; 18:2902-2913. [DOI: 10.1039/d0ob00437e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
GM3 gangliosides have been synthesized via late-stage α-sialylation using a macro-bicyclic sialyl donor. 19F solid-state NMR analysis of the C5-NHTFAc GM3 analog on a model membrane revealed the influence of cholesterol on glycan dynamics.
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Affiliation(s)
- Maina Takahashi
- Department of Applied Bioorganic Chemistry
- Gifu University
- Gifu 501-1193
- Japan
| | - Junya Shirasaki
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN)
- Gifu University
- Gifu 501-1193
- Japan
| | - Naoko Komura
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN)
- Gifu University
- Gifu 501-1193
- Japan
| | - Katsuaki Sasaki
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Hide-Nori Tanaka
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN)
- Gifu University
- Gifu 501-1193
- Japan
| | - Akihiro Imamura
- Department of Applied Bioorganic Chemistry
- Gifu University
- Gifu 501-1193
- Japan
| | - Hideharu Ishida
- Department of Applied Bioorganic Chemistry
- Gifu University
- Gifu 501-1193
- Japan
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN)
| | - Shinya Hanashima
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Michio Murata
- Department of Chemistry
- Graduate School of Science
- Osaka University
- Toyonaka
- Japan
| | - Hiromune Ando
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN)
- Gifu University
- Gifu 501-1193
- Japan
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4
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Small structural alterations greatly influence the membrane affinity of lipophilic ligands: Membrane interactions of bafilomycin A1 and its desmethyl derivative bearing 19F-labeling. Bioorg Med Chem 2019; 27:1677-1682. [DOI: 10.1016/j.bmc.2019.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 11/20/2022]
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5
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Lee JH, Kim MS, Lee HW, Lee IYC, Kim HK, Kim ND, Lee S, Seo H, Paik Y. The Application of REDOR NMR to Understand the Conformation of Epothilone B. Int J Mol Sci 2017; 18:E1472. [PMID: 28698492 PMCID: PMC5535963 DOI: 10.3390/ijms18071472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/22/2022] Open
Abstract
The structural information of small therapeutic compounds complexed in biological matrices is important for drug developments. However, structural studies on ligands bound to such a large and dynamic system as microtubules are still challenging. This article reports an application of the solid-state NMR technique to investigating the bioactive conformation of epothilone B, a microtubule stabilizing agent, whose analog ixabepilone was approved by the U.S. Food and Drug Administration (FDA) as an anticancer drug. First, an analog of epothilone B was designed and successfully synthesized with deuterium and fluorine labels while keeping the high potency of the drug; Second, a lyophilization protocol was developed to enhance the low sensitivity of solid-state NMR; Third, molecular dynamics information of microtubule-bound epothilone B was revealed by high-resolution NMR spectra in comparison to the non-bound epothilone B; Last, information for the macrolide conformation of microtubule-bound epothilone B was obtained from rotational-echo double-resonance (REDOR) NMR data, suggesting the X-ray crystal structure of the ligand in the P450epoK complex as a possible candidate for the conformation. Our results are important as the first demonstration of using REDOR for studying epothilones.
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Affiliation(s)
- Jae-Ho Lee
- Department of Chemistry, Chungbuk National University, 1 Chungdae-ro, Cheongju, Chungbuk 28644, Korea.
| | - Moon-Su Kim
- Department of Chemistry, Chungbuk National University, 1 Chungdae-ro, Cheongju, Chungbuk 28644, Korea.
| | - Hyo Won Lee
- Department of Chemistry, Chungbuk National University, 1 Chungdae-ro, Cheongju, Chungbuk 28644, Korea.
| | - Ihl-Young C Lee
- Drug Discovery Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea.
| | - Hyun Kyoung Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, 88 Dongnae-ro, Dong-gu, Daegu 41061, Korea.
| | - Nam Doo Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, 88 Dongnae-ro, Dong-gu, Daegu 41061, Korea.
| | - SangGap Lee
- Spin Physics & Engineering Team, Korea Basic Science Institute, 169-148 Gwahak-ro, Yuseong-gu, Daejeon 34133, Korea.
| | - Hwajeong Seo
- Daegu Center, Korea Basic Science Institute, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea.
| | - Younkee Paik
- Spin Physics & Engineering Team, Korea Basic Science Institute, 169-148 Gwahak-ro, Yuseong-gu, Daejeon 34133, Korea.
- Daegu Center, Korea Basic Science Institute, 80 Daehak-ro, Buk-gu, Daegu 41566, Korea.
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6
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Dynamic regulation of lipid-protein interactions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1849-59. [PMID: 25666872 DOI: 10.1016/j.bbamem.2015.01.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/27/2015] [Accepted: 01/29/2015] [Indexed: 02/07/2023]
Abstract
We review the importance of helix motions for the function of several important categories of membrane proteins and for the properties of several model molecular systems. For voltage-gated potassium or sodium channels, sliding, tilting and/or rotational movements of the S4 helix accompanied by a swapping of cognate side-chain ion-pair interactions regulate the channel gating. In the seven-helix G protein-coupled receptors, exemplified by the rhodopsins, collective helix motions serve to activate the functional signaling. Peptides which initially associate with lipid-bilayer membrane surfaces may undergo dynamic transitions from surface-bound to tilted-transmembrane orientations, sometimes accompanied by changes in the molecularity, formation of a pore or, more generally, the activation of biological function. For single-span membrane proteins, such as the tyrosine kinases, an interplay between juxtamembrane and transmembrane domains is likely to be crucial for the regulation of dimer assembly that in turn is associated with the functional responses to external signals. Additionally, we note that experiments with designed single-span transmembrane helices offer fundamental insights into the molecular features that govern protein-lipid interactions. This article is part of a Special Issue entitled: Lipid-protein interactions.
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7
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Grage SL, Xu X, Schmitt M, Wadhwani P, Ulrich AS. (19)F-Labeling of Peptides Revealing Long-Range NMR Distances in Fluid Membranes. J Phys Chem Lett 2014; 5:4256-4259. [PMID: 26273971 DOI: 10.1021/jz502195t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
NMR distance measurements lie at the heart of structural biology. However, long-range distances could not yet be detected in liquid-crystalline biomembranes, because dipolar couplings are partially averaged by the intrinsic molecular mobility. Using conformationally constrained (19)F-labeled amino acids as reporter groups, we could more than double the accessible interatomic distance range by combining a highly sensitive solid-state multipulse (19)F-NMR scheme with a favorable sample geometry. Two rigid 4F-phenylglycine labels were placed into the helical antimicrobial peptide PGLa embedded in fluid oriented membrane samples. A modified Carr-Purcell-Meiboom-Gill sequence yielded an intramolecular distance of 6.6 Å for the labels spanning one helix turn, and 11.0 Å was obtained when the labels spanned two turns. This approach should now also allow the characterization of conformational changes in membrane-active peptides and of oligomeric assemblies in a biologically relevant lipid environment.
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Affiliation(s)
- Stephan L Grage
- †Institute of Biological Interfaces IBG-2, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Xiaojun Xu
- ‡Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Markus Schmitt
- †Institute of Biological Interfaces IBG-2, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- †Institute of Biological Interfaces IBG-2, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Anne S Ulrich
- †Institute of Biological Interfaces IBG-2, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
- ‡Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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8
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Tkachenko AN, Mykhailiuk PK, Radchenko DS, Babii O, Afonin S, Ulrich AS, Komarov IV. Design and Synthesis of a Monofluoro-Substituted Aromatic Amino Acid as a Conformationally Restricted19F NMR Label for Membrane-Bound Peptides. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301737] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Dürr UHN, Afonin S, Hoff B, de Luca G, Emsley JW, Ulrich AS. Alignment of Druglike Compounds in Lipid Bilayers Analyzed by Solid-State 19F-NMR and Molecular Dynamics, Based on Dipolar Couplings of Adjacent CF3 Groups. J Phys Chem B 2012; 116:4769-82. [DOI: 10.1021/jp212339k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ulrich H. N. Dürr
- Institute
of Organic Chemistry
and CFN, Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg
6, 76131 Karlsruhe, Germany
| | - Sergii Afonin
- Institute
of Organic Chemistry
and CFN, Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg
6, 76131 Karlsruhe, Germany
| | - Barbara Hoff
- Bioprocess Engineering, IMVM, Fritz-Haber-Weg
2, 76131 Karlsruhe, Germany
| | - Giuseppina de Luca
- Dipartimento di Chimica, University of Calabria, Campus di Arcavacata, Via Pietro
Bucci Cubo 12C, I-87036 Rende (Cosenza), Italy
| | - James W. Emsley
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Anne S. Ulrich
- Institute
of Organic Chemistry
and CFN, Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg
6, 76131 Karlsruhe, Germany
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10
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Su Y, DeGrado WF, Hong M. Orientation, dynamics, and lipid interaction of an antimicrobial arylamide investigated by 19F and 31P solid-state NMR spectroscopy. J Am Chem Soc 2010; 132:9197-205. [PMID: 20536141 PMCID: PMC2904348 DOI: 10.1021/ja103658h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A number of arylamides have been synthesized and found to exhibit potent antimicrobial activities against a broad spectrum of Gram-positive and Gram-negative bacteria while exhibiting low toxicity toward eukaryotic cells. These facially amphiphilic foldamers have a relatively rigid intramolecular hydrogen-bonded arylamide as a framework, which places trifluormethyl versus positively charged amino and guanidino groups along opposite faces of the elongated molecule, facilitating interactions with lipid membranes. To better understand the mechanism of action of these antimicrobial foldamers, we have investigated the lipid interaction, depth of insertion, orientation, and dynamics of an arylamide, PMX30016, using (31)P and (19)F solid-state NMR spectroscopy. Static (31)P NMR line shapes of lipid membranes with a range of compositions indicate that PMX30016 does not disrupt the lamellar order of the lipid bilayer but perturbs the lipid headgroup conformation. This headgroup perturbation, manifested as systematic (31)P chemical shift anisotropy increases, is consistent with the well documented "electrometer" effect of lipid membranes in response to the addition of positive charges to membrane surfaces. Paramagnetic relaxation enhancement experiments indicate that the arylamide inserts into the membrane-water interface, just below the headgroup region. Measurement of (19)F-(19)F dipolar couplings within each CF(3) moiety revealed that PMX30016 is oriented with the molecular plane 20 degrees and 30 degrees from the membrane normal of neutral and anionic bilayers, respectively, and the long molecular axis lies parallel to the membrane plane. Thus, this arylamide inserts into the bilayer in a knife-like fashion, consistent with previous vibrational spectroscopy results. Moreover, (19)F NMR line shapes indicate that this molecular knife undergoes fast uniaxial rotation around the bilayer normal. These results suggest that antimicrobial arylamides destabilize anionic lipid membranes primarily by altering the membrane electric potential profile, and the spinning molecular knife may additionally create transient defects in the lipid membrane. Compared to typical antimicrobial peptides, this arylamide has more subtle effects on and is less disruptive of the structure of lipid bilayers.
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Affiliation(s)
- Yongchao Su
- Department of Chemistry, Iowa State University, Ames, IA 50011
| | - William F. DeGrado
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059
| | - Mei Hong
- Department of Chemistry, Iowa State University, Ames, IA 50011
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11
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Stueber D, Yu TY, Hess B, Kremer K, O'Connor RD, Schaefer J. Chain packing in polycarbonate glasses. J Chem Phys 2010; 132:104901. [PMID: 20232984 DOI: 10.1063/1.3330412] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Chain packing in homogeneous blends of carbonate (13)C-labeled bisphenol A polycarbonate with either (i) CF(3)-labeled bisphenol A polycarbonate or (ii) ring-F-labeled bisphenol A polycarbonate has been characterized using (13)C{(19)F} rotational-echo double-resonance (REDOR) nuclear magnetic resonance. In both blends, the (13)C observed spin was at high concentration, and the (19)F dephasing or probe spin was at low concentration. In this situation, an analysis in terms of a distribution of isolated heteronuclear pairs of spins is valid. Nearest-neighbor separation of (13)C and (19)F labels was determined by accurately mapping the initial dipolar evolution using a shifted-pulse version of REDOR. Based on the results of this experiment, the average distance from a ring-fluorine to the nearest (13)C=O is more than 1.2 A greater than the corresponding CF(3)-(13)C=O distance. Next-nearest and more-distant-neighbor separations of labels were measured in a 416-rotor-cycle constant-time version of REDOR for both blends. Statistically significant local order was established for the nearest-neighbor labels in the methyl-labeled blend. These interchain packing results are in qualitative agreement with predictions based on coarse-grained simulations of a specially adapted model for bisphenol A polycarbonate. The model itself has been previously used to determine static and dynamic properties of polycarbonate with results in good agreement with those from rheological and neutron scattering experiments.
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Affiliation(s)
- Dirk Stueber
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
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12
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Waechtler M, Sellin M, Stark A, Akcakayiran D, Findenegg G, Gruenberg A, Breitzke H, Buntkowsky G. 2H and 19F solid-state NMR studies of the ionic liquid [C2Py][BTA]-d10 confined in mesoporous silica materials. Phys Chem Chem Phys 2010; 12:11371-9. [DOI: 10.1039/b926836g] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Afonin S, Grage SL, Ieronimo M, Wadhwani P, Ulrich AS. Temperature-dependent transmembrane insertion of the amphiphilic peptide PGLa in lipid bilayers observed by solid state 19F NMR spectroscopy. J Am Chem Soc 2009; 130:16512-4. [PMID: 19049452 DOI: 10.1021/ja803156d] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Sergii Afonin
- Karlsruhe Institute of Technology, Institute of Biological Interfaces, P.O. Box 3640, 76021 Karlsruhe, Germany
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14
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Aso Y, Yoshioka S, Miyazaki T, Kawanishi T. Feasibility of 19F-NMR for Assessing the Molecular Mobility of Flufenamic Acid in Solid Dispersions. Chem Pharm Bull (Tokyo) 2009; 57:61-4. [DOI: 10.1248/cpb.57.61] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yukio Aso
- National Institute of Health Sciences
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15
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Chekmenev EY, Chow SK, Tofan D, Weitekamp DP, Ross BD, Bhattacharya P. Fluorine-19 NMR chemical shift probes molecular binding to lipid membranes. J Phys Chem B 2008; 112:6285-7. [PMID: 18422359 DOI: 10.1021/jp800646k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The binding of amphiphilic molecules to lipid bilayers is followed by 19F NMR using chemical shift and line shape differences between the solution and membrane-tethered states of -CF 3 and -CHF 2 groups. A chemical shift separation of 1.6 ppm combined with a high natural abundance and high sensitivity of 19F nuclei offers an advantage of using 19F NMR spectroscopy as an efficient tool for rapid time-resolved screening of pharmaceuticals for membrane binding. We illustrate the approach with molecules containing both fluorinated tails and an acrylate moiety, resolving the signals of molecules in solution from those bound to synthetic dimyristoylphosphatidylcholine bilayers both with and without magic angle sample spinning. The potential in vitro and in vivo biomedical applications are outlined. The presented method is applicable with the conventional NMR equipment, magnetic fields of several Tesla, stationary samples, and natural abundance isotopes.
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Affiliation(s)
- Eduard Y Chekmenev
- Enhanced Magnetic Resonance Laboratory, Huntington Medical Research Institutes, Pasadena, CA 91105, USA.
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16
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Grage SL, Dürr UHN, Afonin S, Mikhailiuk PK, Komarov IV, Ulrich AS. Solid state 19F NMR parameters of fluorine-labeled amino acids. Part II: aliphatic substituents. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 191:16-23. [PMID: 18155628 DOI: 10.1016/j.jmr.2007.11.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 10/30/2007] [Accepted: 11/21/2007] [Indexed: 05/25/2023]
Abstract
A representative set of amino acids with aliphatic 19F-labels has been characterized here, following up our previous compilation of NMR parameters for single 19F-substituents on aromatic side chains. Their isotropic chemical shifts, chemical shift tensor parameters, intra-molecular 19F dipole-dipole couplings and temperature-dependent T1 and T2 relaxation times were determined by solid state NMR on twelve polycrystalline amino acid samples, and the corresponding isotropic 19F chemical shifts and scalar couplings were obtained in solution. Of particular interest are amino acids carrying a trifluoromethyl-group, because not only the 19F chemical shift but also the intra-CF3 homonuclear dipolar coupling can be used for structural studies of 19F-labeled peptides and proteins. The CF3-groups are further compared with CH2F-, CD2F-, and CD3-groups, using both 19F and 2H NMR to describe their motional behavior and to examine the respective linebroadening effects of the protonated and deuterated neighbors. We have also characterized two unnatural amino acids in which a CF3-label is rigidly connected to the backbone by a phenyl or bicyclopentyl moiety, and which are particularly well suited for structure analysis of membrane-bound polypeptides. The 19F NMR parameters of the polycrystalline amino acids are compared with data from the correspondingly labeled side chains in synthetic peptides.
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Affiliation(s)
- Stephan L Grage
- Forschungszentrum Karlsruhe, Institute of Biological Interfaces, P.O.B. 3640, 76021 Karlsruhe, Germany
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17
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Solid State NMR Structure Analysis of the Antimicrobial Peptide Gramicidin S in Lipid Membranes: Concentration-Dependent Re-alignment and Self-Assembly as a β-Barrel. Top Curr Chem (Cham) 2008; 273:139-54. [DOI: 10.1007/128_2007_20] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Gor'kov PL, Witter R, Chekmenev EY, Nozirov F, Fu R, Brey WW. Low-E probe for (19)F-(1)H NMR of dilute biological solids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 189:182-189. [PMID: 17920316 DOI: 10.1016/j.jmr.2007.09.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 09/05/2007] [Accepted: 09/13/2007] [Indexed: 05/25/2023]
Abstract
Sample heating induced by radio frequency (RF) irradiation presents a significant challenge to solid state NMR experiments in proteins and other biological systems, causing the sample to dehydrate which may result in distorted spectra and a damaged sample. In this work we describe a large volume, low-E (19)F-(1)H solid state NMR probe, which we developed for the 2D (19)F CPMG studies of dilute membrane proteins in a static and electrically lossy environment at 600MHz field. In (19)FCPMG and related multi-pulse (19)F-(1)H experiments the sample is heated by the conservative electric fields E produced in the sample coil at both (19)F and (1)H frequencies. Instead of using a traditional sample solenoid, our low-E (19)F-(1)H probe utilizes two orthogonal loop-gap resonators in order to minimize the conservative electric fields responsible for sample heating. Absence of the wavelength effects in loop-gap resonators results in homogeneous RF fields and enables the study of large sample volumes, an important feature for the dilute protein preparations. The orthogonal resonators also provide intrinsic isolation between the (19)F and (1)H channels, which is another major challenge for the (19)F-(1)H circuits where Larmor frequencies are only 6% apart. We detail steps to reduce (19)F background signals from the probe, which included careful choice of capacitor lubricants and manufacture of custom non-fluorinated coaxial cables. Application of the probe for two-dimensional (19)F CPMG spectroscopy in oriented lipid membranes is demonstrated with Flufenamic acid (FFA), a non-steroidal anti-inflammatory drug.
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Affiliation(s)
- Peter L Gor'kov
- National High Magnetic Field Laboratory, Tallahassee, FL 32310, USA.
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19
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Oligomeric structure, dynamics, and orientation of membrane proteins from solid-state NMR. Structure 2007; 14:1731-40. [PMID: 17161364 DOI: 10.1016/j.str.2006.10.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2006] [Revised: 10/01/2006] [Accepted: 10/03/2006] [Indexed: 11/27/2022]
Abstract
Solid-state NMR is a versatile and powerful tool for determining the dynamic structure of membrane proteins at atomic resolution. I review the recent progress in determining the orientation, the internal and global protein dynamics, the oligomeric structure, and the ligand-bound structure of membrane proteins with both alpha-helical and beta sheet conformations. Examples are given that illustrate the insights into protein function that can be gained from the NMR structural information.
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20
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Grage SL, Suleymanova AV, Afonin S, Wadhwani P, Ulrich AS. Solid state NMR analysis of the dipolar couplings within and between distant CF3-groups in a membrane-bound peptide. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 183:77-86. [PMID: 16919983 DOI: 10.1016/j.jmr.2006.07.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Revised: 07/11/2006] [Accepted: 07/14/2006] [Indexed: 05/11/2023]
Abstract
Dipolar couplings contain information on internuclear distances as well as orientational constraints. To characterize the structure of the antimicrobial peptide gramicidin S when bound to model membranes, two rigid 4-CF3-phenylglycine labels were attached to the cyclic backbone such that they reflect the behavior of the entire peptide. By solid state 19F NMR we measured the homonuclear dipolar couplings of the two trifluoromethyl-groups in oriented membrane samples. Using the CPMG experiment, both the strong couplings within each CF3-group as well as the weak coupling between the two CF3-groups could be detected. An intra-CF3-group dipolar coupling of 86 Hz and a weak inter-group coupling of 20 Hz were obtained by lineshape simulation of the complex dipolar spectrum. It is thus possible to explore the large distance range provided by 19F-labels and to resolve weak dipolar couplings even in the presence of strong intra-CF3 couplings. We applied this approach to distinguish and assign two epimers of the labeled gramicidin S peptide on the basis of their distinct 19F dipolar coupling patterns.
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Affiliation(s)
- Stephan L Grage
- Institute of Biological Interfaces, Forschungszentrum Karlsruhe, P.O. Box 3640, 76021 Karlsruhe, Germany
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21
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Bender M, Holstein P, Geschke D. Homogeneous and Inhomogeneous Director Dynamics of a Fluorinated Liquid Crystal. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/10587250108025260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Michael Bender
- a Universität Leipzig, Fakultät für Physik und Geowissenschaften , Linnéstraße 5, 04103 , Leipzig , Germany
| | - Peter Holstein
- a Universität Leipzig, Fakultät für Physik und Geowissenschaften , Linnéstraße 5, 04103 , Leipzig , Germany
| | - Dieter Geschke
- a Universität Leipzig, Fakultät für Physik und Geowissenschaften , Linnéstraße 5, 04103 , Leipzig , Germany
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22
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Stueber D, Mehta AK, Chen Z, Wooley KL, Schaefer J. Local order in polycarbonate glasses by 13
C{19
F} rotational-echo double-resonance NMR. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/polb.20931] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Strandberg E, Wadhwani P, Tremouilhac P, Dürr UHN, Ulrich AS. Solid-state NMR analysis of the PGLa peptide orientation in DMPC bilayers: structural fidelity of 2H-labels versus high sensitivity of 19F-NMR. Biophys J 2005; 90:1676-86. [PMID: 16339890 PMCID: PMC1367318 DOI: 10.1529/biophysj.105.073858] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structure and alignment of the amphipathic alpha-helical antimicrobial peptide PGLa in a lipid membrane is determined with high accuracy by solid-state 2H-NMR. Orientational constraints are derived from a series of eight alanine-3,3,3-d3-labeled peptides, in which either a native alanine is nonperturbingly labeled (4x), or a glycine (2x) or isoleucine (2x) is selectively replaced. The concentration dependent realignment of the alpha-helix from the surface-bound "S-state" to a tilted "T-state" by 30 degrees is precisely calculated using the quadrupole splittings of the four nonperturbing labels as constraints. The remaining, potentially perturbing alanine-3,3,3-d3 labels show only minor deviations from the unperturbed peptide structure and help to single out the unique solution. Comparison with previous 19F-NMR constraints from 4-CF3-phenylglycine labels shows that the structure and orientation of the PGLa peptide is not much disturbed even by these bulky nonnatural side chains, which contain CF3 groups that offer a 20-fold better NMR sensitivity than CD3 groups.
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Affiliation(s)
- Erik Strandberg
- Institute for Biological Interfaces, Forschungszentrum Karlsruhe, 76344 Eggenstein-Leopoldshafen, Germany
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Glaser RW, Sachse C, Dürr UHN, Wadhwani P, Ulrich AS. Orientation of the antimicrobial peptide PGLa in lipid membranes determined from 19F-NMR dipolar couplings of 4-CF3-phenylglycine labels. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2004; 168:153-63. [PMID: 15082261 DOI: 10.1016/j.jmr.2004.02.008] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Revised: 02/02/2004] [Indexed: 05/03/2023]
Abstract
A highly sensitive solid state (19)F-NMR strategy is described to determine the orientation and dynamics of membrane-associated peptides from specific fluorine labels. Several analogues of the antimicrobial peptide PGLa were synthesized with the non-natural amino acid 4-trifluoromethyl-phenylglycine (CF(3)-Phg) at different positions throughout the alpha-helical peptide chain. A simple 1-pulse (19)F experiment allows the simultaneous measurement of both the anisotropic chemical shift and the homonuclear dipolar coupling within the rotating CF(3)-group in a macroscopically oriented membrane sample. The value and sign of the dipolar splitting determines the tilt of the CF(3)-rotational axis, which is rigidly attached to the peptide backbone, with respect to the external magnetic field direction. Using four CF(3)-labeled peptide analogues (with L-CF(3)-Phg at Ile9, Ala10, Ile13, and Ala14) we confirmed that PGLa is aligned at the surface of lipid membranes with its helix axis perpendicular to the bilayer normal at a peptide:lipid ratio of 1:200. We also determined the azimuthal rotation angle of the helix, which agrees well with the orientation expected from its amphiphilic character. Peptide analogues with a D-CF(3)-Phg label resulting from racemization of the amino acid during synthesis were separately collected by HPLC. Their spectra provide additional information about the PGLa structure and orientation but allow only to discriminate qualitatively between multiple solutions. The structural and functional characterization of the individual CF(3)-labeled peptides by circular dichroism and antimicrobial assays showed only small effects for our four substitutions on the hydrophobic face of the helix, but a significant disturbance was observed in a fifth analogue where Ala8 on the hydrophilic face had been replaced. Even though the hydrophobic CF(3)-Phg side chain cannot be utilized in all positions, it allows highly sensitive NMR measurements over a wide range of experimental conditions and dynamic regimes of the peptide.
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Affiliation(s)
- Ralf W Glaser
- Institute of Biochemistry and Biophysics, Friedrich-Schiller-Universität Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany
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Afonin S, Glaser RW, Berditchevskaia M, Wadhwani P, Gührs KH, Möllmann U, Perner A, Ulrich AS. 4-fluorophenylglycine as a label for 19F NMR structure analysis of membrane-associated peptides. Chembiochem 2004; 4:1151-63. [PMID: 14613106 DOI: 10.1002/cbic.200300568] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The non-natural amino acid 4-fluorophenylglycine (4F-Phg) was incorporated into several representative membrane-associated peptides for dual purpose. The (19)F-substituted ring is directly attached to the peptide backbone, so it not only provides a well-defined label for highly sensitive (19)F NMR studies but, in addition, the D and L enantiomers of the stiff side chain may serve as reporter groups on the transient peptide conformation during the biological function. Besides peptide synthesis, which is accompanied by racemisation of 4F-Phg, we also describe separation of the epimers by HPLC and removal of trifluoroacetic acid. As a first example, 18 different analogues of the fusogenic peptide "B18" were prepared and tested for induction of vesicle fusion; the results confirmed that hydrophobic sites tolerated 4F-Phg labelling. Similar fusion activities within each pair of epimers suggest that the peptide is less structured in the fusogenic transition state than in the helical ground state. In a second example, five doubly labelled analogues of the antimicrobial peptide gramicidin S were compared by using bacterial growth inhibition assays. This cyclic beta-sheet peptide could accommodate both L and D substituents on its hydrophobic face. As a third example, we tested six analogues of the antimicrobial peptide PGLa. The presence of d-4F-Phg reduced the biological activity of the peptide by interfering with its amphiphilic alpha-helical fold. Finally, to illustrate the numerous uses of l-4F-Phg in (19)F NMR spectroscopy, we characterised the interaction of labelled PGLa with uncharged and negatively charged membranes. Observing the signal of the free peptide in an aqueous suspension of unilamellar vesicles, we found a linear saturation behaviour that was dominated by electrostatic attraction of the cationic PGLa. Once the peptide is bound to the membrane, however, solid-state (19)F NMR spectroscopy of macroscopically oriented samples revealed that the charge density has virtually no further influence on the structure, alignment or mobility of the peptide.
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Affiliation(s)
- Sergii Afonin
- Forschungszentrum Karlsruhe, IFIA, P.O.B. 3640, 76021 Karlsruhe, Germany
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Afonin S, Dürr UHN, Glaser RW, Ulrich AS. 'Boomerang'-like insertion of a fusogenic peptide in a lipid membrane revealed by solid-state 19F NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2004; 42:195-203. [PMID: 14745800 DOI: 10.1002/mrc.1340] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Solid state (19)F NMR revealed the conformation and alignment of the fusogenic peptide sequence B18 from the sea urchin fertilization protein bindin embedded in flat phospholipid bilayers. Single (19)F labels were introduced into nine distinct positions along the wild-type sequence by substituting each hydrophobic amino acid, one by one, with L-4-fluorophenylglycine. Their anisotropic chemical shifts were measured in uniaxially oriented membrane samples and used as orientational constraints to model the peptide structure in the membrane-bound state. Previous (1)H NMR studies of B18 in 30% TFE and in detergent micelles had shown that the peptide structure consists of two alpha-helical segments that are connected by a flexible hinge. This helix-break-helix motif was confirmed here by the solid-state (19)F NMR data, while no other secondary structure (beta-sheet, 3(10)-helix) was compatible with the set of orientational constraints. For both alpha-helical segments we found that the helical conformation extends all the way to the respective N- and C-termini of the peptide. Analysis of the corresponding tilt and azimuthal rotation angles showed that the N-terminal helix of B18 is immersed obliquely into the bilayer (at a tilt angle tau approximately 54 degrees), whereas the C-terminus is peripherally aligned (tau approximately 91 degrees). The azimuthal orientation of the two segments is consistent with the amphiphilic distribution of side-chains. The observed 'boomerang'-like mode of insertion into the membrane may thus explain how peptide binding leads to lipid dehydration and acyl chain perturbation as a prerequisite for bilayer fusion to occur.
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Affiliation(s)
- Sergii Afonin
- Forschungszentrum Karlsruhe, IFIA, POB 3640, 76021 Karlsruhe, Germany
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27
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Glaser RW, Ulrich AS. Susceptibility corrections in solid-state NMR experiments with oriented membrane samples. Part I: applications. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2003; 164:104-114. [PMID: 12932462 DOI: 10.1016/s1090-7807(03)00207-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chemical shift referencing of solid-state NMR experiments on oriented membranes has to compensate for bulk magnetic susceptibility effects that are associated with the non-spherical sample shape, as described in the accompanying paper [J. Magn. Reson. 164 (2003) 115-127]. The resulting frequency deviations can be on the order of 10 ppm, which is serious for nuclei with a narrow chemical shift anisotropy such as 1H or 13C, and in some cases even 19F. Two referencing schemes are proposed here to compensate for these effects: A flat (0.4 mm) glass container with an isotropic reference molecule dissolved in a thin film of liquid is stacked on top of the oriented membrane sample. Alternatively, the intrinsic proton signal of the hydrated lipid can be used for chemical shift referencing. Further aspects related to magnetic susceptibility are discussed, such as air gaps in susceptibility-matched probeheads, the benefits of shimming, and limitations in the accuracy of orientational constraints. A biological application is illustrated by a series of experiments on the antimicrobial peptide PGLa, aimed at understanding its concentration-dependent membranolytic effect. To address a wide range of molar peptide/lipid ratios between 1:3000 and 1:8, multilayers of hydrated DMPC containing a 19F-labeled peptide were oriented between stacked glass plates. Maintaining an approximately constant amount of peptide gives rise to thick samples (18 plates) at low, and thin samples (3 plates) at high peptide/lipid ratio. Accurate referencing was critical to reveal a small but significant change over 5 ppm in the anisotropic chemical shift of the 19F label on the peptide, indicative of a change in the orientation and/or dynamics of PGLa in the membrane.
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Affiliation(s)
- Ralf W Glaser
- Institute of Molecular Biology, Friedrich-Schiller-Universität Jena, Winzerlaer Str. 10, D-07745 Jena, Germany
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