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Stockwald ER, Steger LME, Vollmer S, Gottselig C, Grage SL, Bürck J, Afonin S, Fröbel J, Blümmel AS, Setzler J, Wenzel W, Walther TH, Ulrich AS. Length matters: Functional flip of the short TatA transmembrane helix. Biophys J 2023; 122:2125-2146. [PMID: 36523158 PMCID: PMC10257086 DOI: 10.1016/j.bpj.2022.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The twin arginine translocase (Tat) exports folded proteins across bacterial membranes. The putative pore-forming or membrane-weakening component (TatAd in B. subtilis) is anchored to the lipid bilayer via an unusually short transmembrane α-helix (TMH), with less than 16 residues. Its tilt angle in different membranes was analyzed under hydrophobic mismatch conditions, using synchrotron radiation circular dichroism and solid-state NMR. Positive mismatch (introduced either by reconstitution in short-chain lipids or by extending the hydrophobic TMH length) increased the helix tilt of the TMH as expected. Negative mismatch (introduced either by reconstitution in long-chain lipids or by shortening the TMH), on the other hand, led to protein aggregation. These data suggest that the TMH of TatA is just about long enough for stable membrane insertion. At the same time, its short length is a crucial factor for successful translocation, as demonstrated here in native membrane vesicles using an in vitro translocation assay. Furthermore, when reconstituted in model membranes with negative spontaneous curvature, the TMH was found to be aligned parallel to the membrane surface. This intrinsic ability of TatA to flip out of the membrane core thus seems to play a key role in its membrane-destabilizing effect during Tat-dependent translocation.
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Affiliation(s)
- Eva R Stockwald
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Karlsruhe, Germany
| | - Lena M E Steger
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
| | - Stefanie Vollmer
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Karlsruhe, Germany
| | - Christina Gottselig
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Karlsruhe, Germany
| | - Stephan L Grage
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
| | - Jochen Bürck
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
| | - Sergii Afonin
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany
| | - Julia Fröbel
- University of Freiburg, Institute of Biochemistry and Molecular Biology, Freiburg, Germany
| | - Anne-Sophie Blümmel
- University of Freiburg, Institute of Biochemistry and Molecular Biology, Freiburg, Germany
| | - Julia Setzler
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, Karlsruhe, Germany
| | - Wolfgang Wenzel
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology, Karlsruhe, Germany
| | - Torsten H Walther
- Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany.
| | - Anne S Ulrich
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Karlsruhe, Germany; Karlsruhe Institute of Technology (KIT), Institute of Biological Interfaces (IBG-2), Karlsruhe, Germany.
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Head-to-Tail and Head-to-Head Molecular Chains of Poly(p-Anisidine): Combined Experimental and Theoretical Evaluation. Molecules 2022; 27:molecules27196326. [PMID: 36234863 PMCID: PMC9571860 DOI: 10.3390/molecules27196326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 12/02/2022] Open
Abstract
Poly(p-anisidine) (PPA) is a polyaniline derivative presenting a methoxy (–OCH3) group at the para position of the phenyl ring. Considering the important role of conjugated polymers in novel technological applications, a systematic, combined experimental and theoretical investigation was performed to obtain more insight into the crystallization process of PPA. Conventional oxidative polymerization of p-anisidine monomer was based on a central composite rotational design (CCRD). The effects of the concentration of the monomer, ammonium persulfate (APS), and HCl on the percentage of crystallinity were considered. Several experimental techniques such as X-ray Diffraction (XRD), Scanning Electron Microscopy (SEM), multifractal analysis, Nuclear Magnetic Resonance (13C NMR), Fourier-transform Infrared spectroscopy (FTIR), and complex impedance spectroscopy analysis, in addition to Density Functional Theory (DFT), were employed to perform a systematic investigation of PPA. The experimental treatments resulted in different crystal structures with a percentage of crystallinity ranging from (29.2 ± 0.6)% (PPA1HT) to (55.1 ± 0.2)% (PPA16HT-HH). A broad halo in the PPA16HT-HH pattern from 2θ = 10.0–30.0° suggested a reduced crystallinity. Needle and globular-particle morphologies were observed in both samples; the needle morphology might have been related to the crystalline contribution. A multifractal analysis showed that the PPA surface became more complex when the crystallinity was reduced. The proposed molecular structures of PPA were supported by the high-resolution 13C NMR results, allowing us to access the percentage of head-to-tail (HT) and head-to-head (HH) molecular structures. When comparing the calculated and experimental FTIR spectra, the most pronounced changes were observed in ν(C–H), ν(N–H), ν(C–O), and ν(C–N–C) due to the influence of counterions on the polymer backbone as well as the different mechanisms of polymerization. Finally, a significant difference in the electrical conductivity was observed in the range of 1.00 × 10−9 S.cm−1 and 3.90 × 10−14 S.cm−1, respectively, for PPA1HT and PPA16HT-HH.
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Facchinatto WM, Dos Santos DM, de Lacerda Bukzem A, Moraes TB, Habitzreuter F, de Azevedo ER, Colnago LA, Campana-Filho SP. Insight into morphological, physicochemical and spectroscopic properties of β-chitin nanocrystalline structures. Carbohydr Polym 2021; 273:118563. [PMID: 34560974 DOI: 10.1016/j.carbpol.2021.118563] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/14/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
We systematically investigated the effect of β-chitin (BCH) particle size on the preparation of nanocrystals/nanowhiskers (CWH) by acid hydrolysis. Regardless this variable, CWH aqueous suspension exhibited outstanding stability and the average degree of acetylation remained nearly constant after the acid treatment. In contrast, the morphology, dimensions, crystallinity, and molecular weight of CHW were significantly affect by the particle size. Although needle-like crystals have predominated, BCH particles sizes significantly affected the dimensions and asymmetry of CWH, as confirmed by the rheological and NMR relaxation (T2) behaviors. According to different SSNMR approaches, the acid hydrolysis meaningless affected the local chain conformation, while the spatial freedom of BCH intersheets, rated upon the mobility of methyl segments, was taken as evidence of higher permeability of acid into small particle sizes. Thus, this study demonstrated the importance of standardizing the surface/bulk proportions of β-chitin aiming to predict and control the CWH morphology and related properties.
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Affiliation(s)
- William Marcondes Facchinatto
- São Carlos Institute of Chemistry, University of São Paulo, Avenida Trabalhador sao-carlense 400, Zip Code 13560-590, PO Box 780, São Carlos, SP, Brazil.
| | - Danilo Martins Dos Santos
- Brazilian Corporation for Agricultural Research, Embrapa Instrumentation, Rua XV de Novembro 1452, Zip Code 13560-970, PO Box 741, São Carlos, SP, Brazil
| | - Andrea de Lacerda Bukzem
- São Carlos Institute of Chemistry, University of São Paulo, Avenida Trabalhador sao-carlense 400, Zip Code 13560-590, PO Box 780, São Carlos, SP, Brazil
| | - Tiago Bueno Moraes
- Department of Chemistry, Institute of Exact Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, 6627, Zip Code 31270-901, PO Box 702, Belo Horizonte, MG, Brazil
| | - Filipe Habitzreuter
- São Carlos Institute of Chemistry, University of São Paulo, Avenida Trabalhador sao-carlense 400, Zip Code 13560-590, PO Box 780, São Carlos, SP, Brazil
| | - Eduardo Ribeiro de Azevedo
- São Carlos Institute of Physics, University of São Paulo, Avenida Trabalhador São-carlense 400, Zip Code 13560-590, PO Box 369, São Carlos, SP, Brazil
| | - Luiz Alberto Colnago
- Brazilian Corporation for Agricultural Research, Embrapa Instrumentation, Rua XV de Novembro 1452, Zip Code 13560-970, PO Box 741, São Carlos, SP, Brazil
| | - Sérgio Paulo Campana-Filho
- São Carlos Institute of Chemistry, University of São Paulo, Avenida Trabalhador sao-carlense 400, Zip Code 13560-590, PO Box 780, São Carlos, SP, Brazil
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Long Z, Ruthford J, Opella SJ. 3D printed sample tubes for solid-state NMR experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 327:106957. [PMID: 33798799 PMCID: PMC8141027 DOI: 10.1016/j.jmr.2021.106957] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
The availability of 3D printers and an assortment of polymers that can be fashioned into a wide variety of shapes provides opportunities to rethink the design and construction of probes for NMR spectroscopy. The direct interfacing of computer aided design (CAD) with precise 3D printing enables the simplification and optimization of probes through the rapid production of components. Here we demonstrate the use of 3D printing to fully integrate a permanent former for the radiofrequency (RF) coil with the sample chamber (equivalent to the sample tube). This simultaneously increases the sample volume and improves the filling factor within a fixed outer diameter (OD). It also reduces the space lost in dual coil arrangements where a high frequency resonator is positioned outside a solenoid coil tuned to one or more lower frequencies, making multiple-resonance experiments more efficient. The initial applications demonstrate the possibilities for future designs that reimagine the interface between resonators and the liquid, solid, and heterogeneous samples encountered in NMR studies of biomolecules, polymers, surfaces, and spectroscopy (MRS) and imaging (MRI) of biological organs and intact organisms.
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Affiliation(s)
- Zheng Long
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307, United States
| | - Jamie Ruthford
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307, United States
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0307, United States.
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Facchinatto WM, Dos Santos Garcia RH, Dos Santos DM, Fiamingo A, Menezes Flores DW, Campana-Filho SP, de Azevedo ER, Colnago LA. Fast-forward approach of time-domain NMR relaxometry for solid-state chemistry of chitosan. Carbohydr Polym 2021; 256:117576. [PMID: 33483071 DOI: 10.1016/j.carbpol.2020.117576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/11/2020] [Accepted: 12/27/2020] [Indexed: 11/19/2022]
Abstract
Chitosans with different average degrees of acetylation and weight molecular weight were analyzed by time-domain NMR relaxometry using the recently proposed pulse sequence named Rhim and Kessemeier - Radiofrequency Optimized Solid-Echo (RK-ROSE) to acquire 1H NMR signal of solid-state materials. The NMR signal decay was composed of faster (tenths of μs) and longer components, where the mobile-part fraction exhibited an effective relaxation transverse time assigned to methyl hydrogens from N-acetyl-d-glucosamine (GlcNAc) units. The higher intrinsic mobility of methyl groups was confirmed via DIPSHIFT experiments by probing the 1H-13C dipolar interaction. RK-ROSE data were modeled by using Partial Least Square (PLS) multivariate regression, which showed a high coefficient of determination (R2 > 0.93) between RK-ROSE signal profile and average degrees of acetylation and crystallinity index, thus indicating that time-domain NMR consists in a promising tool for structural and morphological characterization of chitosan.
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Affiliation(s)
- William Marcondes Facchinatto
- Sao Carlos Institute of Chemistry, University of Sao Paulo, Av. Trabalhador sao-carlense 400, CEP 13566-590, Caixa Postal 780, Sao Carlos, SP, Brazil.
| | - Rodrigo Henrique Dos Santos Garcia
- Sao Carlos Institute of Chemistry, University of Sao Paulo, Av. Trabalhador sao-carlense 400, CEP 13566-590, Caixa Postal 780, Sao Carlos, SP, Brazil
| | - Danilo Martins Dos Santos
- Brazilian Corporation for Agricultural Research, Embrapa Instrumentation, Rua XV de Novembro 1452, CEP 13560-970, Caixa Postal 741, Sao Carlos, SP, Brazil
| | - Anderson Fiamingo
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador sao-carlense 400, CEP 13566-590, Caixa Postal 369, Sao Carlos, SP, Brazil
| | - Douglas William Menezes Flores
- Superior College of Agriculture "Luiz de Queiroz", University of Sao Paulo, Av. Padua Dias 11, CEP 13418-900, Caixa Postal 9, Piracicaba, SP, Brazil
| | - Sérgio Paulo Campana-Filho
- Sao Carlos Institute of Chemistry, University of Sao Paulo, Av. Trabalhador sao-carlense 400, CEP 13566-590, Caixa Postal 780, Sao Carlos, SP, Brazil
| | - Eduardo Ribeiro de Azevedo
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Trabalhador sao-carlense 400, CEP 13566-590, Caixa Postal 369, Sao Carlos, SP, Brazil
| | - Luiz Alberto Colnago
- Brazilian Corporation for Agricultural Research, Embrapa Instrumentation, Rua XV de Novembro 1452, CEP 13560-970, Caixa Postal 741, Sao Carlos, SP, Brazil
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Facchinatto WM, Santos DMD, Fiamingo A, Bernardes-Filho R, Campana-Filho SP, Azevedo ERD, Colnago LA. Evaluation of chitosan crystallinity: A high-resolution solid-state NMR spectroscopy approach. Carbohydr Polym 2020; 250:116891. [DOI: 10.1016/j.carbpol.2020.116891] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/26/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022]
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Schneemann A, Wan LF, Lipton AS, Liu YS, Snider JL, Baker AA, Sugar JD, Spataru CD, Guo J, Autrey TS, Jørgensen M, Jensen TR, Wood BC, Allendorf MD, Stavila V. Nanoconfinement of Molecular Magnesium Borohydride Captured in a Bipyridine-Functionalized Metal-Organic Framework. ACS NANO 2020; 14:10294-10304. [PMID: 32658451 DOI: 10.1021/acsnano.0c03764] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The lower limit of metal hydride nanoconfinement is demonstrated through the coordination of a molecular hydride species to binding sites inside the pores of a metal-organic framework (MOF). Magnesium borohydride, which has a high hydrogen capacity, is incorporated into the pores of UiO-67bpy (Zr6O4(OH)4(bpydc)6 with bpydc2- = 2,2'-bipyridine-5,5'-dicarboxylate) by solvent impregnation. The MOF retained its long-range order, and transmission electron microscopy and elemental mapping confirmed the retention of the crystal morphology and revealed a homogeneous distribution of the hydride within the MOF host. Notably, the B-, N-, and Mg-edge XAS data confirm the coordination of Mg(II) to the N atoms of the chelating bipyridine groups. In situ 11B MAS NMR studies helped elucidate the reaction mechanism and revealed that complete hydrogen release from Mg(BH4)2 occurs as low as 200 °C. Sieverts and thermogravimetric measurements indicate an increase in the rate of hydrogen release, with the onset of hydrogen desorption as low as 120 °C, which is approximately 150 °C lower than that of the bulk material. Furthermore, density functional theory calculations support the improved dehydrogenation properties and confirm the drastically lower activation energy for B-H bond dissociation.
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Affiliation(s)
- Andreas Schneemann
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Liwen F Wan
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Andrew S Lipton
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Yi-Sheng Liu
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jonathan L Snider
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Alexander A Baker
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Joshua D Sugar
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Catalin D Spataru
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Jinghua Guo
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tom S Autrey
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Mathias Jørgensen
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
- Center for Materials Crystallography at the Department of Chemistry and the Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Torben R Jensen
- Center for Materials Crystallography at the Department of Chemistry and the Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Brandon C Wood
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - Mark D Allendorf
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
| | - Vitalie Stavila
- Sandia National Laboratories, 7011 East Avenue, Livermore, California 94550, United States
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Long Z, Park SH, Opella SJ. Effects of deuteration on solid-state NMR spectra of single peptide crystals and oriented protein samples. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 309:106613. [PMID: 31677452 PMCID: PMC7326366 DOI: 10.1016/j.jmr.2019.106613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/18/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Extensive deuteration can be used to simplify NMR spectra by "diluting" and minimizing the effects of the abundant 1H nuclei. In solution-state NMR and magic angle spinning solid-state NMR of proteins, perdeuteration has been widely applied and its effects are well understood. Oriented sample solid-state NMR of proteins, however, is at a much earlier stage of development. In spite of the promise of the approach, the effects of sample deuteration are largely unknown. Here we map out the effects of perdeuteration on solid-state NMR spectra of aligned samples by closely examining differences in results obtained on fully protiated and perdeuterated samples, where all of the carbon sites have either 1H or 2H bonded to them, respectively. The 2H and 15N labeled samples are back-exchanged in 1H2O solution so that the amide 15N sites have a bonded 1H. Line-widths in the 15N chemical shift, 1H chemical shift, and 1H-15N dipolar coupling frequency dimensions were compared for peptide single crystals as well as membrane proteins aligned along with the phospholipids in bilayers with their normals perpendicular to the direction of the magnetic field. Remarkably, line-width differences were not found between fully protiated and perdeuterated samples. However, in the absence of effective 1H-1H homonuclear decoupling, the line-widths in the 1H-15N heteronuclear dipolar coupling frequency dimension were greatly narrowed in the perdeuterated samples. In proton-driven spin diffusion (PDSD) experiments, no effects of perdeuteration were observed. In contrast, in mismatched Hartmann-Hahn experiments, perdeuteration enhances cross-peak intensities by allowing more efficient spin-exchange with less polarization transfer back to the carbon-bound 1H. Here we show that in oriented sample solid-state NMR, the effects of perdeuteration can be exploited in experiments where 1H-1H homonuclear decoupling cannot be applied. These data also provide evidence for the possible contribution of direct 15N-15N dilute-spin mixing mechanism in proton-driven spin diffusion experiments.
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Affiliation(s)
- Zheng Long
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0309, United States
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0309, United States
| | - Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0309, United States.
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Stavila V, Foster ME, Brown JW, Davis RW, Edgington J, Benin AI, Zarkesh RA, Parthasarathi R, Hoyt DW, Walter ED, Andersen A, Washton NM, Lipton AS, Allendorf MD. IRMOF-74( n)-Mg: a novel catalyst series for hydrogen activation and hydrogenolysis of C-O bonds. Chem Sci 2019; 10:9880-9892. [PMID: 32015812 PMCID: PMC6977460 DOI: 10.1039/c9sc01018a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/02/2019] [Indexed: 12/15/2022] Open
Abstract
Metal-Organic Frameworks (MOFs) that catalyze hydrogenolysis reactions are rare and there is little understanding of how the MOF, hydrogen, and substrate molecules interact. In this regard, the isoreticular IRMOF-74 series, two of which are known catalysts for hydrogenolysis of aromatic C-O bonds, provides an unusual opportunity for systematic probing of these reactions. The diameter of the 1D open channels can be varied within a common topology owing to the common secondary building unit (SBU) and controllable length of the hydroxy-carboxylate struts. We show that the first four members of the IRMOF-74(Mg) series are inherently catalytic for aromatic C-O bond hydrogenolysis and that the conversion varies non-monotonically with pore size. These catalysts are recyclable and reusable, retaining their crystallinity and framework structure after the hydrogenolysis reaction. The hydrogenolysis conversion of phenylethylphenyl ether (PPE), benzylphenyl ether (BPE), and diphenyl ether (DPE) varies as PPE > BPE > DPE, consistent with the strength of the C-O bond. Counterintuitively, however, the conversion also follows the trend IRMOF-74(III) > IRMOF-74(IV) > IRMOF-74(II) > IRMOF-74(I), with little variation in the corresponding selectivity. DFT calculations suggest the unexpected behavior is due to much stronger ether and phenol binding to the Mg(ii) open metal sites (OMS) of IRMOF-74(III), resulting from a structural distortion that moves the Mg2+ ions toward the interior of the pore. Solid-state 25Mg NMR data indicate that both H2 and ether molecules interact with the Mg(ii) OMS and hydrogen-deuterium exchange reactions show that these MOFs activate dihydrogen bonds. The results suggest that both confinement and the presence of reactive metals are essential for achieving the high catalytic activity, but that subtle variations in pore structure can significantly affect the catalysis. Moreover, they challenge the notion that simply increasing MOF pore size within a constant topology will lead to higher conversions.
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Affiliation(s)
- Vitalie Stavila
- Chemistry, Combustion, and Materials Center , Sandia National Laboratories , Livermore , California 94551 , USA . ;
| | - Michael E Foster
- Chemistry, Combustion, and Materials Center , Sandia National Laboratories , Livermore , California 94551 , USA . ;
| | - Jonathan W Brown
- Chemistry, Combustion, and Materials Center , Sandia National Laboratories , Livermore , California 94551 , USA . ;
| | - Ryan W Davis
- Chemistry, Combustion, and Materials Center , Sandia National Laboratories , Livermore , California 94551 , USA . ;
| | - Jane Edgington
- Chemistry, Combustion, and Materials Center , Sandia National Laboratories , Livermore , California 94551 , USA . ;
| | - Annabelle I Benin
- Chemistry, Combustion, and Materials Center , Sandia National Laboratories , Livermore , California 94551 , USA . ;
| | - Ryan A Zarkesh
- Chemistry, Combustion, and Materials Center , Sandia National Laboratories , Livermore , California 94551 , USA . ;
| | - Ramakrishnan Parthasarathi
- Chemistry, Combustion, and Materials Center , Sandia National Laboratories , Livermore , California 94551 , USA . ;
| | - David W Hoyt
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , USA
| | - Eric D Walter
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , USA
| | - Amity Andersen
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , USA
| | - Nancy M Washton
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , USA
| | - Andrew S Lipton
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99354 , USA
| | - Mark D Allendorf
- Chemistry, Combustion, and Materials Center , Sandia National Laboratories , Livermore , California 94551 , USA . ;
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Ranjan R, Sinha N. Nuclear magnetic resonance (NMR)-based metabolomics for cancer research. NMR IN BIOMEDICINE 2019; 32:e3916. [PMID: 29733484 DOI: 10.1002/nbm.3916] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/01/2018] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Nuclear magnetic resonance (NMR) has emerged as an effective tool in various spheres of biomedical research, amongst which metabolomics is an important method for the study of various types of disease. Metabolomics has proved its stronghold in cancer research by the development of different NMR methods over time for the study of metabolites, thus identifying key players in the aetiology of cancer. A plethora of one-dimensional and two-dimensional NMR experiments (in solids, semi-solids and solution phases) are utilized to obtain metabolic profiles of biofluids, cell extracts and tissue biopsy samples, which can further be subjected to statistical analysis. Any alteration in the assigned metabolite peaks gives an indication of changes in metabolic pathways. These defined changes demonstrate the utility of NMR in the early diagnosis of cancer and provide further measures to combat malignancy and its progression. This review provides a snapshot of the trending NMR techniques and the statistical analysis involved in the metabolomics of diseases, with emphasis on advances in NMR methodology developed for cancer research.
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Affiliation(s)
- Renuka Ranjan
- Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow, India
- School of Biotechnology, Institute of Science Banaras Hindu University, Varanasi, India
| | - Neeraj Sinha
- Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow, India
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Lee TH, Sani MA, Overall S, Separovic F, Aguilar MI. Effect of phosphatidylcholine bilayer thickness and molecular order on the binding of the antimicrobial peptide maculatin 1.1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:300-309. [DOI: 10.1016/j.bbamem.2017.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/18/2017] [Accepted: 10/08/2017] [Indexed: 01/01/2023]
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Grage SL, Sani MA, Cheneval O, Henriques ST, Schalck C, Heinzmann R, Mylne JS, Mykhailiuk PK, Afonin S, Komarov IV, Separovic F, Craik DJ, Ulrich AS. Orientation and Location of the Cyclotide Kalata B1 in Lipid Bilayers Revealed by Solid-State NMR. Biophys J 2017; 112:630-642. [PMID: 28256223 PMCID: PMC5340158 DOI: 10.1016/j.bpj.2016.12.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 12/23/2016] [Accepted: 12/29/2016] [Indexed: 02/04/2023] Open
Abstract
Cyclotides are ultra-stable cyclic disulfide-rich peptides from plants. Their biophysical effects and medically interesting activities are related to their membrane-binding properties, with particularly high affinity for phosphatidylethanolamine lipids. In this study we were interested in understanding the molecular details of cyclotide-membrane interactions, specifically with regard to the spatial orientation of the cyclotide kalata B1 from Oldenlandia affinis when embedded in a lipid bilayer. Our experimental approach was based on the use of solid-state 19F-NMR of oriented bilayers in conjunction with the conformationally restricted amino acid L-3-(trifluoromethyl)bicyclopent-[1.1.1]-1-ylglycine as an orientation-sensitive 19F-NMR probe. Its rigid connection to the kalata B1 backbone scaffold, together with the well-defined structure of the cyclotide, allowed us to calculate the protein alignment in the membrane directly from the orientation-sensitive 19F-NMR signal. The hydrophobic and polar residues on the surface of kalata B1 form well-separated patches, endowing this cyclotide with a pronounced amphipathicity. The peptide orientation, as determined by NMR, showed that this amphipathic structure matches the polar/apolar interface of the lipid bilayer very well. A location in the amphiphilic headgroup region of the bilayer was supported by 15N-NMR of uniformly labeled protein, and confirmed using solid-state 31P- and 2H-NMR. 31P-NMR relaxation data indicated a change in lipid headgroup dynamics induced by kalata B1. Changes in the 2H-NMR order parameter profile of the acyl chains suggest membrane thinning, as typically observed for amphiphilic peptides embedded near the polar/apolar bilayer interface. Furthermore, from the 19F-NMR analysis two important charged residues, E7 and R28, were found to be positioned equatorially. The observed location thus would be favorable for the postulated binding of E7 to phosphatidylethanolamine lipid headgroups. Furthermore, it may be speculated that this pair of side chains could promote oligomerization of kalata B1 through electrostatic intermolecular contacts via their complementary charges.
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Affiliation(s)
- Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Olivier Cheneval
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Constantin Schalck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ralf Heinzmann
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Joshua S Mylne
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Pavel K Mykhailiuk
- Chemistry Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine; Enamine Ltd., Kyiv, Ukraine
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Igor V Komarov
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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Wang Q, Li Y, Trébosc J, Lafon O, Xu J, Hu B, Feng N, Chen Q, Amoureux JP, Deng F. Population transfer HMQC for half-integer quadrupolar nuclei. J Chem Phys 2015; 142:094201. [DOI: 10.1063/1.4913683] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Qiang Wang
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yixuan Li
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
- Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR-8181, University of Lille, 59652 Villeneuve d’Ascq, France
- Physics Department and Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - Julien Trébosc
- Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR-8181, University of Lille, 59652 Villeneuve d’Ascq, France
| | - Olivier Lafon
- Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR-8181, University of Lille, 59652 Villeneuve d’Ascq, France
| | - Jun Xu
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Bingwen Hu
- Physics Department and Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - Ningdong Feng
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qun Chen
- Physics Department and Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - Jean-Paul Amoureux
- Unit of Catalysis and Chemistry of Solids (UCCS), CNRS UMR-8181, University of Lille, 59652 Villeneuve d’Ascq, France
- Physics Department and Shanghai Key Laboratory of Magnetic Resonance, East China Normal University, Shanghai 200062, China
| | - Feng Deng
- National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
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14
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Opella SJ. Structure determination of membrane proteins by nuclear magnetic resonance spectroscopy. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2013; 6:305-28. [PMID: 23577669 PMCID: PMC3980955 DOI: 10.1146/annurev-anchem-062012-092631] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many biological membranes consist of 50% or more (by weight) membrane proteins, which constitute approximately one-third of all proteins expressed in biological organisms. Helical membrane proteins function as receptors, enzymes, and transporters, among other unique cellular roles. Additionally, most drugs have membrane proteins as their receptors, notably the superfamily of G protein-coupled receptors with seven transmembrane helices. Determining the structures of membrane proteins is a daunting task because of the effects of the membrane environment; specifically, it has been difficult to combine biologically compatible environments with the requirements for the established methods of structure determination. There is strong motivation to determine the structures in their native phospholipid bilayer environment so that perturbations from nonnatural lipids and phases do not have to be taken into account. At present, the only method that can work with proteins in liquid crystalline phospholipid bilayers is solid-state NMR spectroscopy.
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Affiliation(s)
- Stanley J Opella
- Department of Chemistry and Biochemistry, University of California, San Diego 92093, USA.
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15
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Shahid SA, Markovic S, Linke D, van Rossum BJ. Assignment and secondary structure of the YadA membrane protein by solid-state MAS NMR. Sci Rep 2012; 2:803. [PMID: 23150774 PMCID: PMC3495290 DOI: 10.1038/srep00803] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/15/2012] [Indexed: 11/11/2022] Open
Abstract
We report the complete solid-state MAS NMR resonance assignment of a medium-sized, trimeric membrane protein, YadA-M. The protein YadA (Yersinia adhesin A) is an important virulence factor of enteropathogenic Yersinia species (such as Yersinia enterocolitica and Yersinia pseudotuberculosis). YadA is localized on the bacterial cell surface and is involved in adhesion to host cells and tissues. It is anchored in the outer membrane by a transmembrane anchor domain (YadA-M). This domain hosts the so-called autotransporter function of YadA: it transports its own N-terminal domain through the outer membrane. The assignment is based on a dataset that consisted of several MAS NMR correlation spectra, recorded on a single, uniformly (13)C, (15)N- labelled microcrystalline preparation. Except for the single C-terminal residue and the mobile strep tag, we were able to completely assign YadA-M. From this, secondary structure elements were predicted, which, combined with several long-range interstrand restraints, yielded the architecture of the β-sheet.
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Affiliation(s)
- Shakeel A. Shahid
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Max Planck Institute for Developmental Biology; Spemannstraße 35, 72076 Tübingen, Germany
| | - Stefan Markovic
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Dirk Linke
- Max Planck Institute for Developmental Biology; Spemannstraße 35, 72076 Tübingen, Germany
| | - Barth-Jan van Rossum
- Leibniz-Institut für Molekulare Pharmakologie (FMP); Robert-Rössle-Straße 10, 13125 Berlin, Germany
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16
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Membrane-protein structure determination by solid-state NMR spectroscopy of microcrystals. Nat Methods 2012; 9:1212-7. [DOI: 10.1038/nmeth.2248] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 10/10/2012] [Indexed: 11/08/2022]
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17
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Lin EC, Opella SJ. 1H assisted 13C/15N heteronuclear correlation spectroscopy in oriented sample solid-state NMR of single crystal and magnetically aligned samples. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 211:37-44. [PMID: 21543244 PMCID: PMC3236683 DOI: 10.1016/j.jmr.2011.03.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 03/23/2011] [Accepted: 03/29/2011] [Indexed: 05/30/2023]
Abstract
(1)H-irradiation under mismatched Hartmann-Hahn conditions provides an alternative mechanism for carrying out (15)N/(13)C transfers in triple-resonance heteronuclear correlation spectroscopy (HETCOR) on stationary samples of single crystals and aligned samples of biopolymers, which improve the efficiency especially when the direct (15)N-(13)C dipolar couplings are small. In many cases, the sensitivity is improved by taking advantage of the (13)C(α) labeled sites in peptides and proteins with (13)C detection. The similarities between experimental and simulated spectra demonstrate the validity of the recoupling mechanism and identify the potential for applying these experiments to virus particles or membrane proteins in phospholipid bilayers; however, further development is needed in order to derive quantitative distance and angular constraints from these measurements.
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Affiliation(s)
| | - Stanley J. Opella
- Corresponding Author: Stanley J. Opella, , phone 858 822-4820, FAX 858 822-4821
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18
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Comellas G, Lopez JJ, Nieuwkoop AJ, Lemkau LR, Rienstra CM. Straightforward, effective calibration of SPINAL-64 decoupling results in the enhancement of sensitivity and resolution of biomolecular solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 209:131-5. [PMID: 21296014 PMCID: PMC3065959 DOI: 10.1016/j.jmr.2010.12.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 12/21/2010] [Accepted: 12/28/2010] [Indexed: 05/11/2023]
Abstract
We describe a simple yet highly effective optimization strategy for SPINAL-64 ¹H decoupling conditions for magic-angle spinning solid-state NMR. With adjustment of the phase angles in a coupled manner, the optimal conditions resulting from three parameter optimizations can be determined with adjustment of a single phase. Notably, echo T₂ relaxation times for ¹³C and ¹⁵N show significant enhancement (up to 64%), relative to the previous described SPINAL-64 conditions, under the moderate ¹H decoupling levels (60-100 kHz) and MAS rate (13.3 kHz) commonly employed for high-resolution SSNMR spectroscopy of proteins. Additionally, we also investigated the effect at higher spinning rate (33.3 kHz) and compared the results with other ¹H decoupling schemes (TPPM, XiX), as well as SPINAL-64 with the originally reported optimal values.
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Affiliation(s)
- Gemma Comellas
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Jakob J. Lopez
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Andrew J. Nieuwkoop
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Luisel R. Lemkau
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
| | - Chad M. Rienstra
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801
- Corresponding author information: Chad M. Rienstra, Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA. Telephone: (+01) 217 244-4655. Fax: 217 244-3186.
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19
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Lu GJ, Son WS, Opella SJ. A general assignment method for oriented sample (OS) solid-state NMR of proteins based on the correlation of resonances through heteronuclear dipolar couplings in samples aligned parallel and perpendicular to the magnetic field. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 209:195-206. [PMID: 21316275 PMCID: PMC3109902 DOI: 10.1016/j.jmr.2011.01.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 01/08/2011] [Indexed: 05/11/2023]
Abstract
A general method for assigning oriented sample (OS) solid-state NMR spectra of proteins is demonstrated. In principle, this method requires only a single sample of a uniformly ¹⁵N-labeled membrane protein in magnetically aligned bilayers, and a previously assigned isotropic chemical shift spectrum obtained either from solution NMR on micelle or isotropic bicelle samples or from magic angle spinning (MAS) solid-state NMR on unoriented proteoliposomes. The sequential isotropic resonance assignments are transferred to the OS solid-state NMR spectra of aligned samples by correlating signals from the same residue observed in protein-containing bilayers aligned with their normals parallel and perpendicular to the magnetic field. The underlying principle is that the resonances from the same residue have heteronuclear dipolar couplings that differ by exactly a factor of two between parallel and perpendicular alignments. The method is demonstrated on the membrane-bound form of Pf1 coat protein in phospholipid bilayers, whose assignments have been previously made using an earlier generation of methods that relied on the preparation of many selectively labeled (by residue type) samples. The new method provides the correct resonance assignments using only a single uniformly ¹⁵N-labeled sample, two solid-state NMR spectra, and a previously assigned isotropic spectrum. Significantly, this approach is equally applicable to residues in alpha helices, beta sheets, loops, and any other elements of tertiary structure. Moreover, the strategy bridges between OS solid-state NMR of aligned samples and solution NMR or MAS solid-state NMR of unoriented samples. In combination with the development of complementary experimental methods, it provides a step towards unifying these apparently different NMR approaches.
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20
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Toke O, Bánóczi Z, Király P, Heinzmann R, Bürck J, Ulrich AS, Hudecz F. A kinked antimicrobial peptide from Bombina maxima. I. Three-dimensional structure determined by NMR in membrane-mimicking environments. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:447-62. [DOI: 10.1007/s00249-010-0657-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/09/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022]
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21
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Cook G, Stefer S, Opella SJ. Expression and purification of the membrane protein p7 from hepatitis C virus. Biopolymers 2011; 96:32-40. [PMID: 20560141 PMCID: PMC2954269 DOI: 10.1002/bip.21453] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A small 63-residue membrane protein, p7, has essential roles in the infectivity of the hepatitis C virus in humans. This hydrophobic membrane protein forms homo-oligomeric ion channels in bilayers, which can be blocked by known channel-blocking compounds. To perform structural studies of p7 by nuclear magnetic resonance (NMR) spectroscopy, it is necessary to produce milligram quantities of isotopically labeled protein; as is the case for most membrane-associated proteins, this is challenging. We describe the successful expression of full-length p7 and two truncated constructs in Escherichia coli using a fusion partner that directs the overexpressed protein to inclusion bodies. Following isolation of the fusion proteins by affinity chromatography, they were chemically cleaved with cyanogen bromide. The p7-polypeptides were purified by size-exclusion chromatography. Solution NMR two-dimensional heteronuclear single quantum coherence spectra of uniformly (15) N-labeled p7-polypeptides in 1,2-dihexyl-1-sn-glycero-3-phosphocholine isotropic micelles are fully resolved, with a single resonance for each amide site. The solid-state NMR spectra of the same polypeptides in magnetically aligned 14-O-PC/6-O-PC bicelles demonstrate their reconstitution into planar phospholipid bilayers.
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Affiliation(s)
- Gabriel Cook
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0307 USA
| | - Susanne Stefer
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0307 USA
| | - Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0307 USA
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22
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Walther TH, Grage SL, Roth N, Ulrich AS. Membrane Alignment of the Pore-Forming Component TatAd of the Twin-Arginine Translocase from Bacillus subtilis Resolved by Solid-State NMR Spectroscopy. J Am Chem Soc 2010; 132:15945-56. [DOI: 10.1021/ja106963s] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Torsten H. Walther
- DFG-Center for Functional Nanostructures (CFN), Institute of Biological Interfaces (IBG-2), and Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Stephan L. Grage
- DFG-Center for Functional Nanostructures (CFN), Institute of Biological Interfaces (IBG-2), and Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Nadine Roth
- DFG-Center for Functional Nanostructures (CFN), Institute of Biological Interfaces (IBG-2), and Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Anne S. Ulrich
- DFG-Center for Functional Nanostructures (CFN), Institute of Biological Interfaces (IBG-2), and Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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23
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Lin EC, Wu CH, Yang Y, Grant CV, Opella SJ. 1H-13C separated local field spectroscopy of uniformly 13C labeled peptides and proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 206:105-11. [PMID: 20637662 PMCID: PMC2926282 DOI: 10.1016/j.jmr.2010.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 06/22/2010] [Accepted: 06/22/2010] [Indexed: 05/17/2023]
Abstract
By incorporating homonuclear decoupling on both the (1)H and (13)C channels it is feasible to obtain high-resolution two-dimensional separated local field spectra of peptides and proteins that are 100% labeled with (13)C. Dual-PISEMO (Polarization Inversion Spin Exchange Modulated Observation) can be performed as a conventional two-dimensional experiment, or with windowed detection as a one-dimensional experiment that offers flexibility as a building block for shiftless and other multidimensional triple-resonance experiments with the inclusion of (15)N irradiation. The triple-resonance MAGC probe used to perform these experiments at 500 MHz is described.
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24
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Mahalakshmi R, Marassi FM. Orientation of the Escherichia coli outer membrane protein OmpX in phospholipid bilayer membranes determined by solid-State NMR. Biochemistry 2010; 47:6531-8. [PMID: 18512961 DOI: 10.1021/bi800362b] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solid-state NMR orientation-dependent frequencies measured for membrane proteins in macroscopically oriented lipid bilayers provide precise orientation restraints for structure determination in membranes. Here we show that this information can also be used to supplement crystallographic structural data to establish the orientation of a membrane protein in the membrane. This is achieved by incorporating a few orientation restraints, measured for the Escherichia coli outer membrane protein OmpX in magnetically oriented lipid bilayers (bicelles), in a simulated annealing calculation with the coordinates of the OmpX crystal structure. The (1)H-(15)N dipolar couplings measured for the seven Phe residues of OmpX in oriented bilayers can be assigned by back-calculation of the NMR spectrum from the crystal structure and are sufficient to establish the three-dimensional orientation of the protein in the membrane, while the (15)N chemical shifts provide a measure of cross-validation for the analysis. In C14 lipid bilayers, OmpX adopts a transmembrane orientation with a 7 degrees tilt of its beta-barrel axis relative to the membrane normal, matching the hydrophobic thickness of the barrel with that of the membrane.
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Affiliation(s)
- Radhakrishnan Mahalakshmi
- Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
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25
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Wu CH, Das BB, Opella SJ. (1)H-(13)C Hetero-nuclear dipole-dipole couplings of methyl groups in stationary and magic angle spinning solid-state NMR experiments of peptides and proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 202:127-34. [PMID: 19896874 PMCID: PMC2888030 DOI: 10.1016/j.jmr.2009.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 10/16/2009] [Accepted: 10/16/2009] [Indexed: 05/16/2023]
Abstract
(13)C NMR of isotopically labeled methyl groups has the potential to combine spectroscopic simplicity with ease of labeling for protein NMR studies. However, in most high resolution separated local field experiments, such as polarization inversion spin exchange at the magic angle (PISEMA), that are used to measure (1)H-(13)C hetero-nuclear dipolar couplings, the four-spin system of the methyl group presents complications. In this study, the properties of the (1)H-(13)C hetero-nuclear dipolar interactions of (13)C-labeled methyl groups are revealed through solid-state NMR experiments on a range of samples, including single crystals, stationary powders, and magic angle spinning of powders, of (13)C(3) labeled alanine alone and incorporated into a protein. The spectral simplifications resulting from proton detected local field (PDLF) experiments are shown to enhance resolution and simplify the interpretation of results on single crystals, magnetically aligned samples, and powders. The complementarity of stationary sample and magic angle spinning (MAS) measurements of dipolar couplings is demonstrated by applying polarization inversion spin exchange at the magic angle and magic angle spinning (PISEMAMAS) to unoriented samples.
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26
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Efficient heteronuclear dipolar decoupling in NMR of static solid samples using phase-wiggled two-pulse phase modulation. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.10.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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Cook GA, Opella SJ. NMR studies of p7 protein from hepatitis C virus. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:1097-104. [PMID: 19727701 PMCID: PMC2878448 DOI: 10.1007/s00249-009-0533-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 07/22/2009] [Accepted: 08/04/2009] [Indexed: 01/10/2023]
Abstract
The p7 protein of hepatitis C virus (HCV) plays an important role in the viral lifecycle. Like other members of the viroporin family of small membrane proteins, the amino acid sequence of p7 is largely conserved over the entire range of genotypes, and it forms ion channels that can be blocked by a number of established channel-blocking compounds. Its characteristics as a membrane protein make it difficult to study by most structural techniques, since it requires the presence of lipids to fold and function properly. Purified p7 can be incorporated into phospholipid bilayers and micelles. Initial solid-state nuclear magnetic resonance (NMR) studies of p7 in 14-O-PC/6-O-PC bicelles indicate that the protein contains helical segments that are tilted approximately 10° and 25° relative to the bilayer normal. A truncated construct corresponding to the second transmembrane domain of p7 is shown to have properties similar to those of the full-length protein, and was used to determine that the helix segment tilted at 10° is in the C-terminal portion of the protein. The addition of the channel blocker amantadine to the full-length protein resulted in selective chemical shift changes, demonstrating that NMR has a potential role in the development of drugs targeted to p7.
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Affiliation(s)
- Gabriel A Cook
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
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28
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Abstract
The acquisition and analysis of high resolution one- and two-dimensional solid-state nuclear magnetic resonance (NMR) spectra without chemical shift frequencies are described. Many variations of shiftless NMR spectroscopy are feasible. A two-dimensional experiment that correlates the dipole-dipole and dipole-dipole couplings in the model peptide , (15)N labeled N-acetyl-leucine is demonstrated. In addition to the resolution of resonances from individual sites in a single crystal sample, the bond lengths and angles are characterized by the two-dimensional powder pattern obtained from a polycrystalline sample.
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Affiliation(s)
- Chin H Wu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0307, USA
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Wu CH, Opella SJ. Proton-detected separated local field spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 190:165-70. [PMID: 17981481 PMCID: PMC3486921 DOI: 10.1016/j.jmr.2007.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 09/29/2007] [Accepted: 10/04/2007] [Indexed: 05/17/2023]
Abstract
PISEMO, a separated local field experiment that can be performed with either direct (15)N (or (13)C) detection or indirect (1)H detection, is demonstrated on a single crystal of a model peptide. The (1)H signals modulated by (1)H-(15)N heteronuclear dipole-dipole couplings are observed stroboscopically in the windows of the multiple-pulse sequence used to attenuate (1)H-(1)H homonuclear dipole-dipole couplings. (1)H-detection yields spectra with about 2.5 times the signal to noise ratio observed with (15)N-detection under equivalent conditions. Resolution in both the (15)N chemical shift and (1)H-(15)N heteronuclear dipole-dipole coupling dimensions is similar to that observed with PISEMA, however, since only on-resonance pulses are utilized, the bandwidth is better.
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Structural characterization of the pore forming protein TatAd of the twin-arginine translocase in membranes by solid-state 15N-NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3071-9. [DOI: 10.1016/j.bbamem.2007.09.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 09/12/2007] [Accepted: 09/13/2007] [Indexed: 11/23/2022]
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Mahalakshmi R, Franzin CM, Choi J, Marassi FM. NMR structural studies of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3216-24. [PMID: 17916325 DOI: 10.1016/j.bbamem.2007.08.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/01/2007] [Accepted: 08/02/2007] [Indexed: 10/22/2022]
Abstract
The beta-barrels found in the outer membranes of prokaryotic and eukaryotic organisms constitute an important functional class of proteins. Here we present solid-state NMR spectra of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes. We show that OmpX is folded in both glass-supported oriented lipid bilayers and in lipid bicelles that can be magnetically oriented with the membrane plane parallel or perpendicular to the direction of the magnetic field. The presence of resolved peaks in these spectra demonstrates that OmpX undergoes rotational diffusion around an axis perpendicular to the membrane surface. A tightly hydrogen-bonded domain of OmpX resists exchange with D2O for days and is assigned to the transmembrane beta-barrel, while peaks at isotropic resonance frequencies that disappear rapidly in D2O are assigned to the extracellular and periplasmic loops. The two-dimensional 1H/15N separated local field spectra of OmpX have several resolved peaks, and agree well with the spectra calculated from the crystal structure of OmpX rotated with the barrel axis nearly parallel (5 degrees tilt) to the direction of the magnetic field. The data indicate that it will be possible to obtain site-specific resonance assignments and to determine the structure, tilt, and rotation of OmpX in membranes using the solid-state NMR methods that are currently being applied to alpha-helical membrane proteins.
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32
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Sinha N, Grant CV, Park SH, Brown JM, Opella SJ. Triple resonance experiments for aligned sample solid-state NMR of (13)C and (15)N labeled proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 186:51-64. [PMID: 17293139 PMCID: PMC3760591 DOI: 10.1016/j.jmr.2007.01.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Revised: 01/11/2007] [Accepted: 01/21/2007] [Indexed: 05/11/2023]
Abstract
Initial steps in the development of a suite of triple-resonance (1)H/(13)C/(15)N solid-state NMR experiments applicable to aligned samples of (13)C and (15)N labeled proteins are described. The experiments take advantage of the opportunities for (13)C detection without the need for homonuclear (13)C/(13)C decoupling presented by samples with two different patterns of isotopic labeling. In one type of sample, the proteins are approximately 20% randomly labeled with (13)C in all backbone and side chain carbon sites and approximately 100% uniformly (15)N labeled in all nitrogen sites; in the second type of sample, the peptides and proteins are (13)C labeled at only the alpha-carbon and (15)N labeled at the amide nitrogen of a few residues. The requirement for homonuclear (13)C/(13)C decoupling while detecting (13)C signals is avoided in the first case because of the low probability of any two (13)C nuclei being bonded to each other; in the second case, the labeled (13)C(alpha) sites are separated by at least three bonds in the polypeptide chain. The experiments enable the measurement of the (13)C chemical shift and (1)H-(13)C and (15)N-(13)C heteronuclear dipolar coupling frequencies associated with the (13)C(alpha) and (13)C' backbone sites, which provide orientation constraints complementary to those derived from the (15)N labeled amide backbone sites. (13)C/(13)C spin-exchange experiments identify proximate carbon sites. The ability to measure (13)C-(15)N dipolar coupling frequencies and correlate (13)C and (15)N resonances provides a mechanism for making backbone resonance assignments. Three-dimensional combinations of these experiments ensure that the resolution, assignment, and measurement of orientationally dependent frequencies can be extended to larger proteins. Moreover, measurements of the (13)C chemical shift and (1)H-(13)C heteronuclear dipolar coupling frequencies for nearly all side chain sites enable the complete three-dimensional structures of proteins to be determined with this approach.
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Affiliation(s)
- Neeraj Sinha
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307 La Jolla, CA 92093-0307, USA
| | - Christopher V. Grant
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307 La Jolla, CA 92093-0307, USA
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307 La Jolla, CA 92093-0307, USA
| | | | - Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307 La Jolla, CA 92093-0307, USA
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Bertelsen K, Pedersen JM, Nielsen NC, Vosegaard T. 2D separated-local-field spectra from projections of 1D experiments. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 184:330-6. [PMID: 17084651 DOI: 10.1016/j.jmr.2006.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 10/02/2006] [Accepted: 10/16/2006] [Indexed: 05/12/2023]
Abstract
A novel procedure for reconstruction of 2D separated-local-field (SLF) NMR spectra from projections of 1D NMR data is presented. The technique, dubbed SLF projection reconstruction from one-dimensional spectra (SLF-PRODI), is particularly useful for uniaxially oriented membrane protein samples and represents a fast and robust alternative to the popular PISEMA experiment which correlates (1)H-(15)N dipole-dipole couplings with (15)N chemical shifts. The different 1D projections in the SLF-PRODI experiment are obtained from 1D spectra recorded under influence of homonuclear decoupling sequences with different scaling factors for the heteronuclear dipolar couplings. We demonstrate experimentally and numerically that as few as 2-4 1D projections will normally be sufficient to reconstruct a 2D SLF-PRODI spectrum with a quality resembling typical PISEMA spectra, leading to significant reduction of the acquisition time.
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Affiliation(s)
- Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, DK-8000 Aarhus C, Denmark
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34
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Dvinskikh SV, Yamamoto K, Dürr UHN, Ramamoorthy A. Sensitivity and resolution enhancement in solid-state NMR spectroscopy of bicelles. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 184:228-35. [PMID: 17084096 PMCID: PMC1861833 DOI: 10.1016/j.jmr.2006.10.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Revised: 10/03/2006] [Accepted: 10/16/2006] [Indexed: 05/12/2023]
Abstract
Magnetically aligned bicelles are becoming attractive model membranes to investigate the structure, dynamics, geometry, and interaction of membrane-associated peptides and proteins using solution- and solid-state NMR experiments. Recent studies have shown that bicelles are more suitable than mechanically aligned bilayers for multidimensional solid-state NMR experiments. In this work, we describe experimental aspects of the natural abundance (13)C and (14)N NMR spectroscopy of DMPC/DHPC bicelles. In particular, approaches to enhance the sensitivity and resolution and to quantify radio-frequency heating effects are presented. Sensitivity of (13)C detection using single pulse excitation, conventional cross-polarization (CP), ramp-CP, and NOE techniques are compared. Our results suggest that the proton decoupling efficiency of the FLOPSY pulse sequence is better than that of continuous wave decoupling, TPPM, SPINAL, and WALTZ sequences. A simple method of monitoring the water proton chemical shift is demonstrated for the measurement of sample temperature and calibration of the radio-frequency-induced heating in the sample. The possibility of using (14)N experiments on bicelles is also discussed.
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Affiliation(s)
| | - Kazutoshi Yamamoto
- Biophysics Research Division and Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ulrich H. N. Dürr
- Biophysics Research Division and Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Research Division and Department of Chemistry, The University of Michigan, Ann Arbor, MI 48109-1055, USA
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35
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Nevzorov AA, Park SH, Opella SJ. Three-dimensional experiment for solid-state NMR of aligned protein samples in high field magnets. JOURNAL OF BIOMOLECULAR NMR 2007; 37:113-6. [PMID: 17216304 DOI: 10.1007/s10858-006-9121-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Accepted: 10/27/2006] [Indexed: 05/13/2023]
Abstract
A pulse sequence that yields three-dimensional (1)H chemical shift/(1)H-(15)N heteronuclear dipolar coupling/(15)N chemical shift solid-state NMR spectra is demonstrated on a uniformly (15)N labeled membrane protein in magnetically aligned phospholipid bilayers. Based on SAMPI4, the pulse sequence yields high resolution in all three dimensions at a (1)H resonance frequency of 900 MHz with the relatively low rf field strength (33 kHz) available for a lossy aqueous sample with a commercial spectrometer and probe. The (1)H chemical shift frequency dimension is shown to select among amide resonances, which will be useful in studies of larger polytopic membrane proteins where the resonances overlap in two-dimensional spectra. Moreover, the (1)H chemical shift, which can be measured from these spectra, provides an additional orientationally dependent frequency as input for structure calculations.
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Affiliation(s)
- Alexander A Nevzorov
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0307, USA
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36
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Pan YL, Cheng JTJ, Hale J, Pan J, Hancock REW, Straus SK. Characterization of the structure and membrane interaction of the antimicrobial peptides aurein 2.2 and 2.3 from Australian southern bell frogs. Biophys J 2007; 92:2854-64. [PMID: 17259271 PMCID: PMC1831713 DOI: 10.1529/biophysj.106.097238] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The structure and membrane interaction of the antimicrobial peptide aurein 2.2 (GLFDIVKKVVGALGSL-CONH(2)), aurein 2.3 (GLFDIVKKVVGAIGSL-CONH(2)), both from Litoria aurea, and a carboxy C-terminal analog of aurein 2.3 (GLFDIVKKVVGAIGSL-COOH) were studied to determine which features of this class of peptides are key to activity. Circular dichroism and solution-state NMR data indicate that all three peptides adopt an alpha-helical structure in the presence of trifluoroethanol or lipids such as 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and a 1:1 mixture of DMPC and 1,2-dimyristoyl-sn-glycero-3-[phospho-rac-(1-glycerol)] (DMPG). Oriented circular dichroism was used to determine the orientation of the peptides in lipid bilayers over a range of concentrations (peptide/lipid molar ratios (P/L) = 1:15-1:120) in DMPC and 1:1 DMPC/DMPG, in the liquid crystalline state. The results demonstrate that in DMPC all three peptides are surface adsorbed over a range of low peptide concentrations but insert into the bilayers at high peptide concentrations. This finding is corroborated by (31)P-solid-state NMR data of the three peptides in DMPC, which shows that at high peptide concentrations the peptides perturb the membrane. Oriented circular dichroism data of the aurein peptides in 1:1 DMPC/DMPG, on the other hand, show that the peptides with amidated C-termini readily insert into the membrane bilayers over the concentration range studied (P/L = 1:15-1:120), whereas the aurein 2.3 peptide with a carboxy C-terminus inserts at a threshold concentration of P/L* between 1:80 and 1:120. Overall, the data presented here suggest that all three peptides studied interact with phosphatidylcholine membranes in a manner which is similar to aurein 1.2 and citropin 1.1, as reported in the literature, with no correlation to the reported activity. On the other hand, both aurein 2.2 and aurein 2.3 behave similarly in phosphatidylcholine/phosphatidylglycerol (PC/PG) membranes, whereas aurein 2.3-COOH inserts less readily. As this does not correlate with reported activities, minimal inhibitory concentrations of the three peptides against Staphylococcus aureus (strain C622, ATCC 25923) and Staphylococcus epidermidis (strain C621--clinical isolate) were determined. The correlation between structure, membrane interaction, and activity are discussed in light of these results.
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Affiliation(s)
- Yeang-Ling Pan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
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37
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Doty FD, Kulkarni J, Turner C, Entzminger G, Bielecki A. Using a cross-coil to reduce RF heating by an order of magnitude in triple-resonance multinuclear MAS at high fields. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 182:239-53. [PMID: 16860580 DOI: 10.1016/j.jmr.2006.06.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2006] [Revised: 06/13/2006] [Accepted: 06/26/2006] [Indexed: 05/11/2023]
Abstract
Four different coil designs for use with MAS in triple-resonance multi-nuclear experiments at high fields are compared, using a combination of finite element analysis (FEA) software and NMR experiments, with respect to RF field strength per unit power and relative sample heating, as governed by mean E/B(1) within the sample region. A commercial FEA package, Microwave Studio 5.1 by Computer Simulation Technology (CST) is shown to obtain remarkably accurate agreement with the experiments in Q(L), L, B, E, and mode frequencies in all cases. A simplified treatment of RF heating in NMR MAS samples is derived and shown to agree with the NMR experimental results within about 10% for two representative stator designs. The coil types studied include: (1) a variable-pitch solenoid outside a ceramic coilform, (2) a conventional solenoid very closely spaced to the MAS rotor, (3) a scroll coil, and (4) a segmented saddle cross coil (XC) for (1)H with an additional solenoid over it for the two lower-frequency channels. The XC/solenoid is shown to offer substantial advantages in reduced decoupler heating, improved S/N, and improved compatibility with multinuclear tuning and high-power decoupling. This seems largely because the division of labor between two orthogonal coils allows them each, and their associated circuitry, to be separately optimized for their respective regimes.
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38
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Park SH, De Angelis AA, Nevzorov AA, Wu CH, Opella SJ. Three-dimensional structure of the transmembrane domain of Vpu from HIV-1 in aligned phospholipid bicelles. Biophys J 2006; 91:3032-42. [PMID: 16861273 PMCID: PMC1578490 DOI: 10.1529/biophysj.106.087106] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The three-dimensional backbone structure of the transmembrane domain of Vpu from HIV-1 was determined by solid-state NMR spectroscopy in two magnetically-aligned phospholipid bilayer environments (bicelles) that differed in their hydrophobic thickness. Isotopically labeled samples of Vpu(2-30+), a 36-residue polypeptide containing residues 2-30 from the N-terminus of Vpu, were incorporated into large (q = 3.2 or 3.0) phospholipid bicelles composed of long-chain ether-linked lipids (14-O-PC or 16-O-PC) and short-chain lipids (6-O-PC). The protein-containing bicelles are aligned in the static magnetic field of the NMR spectrometer. Wheel-like patterns of resonances characteristic of tilted transmembrane helices were observed in two-dimensional (1)H/(15)N PISEMA spectra of uniformly (15)N-labeled Vpu(2-30+) obtained on bicelle samples with their bilayer normals aligned perpendicular or parallel to the direction of the magnetic field. The NMR experiments were performed at a (1)H resonance frequency of 900 MHz, and this resulted in improved data compared to lower-resonance frequencies. Analysis of the polarity-index slant-angle wheels and dipolar waves demonstrates the presence of a transmembrane alpha-helix spanning residues 8-25 in both 14-O-PC and 16-O-PC bicelles, which is consistent with results obtained previously in micelles by solution NMR and mechanically aligned lipid bilayers by solid-state NMR. The three-dimensional backbone structures were obtained by structural fitting to the orientation-dependent (15)N chemical shift and (1)H-(15)N dipolar coupling frequencies. Tilt angles of 30 degrees and 21 degrees are observed in 14-O-PC and 16-O-PC bicelles, respectively, which are consistent with the values previously determined for the same polypeptide in mechanically-aligned DMPC and DOPC bilayers. The difference in tilt angle in C14 and C16 bilayer environments is also consistent with previous results indicating that the transmembrane helix of Vpu responds to hydrophobic mismatch by changing its tilt angle. The kink found in the middle of the helix in the longer-chain C18 bilayers aligned on glass plates was not found in either of these shorter-chain (C14 or C16) bilayers.
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Affiliation(s)
- Sang Ho Park
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0307, USA
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39
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Park SH, Prytulla S, De Angelis AA, Brown JM, Kiefer H, Opella SJ. High-resolution NMR spectroscopy of a GPCR in aligned bicelles. J Am Chem Soc 2006; 128:7402-3. [PMID: 16756269 PMCID: PMC3236030 DOI: 10.1021/ja0606632] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Solid-state NMR spectra with single-site resolution of CXCR1, a G protein-coupled receptor (GPCR), were obtained in magnetically aligned phospholipid bicelles. These results demonstrate that GPCRs in phospholipid bilayers are suitable samples for structure determination by solid-state NMR. The spectra also enable studies of drug-receptor interactions.
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Affiliation(s)
- Sang Ho Park
- Department of Chemistry and Biochemistry. University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0307, USA
| | - Stefan Prytulla
- m-phasys GmbH, Vor dem Kreuzberg 17, Tubingen 72070, Germany
| | - Anna A. De Angelis
- Department of Chemistry and Biochemistry. University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0307, USA
| | | | - Hans Kiefer
- m-phasys GmbH, Vor dem Kreuzberg 17, Tubingen 72070, Germany
| | - Stanley J. Opella
- Department of Chemistry and Biochemistry. University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0307, USA
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40
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Affiliation(s)
- Cecil Dybowski
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716-2522, USA
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41
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Jones DH, Opella SJ. Application of Maximum Entropy reconstruction to PISEMA spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 179:105-13. [PMID: 16343957 DOI: 10.1016/j.jmr.2005.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2005] [Revised: 11/21/2005] [Accepted: 11/22/2005] [Indexed: 05/05/2023]
Abstract
Maximum Entropy reconstruction is applied to two-dimensional PISEMA spectra of stationary samples of peptide crystals and proteins in magnetically aligned virus particles and membrane bilayers. Improvements in signal-to-noise ratios were observed with minimal distortion of the spectra when Maximum Entropy reconstruction was applied to non-linearly sampled data in the indirect dimension. Maximum Entropy reconstruction was also applied in the direct dimension by selecting sub-sets of data from the free induction decays. Because the noise is uncorrelated in the spectra obtained by Maximum Entropy reconstruction of data with different non-linear sampling schedules, it is possible to improve the signal-to-noise ratios by co-addition of multiple spectra derived from one experimental data set. The combined application of Maximum Entropy to data in the indirect and direct dimensions has the potential to lead to substantial reductions in the total amount of experimental time required for acquisition of data in multidimensional NMR experiments.
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Affiliation(s)
- D H Jones
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307 La Jolla, CA 92093-0307, USA
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