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Jayanthi S, Ramanathan KV. 2n-SEMA-a robust solid state nuclear magnetic resonance experiment for measuring heteronuclear dipolar couplings in static oriented systems using effective transverse spin-lock. J Chem Phys 2010; 132:134501. [DOI: 10.1063/1.3336815] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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52
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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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53
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Jayanthi S, Madhu PK, Ramanathan KV. Measurement of Carbon−Proton Dipolar Couplings in Liquid Crystals Using DAPT. J Phys Chem A 2008; 112:11159-64. [DOI: 10.1021/jp804764q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S. Jayanthi
- Department of Physics, Indian Institute of Science, Bangalore, 560 012 India, Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai. 400 005 India, and NMR Research Centre, Indian Institute of Science, Bangalore, 560 012 India
| | - P. K. Madhu
- Department of Physics, Indian Institute of Science, Bangalore, 560 012 India, Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai. 400 005 India, and NMR Research Centre, Indian Institute of Science, Bangalore, 560 012 India
| | - K. V. Ramanathan
- Department of Physics, Indian Institute of Science, Bangalore, 560 012 India, Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai. 400 005 India, and NMR Research Centre, Indian Institute of Science, Bangalore, 560 012 India
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54
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Dvinskikh SV, Yamamoto K, Scanu D, Deschenaux R, Ramamoorthy A. High-resolution characterization of liquid-crystalline [60]fullerenes using solid-state nuclear magnetic resonance spectroscopy. J Phys Chem B 2008; 112:12347-53. [PMID: 18781716 DOI: 10.1021/jp803265z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Liquid-crystalline materials containing fullerenes are valuable in the development of supramolecular switches and in solar cell technology. In this study, we characterize the liquid-crystalline and dynamic properties of fullerene-containing thermotropic compounds using solid-state natural abundance (13)C NMR experiments under stationary and magic angle spinning sample conditions. Chemical shifts spectra were measured in isotropic, liquid-crystalline nematic and smectic A and crystalline phases using one-dimensional (13)C experiments, while two-dimensional separated local-field experiments were used to measure the (1)H- (13)C dipolar couplings in mesophases. Chemical shift and dipolar coupling parameters were used to characterize the structure and dynamics of the liquid-crystalline dyads. NMR data of fullerene-containing thermotropic liquid crystals are compared to that of basic mesogenic unit and mesomorphic promoter compounds. Our NMR results suggest that the fullerene-ferrocene dyads form highly dynamic liquid-crystalline phases in which molecules rotate fast around the symmetry axis on the characteristic NMR time scale of approximately 10 (-4) s.
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Affiliation(s)
- Sergey V Dvinskikh
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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55
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Das BB, Ajithkumar TG, Ramanathan KV. Improved pulse schemes for separated local field spectroscopy for static and spinning samples. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2008; 33:57-63. [PMID: 18406111 DOI: 10.1016/j.ssnmr.2008.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 02/06/2008] [Accepted: 02/27/2008] [Indexed: 05/26/2023]
Abstract
An improved pulse sequence for SLF experiments based on the magic sandwich (MS) scheme for homo-nuclear dipolar decoupling is proposed. The sequence incorporates a double MS, both on I and S spins and has been named as EXE-MS2. The proposed scheme which has a scaling factor of 1 is observed to be free from low intensity artifacts and provides better line-widths particularly for S spins labeled at multiple sites. The pulse sequence which has been applied on static oriented samples incorporates the EXE scheme where direct polarization of the S spin in the B(0) field is utilized in the place of polarization inversion and is observed to perform well without any loss of sensitivity while ensuring considerable reduction in rf power input into the sample. The EXE scheme has also been tested for solid samples under MAS.
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Affiliation(s)
- Bibhuti B Das
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
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56
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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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57
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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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58
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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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59
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Dürr UH, Waskell L, Ramamoorthy A. The cytochromes P450 and b5 and their reductases—Promising targets for structural studies by advanced solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3235-59. [DOI: 10.1016/j.bbamem.2007.08.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 08/08/2007] [Indexed: 02/02/2023]
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60
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Fu R, Truong M, Saager RJ, Cotten M, Cross TA. High-resolution heteronuclear correlation spectroscopy in solid state NMR of aligned samples. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 188:41-8. [PMID: 17606394 DOI: 10.1016/j.jmr.2007.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Revised: 06/12/2007] [Accepted: 06/15/2007] [Indexed: 05/16/2023]
Abstract
A new two-dimensional scheme is proposed for accurate measurements of high-resolution chemical shifts and heteronuclear dipolar couplings in NMR of aligned samples. Both the (1)H chemical shifts and the (1)H-(15)N dipolar couplings are evolved in the indirect dimension while the (15)N chemical shifts are detected. This heteronuclear correlation (HETCOR) spectroscopy yields high-resolution (1)H chemical shifts split by the (1)H-(15)N dipolar couplings in the indirect dimension and the (15)N chemical shifts in the observed dimension. The advantages of the HETCOR technique are illustrated for a static (15)N-acetyl-valine crystal sample and a (15)N-labeled helical peptide sample aligned in hydrated lipid bilayers.
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Affiliation(s)
- Riqiang Fu
- Center for Interdisciplinary Magnetic Resonance, National High Magnetic Field Laboratory, 1800 E. Paul Dirac Drive, Tallahassee, FL 32310, USA.
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61
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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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62
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Heteronuclear polarization transfer in static oriented systems using a windowless multiple-pulse sequence. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.03.104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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63
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Das BB, Ajithkumar TG, Sinha N, Opella SJ, Ramanathan KV. Cross- and axial-peak intensities in 2D-SLF experiments based on cross-polarization--the role of the initial density matrix. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 185:308-17. [PMID: 17280846 DOI: 10.1016/j.jmr.2007.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Revised: 01/08/2007] [Accepted: 01/10/2007] [Indexed: 05/13/2023]
Abstract
Simulations and experiments on simple oriented systems have been used to estimate the relative ratio of cross-peak to axial-peak intensities in 2D-SLF experiments based on dipolar oscillations during cross-polarization (CP). The density matrix prior to dipolar evolution is considered and for an isolated spin pair, it is shown that direct calculations of the ratios match well with simulations and experimental results. Along with the standard CP pulse sequence, two other pulse sequences namely CP with polarization inversion (PI-CP) and another novel variation of the standard CP experiment (EXE-CP) reported recently have been considered. Inclusion of homonuclear dipolar coupling has been observed to increase the axial-peak intensities. In combination with Lee-Goldburg (LG) decoupling, experiments on an oriented liquid crystalline sample have been carried out and the performance of the pulse schemes have been compared. The applicability of the new pulse sequence for different samples and different nuclei is discussed. Such studies are expected to lead to a better understanding of the experiments and to the design of useful pulse sequences.
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Affiliation(s)
- Bibhuti B Das
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
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64
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Nevzorov AA, Opella SJ. Selective averaging for high-resolution solid-state NMR spectroscopy of aligned samples. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 185:59-70. [PMID: 17074522 DOI: 10.1016/j.jmr.2006.09.006] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2006] [Revised: 09/14/2006] [Accepted: 09/15/2006] [Indexed: 05/12/2023]
Abstract
Solid-state NMR experiments benefit from being performed at high fields, and this is essential in order to obtain spectra with the resolution and sensitivity required for applications to protein structure determination in aligned samples. Since the amount of rf power that can be applied is limited, especially for aqueous protein samples, the most important pulse sequences suffer from bandwidth limitations resulting from the same spread in chemical shift frequencies that aids resolution. SAMPI4 is a pulse sequence that addresses these limitations. It yields separated local field spectra with narrower and more uniform linewidths over the entire spectrum than the currently used PISEMA and SAMMY experiments. In addition, it is much easier to set up on commercial spectrometers and can be incorporated as a building block into other multidimensional pulse sequences. This is illustrated with a two-dimensional HETCOR experiment, where it is crucial to transfer polarization from the amide protons to their directly bonded nitrogens over a wide range of chemical shift frequencies. A quantum-mechanical treatment of the spin Hamiltonians under high-power rf pulses is presented which gives the scaling factor for SAMPI4 as well as the durations of the rf pulses to achieve optimal decoupling.
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Affiliation(s)
- Alexander A Nevzorov
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0307, USA
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65
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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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66
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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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67
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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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68
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Dvinskikh SV, Dürr UHN, Yamamoto K, Ramamoorthy A. High-resolution 2D NMR spectroscopy of bicelles to measure the membrane interaction of ligands. J Am Chem Soc 2007; 129:794-802. [PMID: 17243815 PMCID: PMC2527737 DOI: 10.1021/ja065536k] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Magnetically aligned bicelles are increasingly being used as model membranes in solution- and solid-state NMR studies of the structure, dynamics, topology, and interaction of membrane-associated peptides and proteins. These studies commonly utilize the PISEMA pulse sequence to measure dipolar coupling and chemical shift, the two key parameters used in subsequent structural analysis. In the present study, we demonstrate that the PISEMA and other rotating-frame pulse sequences are not suitable for the measurement of long-range heteronuclear dipolar couplings, and that they provide inaccurate values when multiple protons are coupled to a 13C nucleus. Furthermore, we demonstrate that a laboratory-frame separated-local-field experiment is capable of overcoming these difficulties in magnetically aligned bicelles. An extension of this approach to accurately measure 13C-31P and 1H-31P couplings from phospholipids, which are useful to understand the interaction of molecules with the membrane, is also described. In these 2D experiments, natural abundance 13C was observed from bicelles containing DMPC and DHPC lipid molecules. As a first application, these solid-state NMR approaches were utilized to probe the membrane interaction of an antidepressant molecule, desipramine, and its location in the membrane.
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Affiliation(s)
| | - Ulrich H. N. Dürr
- Biophysics Research Division and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, U.S.A
| | - Kazutoshi Yamamoto
- Biophysics Research Division and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, U.S.A
| | - Ayyalusamy Ramamoorthy
- Biophysics Research Division and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, U.S.A
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69
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De Angelis AA, Howell SC, Nevzorov AA, Opella SJ. Structure determination of a membrane protein with two trans-membrane helices in aligned phospholipid bicelles by solid-state NMR spectroscopy. J Am Chem Soc 2006; 128:12256-67. [PMID: 16967977 PMCID: PMC3236029 DOI: 10.1021/ja063640w] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure of the membrane protein MerFt was determined in magnetically aligned phospholipid bicelles by solid-state NMR spectroscopy. With two trans-membrane helices and a 10-residue inter-helical loop, this truncated construct of the mercury transport membrane protein MerF has sufficient structural complexity to demonstrate the feasibility of determining the structures of polytopic membrane proteins in their native phospholipid bilayer environment under physiological conditions. PISEMA, SAMMY, and other double-resonance experiments were applied to uniformly and selectively (15)N-labeled samples to resolve and assign the backbone amide resonances and to measure the associated (15)N chemical shift and (1)H-(15)N heteronuclear dipolar coupling frequencies as orientation constraints for structure calculations. (1)H/(13)C/(15)N triple-resonance experiments were applied to selectively (13)C'- and (15)N-labeled samples to complete the resonance assignments, especially for residues in the nonhelical regions of the protein. A single resonance is observed for each labeled site in one- and two-dimensional spectra. Therefore, each residue has a unique conformation, and all protein molecules in the sample have the same three-dimensional structure and are oriented identically in planar phospholipid bilayers. Combined with the absence of significant intensity near the isotropic resonance frequency, this demonstrates that the entire protein, including the loop and terminal regions, has a well-defined, stable structure in phospholipid bilayers.
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Affiliation(s)
- Anna A. De Angelis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307, La Jolla, California 92093-0307
| | - Stanley C. Howell
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307, La Jolla, California 92093-0307
| | - Alexander A. Nevzorov
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307, La Jolla, California 92093-0307
| | - Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0307, La Jolla, California 92093-0307
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70
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Zujović ZD, Bowmaker GA. Fast proton spin-lattice relaxation time in the rotating frame during the application of time averaged precession frequency. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 181:336-41. [PMID: 16757196 DOI: 10.1016/j.jmr.2006.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 04/19/2006] [Accepted: 05/15/2006] [Indexed: 05/10/2023]
Abstract
A relatively rapid phase alternation of the effective field in the time averaged precession frequency (TAPF) sequence results in averaging of the proton RF spin-lock field. The spin-locking of the proton magnetization becomes less efficient and thus shortens T(1rho)(H), the proton spin-lattice relaxation time in the rotating frame. The relaxation time also depends on the ratio of tau(1) and tau(2) intervals i.e. tau(1)/tau(2) and not only on the number of tau(c)=tau(1)+tau(2) blocks, i.e. the number of the phase transients. Experiments are performed on solid samples of ferrocene and glycine and for some time intervals, T(1rho)(H) is shortened by factors of 9-100 compared to the relaxation times obtained in the standard experiment.
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Affiliation(s)
- Zoran D Zujović
- Department of Chemistry, The University of Auckland, Private Bag 92019, Auckland, New Zealand.
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71
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Prosser RS, Evanics F, Kitevski JL, Al-Abdul-Wahid MS. Current Applications of Bicelles in NMR Studies of Membrane-Associated Amphiphiles and Proteins,. Biochemistry 2006; 45:8453-65. [PMID: 16834319 DOI: 10.1021/bi060615u] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This review covers current trends in studies of membrane amphiphiles and membrane proteins using both fast tumbling bicelles and magnetically aligned bicelle media for both solution state and solid state NMR. The fast tumbling bicelles provide a versatile biologically mimetic membrane model, which in many cases is preferable to micelles, both because of the range of lipids and amphiphiles that may be combined and because radius of curvature effects and strain effects common with micelles may be avoided. Drug and small molecule binding and partitioning studies should benefit from their application in fast tumbling bicelles, tailored to mimic specific membranes. A wide range of topology and immersion depth studies have been shown to be effective in fast tumbling bicelles, while residual dipolar couplings add another dimension to structure refinement possibilities, particularly for situations in which the peptide is uniformly labeled with 15N and 13C. Solid state NMR studies of polytopic transmembrane proteins demonstrate that it is possible to express, purify, and reconstitute membrane proteins, ranging in size from single transmembrane domains to seven-transmembrane GPCRs, into bicelles. The line widths and quality of the resulting 15NH dipole-15N chemical shift spectra demonstrate that there are no insurmountable obstacles to the study of large membrane proteins in magnetically aligned media.
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Affiliation(s)
- R Scott Prosser
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road, North Mississauga, ON, Canada L5L 1C6.
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72
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Dvinskikh S, Dürr U, Yamamoto K, Ramamoorthy A. A high-resolution solid-state NMR approach for the structural studies of bicelles. J Am Chem Soc 2006; 128:6326-7. [PMID: 16683791 PMCID: PMC2529225 DOI: 10.1021/ja061153a] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bicelles are increasingly being used as membrane mimicking systems in NMR experiments to investigate the structure of membrane proteins. In this study, we demonstrate the effectiveness of a 2D solid-state NMR approach that can be used to measure the structural constraints, such as heteronuclear dipolar couplings between 1H, 13C, and 31P nuclei, in bicelles without the need for isotopic enrichment. This method does not require a high radio frequency power unlike the presently used rotating-frame separated-local-field (SLF) techniques, such as PISEMA. In addition, multiple dipolar couplings can be measured accurately, and the presence of a strong dipolar coupling does not suppress the weak couplings. High-resolution spectra obtained from magnetically aligned DMPC:DHPC bicelles even in the presence of peptides suggest that this approach will be useful in understanding lipid-protein interactions that play a vital role in shaping up the function of membrane proteins.
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Affiliation(s)
- Sergey Dvinskikh
- Biophysics Research Division and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Ulrich Dürr
- Biophysics Research Division and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Kazutoshi Yamamoto
- Biophysics Research Division and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Ayyalusamy Ramamoorthy
- Biophysics Research Division and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
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73
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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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74
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Lu JX, Damodaran K, Lorigan GA. Probing membrane topology by high-resolution 1H-13C heteronuclear dipolar solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 178:283-7. [PMID: 16275029 DOI: 10.1016/j.jmr.2005.09.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 09/15/2005] [Accepted: 09/21/2005] [Indexed: 05/05/2023]
Abstract
Membrane topology changes introduced by the association of biologically pertinent molecules with membranes were analyzed utilizing the (1)H-(13)C heteronuclear dipolar solid-state NMR spectroscopy technique (SAMMY) on magnetically aligned phospholipid bilayers (bicelles). The phospholipids (1)H-(13)C dipolar coupling profiles lipid motions at the headgroup, glycerol backbone, and the acyl chain region. The transmembrane segment of phospholamban, the antimicrobial peptide (KIGAKI)(3) and cholesterol were incorporated into the bicelles, respectively. The lipids (1)H-(13)C dipolar coupling profiles exhibit different shifts in the dipolar coupling contour positions upon the addition of these molecules, demonstrating a variety of interaction mechanisms exist between the biological molecules and the membranes. The membrane topology changes revealed by the SAMMY pulse sequence provide a complete screening method for analyzing how these biologically active molecules interact with the membrane.
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Affiliation(s)
- Jun-Xia Lu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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75
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Dvinskikh SV, Yamamoto K, Ramamoorthy A. Separated local field NMR spectroscopy by windowless isotropic mixing. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2005.11.076] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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76
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Sinha N, Grant CV, Rotondi KS, Feduik-Rotondi L, Gierasch LM, Opella SJ. Peptides and the development of double- and triple-resonance solid-state NMR of aligned samples. ACTA ACUST UNITED AC 2005; 65:605-20. [PMID: 15885119 DOI: 10.1111/j.1399-3011.2005.00262.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Peptides have been instrumental in the development of solid-state nuclear magnetic resonance (NMR) spectroscopy, and their roles in the development of solid-state NMR of aligned samples is reviewed. In particular, the roles of synthetic peptides in the development of triple-resonance methods are described. Recent developments of pulse sequences and NMR probes for triple-resonance NMR of aligned samples are presented.
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Affiliation(s)
- N Sinha
- Department of Chemistry and Biochemistry, 9500 Gilman Drive, University of California, San Diego, La Jolla, CA 92093-0307, USA
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77
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Dvinskikh SV, Sandström D. Frequency offset refocused PISEMA-type sequences. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2005; 175:163-9. [PMID: 15949754 DOI: 10.1016/j.jmr.2005.03.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Revised: 03/15/2005] [Accepted: 03/25/2005] [Indexed: 05/02/2023]
Abstract
The popular PISEMA experiment is highly sensitive to the 1H chemical shift dispersion and the choice of the 1H carrier frequency. This is due to the off-resonance 1H irradiation in the FSLG-CP sequence employed during the dipolar evolution period. In the modified approach described in this work, the interfering frequency offset terms are suppressed. In the new pulse schemes, conventional FSLG-CP is intercalated with 180 degrees pulses applied simultaneously to both frequency channels, and with phases set orthogonal to those of the spin-lock fields. The technique is demonstrated on a nematic liquid-crystalline sample. Extensions to amplitude-modulated FSLG-CP recoupling under MAS are also presented.
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Affiliation(s)
- Sergey V Dvinskikh
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden.
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78
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79
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Thiriot DS, Nevzorov AA, Opella SJ. Structural basis of the temperature transition of Pf1 bacteriophage. Protein Sci 2005; 14:1064-70. [PMID: 15741342 PMCID: PMC2253442 DOI: 10.1110/ps.041220305] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The filamentous bacteriophage Pf1 undergoes a reversible temperature-dependent transition that is also influenced by salt concentrations. This structural responsiveness may be a manifestation of the important biological property of flexibility, which is necessary for long, thin filamentous assemblies as a protection against shear forces. To investigate structural changes in the major coat protein, one- and two-dimensional solid-state NMR spectra of concentrated solutions of Pf1 bacteriophage were acquired, and the structure of the coat protein determined at 0 degrees C was compared with the structure previously determined at 30 degrees C. Despite dramatic differences in the NMR spectra, the overall change in the coat protein structure is small. Changes in the orientation of the C-terminal helical segment and the conformation of the first five residues at the N-terminus are apparent. These results are consistent with prior studies by X-ray fiber diffraction and other biophysical methods.
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Affiliation(s)
- David S Thiriot
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0307, USA
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80
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De Angelis AA, Jones DH, Grant CV, Park SH, Mesleh MF, Opella SJ. NMR experiments on aligned samples of membrane proteins. Methods Enzymol 2005; 394:350-82. [PMID: 15808228 DOI: 10.1016/s0076-6879(05)94014-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
NMR methods can be used to determine the structures of membrane proteins. Lipids can be chosen so that protein-containing micelles, bicelles, or bilayers are available as samples. All three types of samples can be aligned weakly or strongly, depending on their rotational correlation time. Solution NMR methods can be used with weakly aligned micelle and small bicelle samples. Solid-state NMR methods can be used with mechanically aligned bilayer and magnetically aligned bicelle samples.
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Affiliation(s)
- A A De Angelis
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093, USA
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81
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Thiriot DS, Nevzorov AA, Zagyanskiy L, Wu CH, Opella SJ. Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy. J Mol Biol 2004; 341:869-79. [PMID: 15288792 DOI: 10.1016/j.jmb.2004.06.038] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2003] [Revised: 05/24/2004] [Accepted: 06/07/2004] [Indexed: 10/26/2022]
Abstract
The atomic resolution structure of Pf1 coat protein determined by solid-state NMR spectroscopy of magnetically aligned filamentous bacteriophage particles in solution is compared to the structures previously determined by X-ray fiber and neutron diffraction, the structure of its membrane-bound form, and the structure of fd coat protein. These structural comparisons provide insights into several biological properties, differences between class I and class II filamentous bacteriophages, and the assembly process. The six N-terminal amino acid residues adopt an unusual "double hook" conformation on the outside of the bacteriophage particle. The solid-state NMR results indicate that at 30 degrees C, some of the coat protein subunits assume a single, fully structured conformation, and some have a few mobile residues that provide a break between two helical segments, in agreement with structural models from X-ray fiber and neutron diffraction, respectively. The atomic resolution structure determined by solid-state NMR for residues 7-14 and 18-46, which excludes the N-terminal double hook and the break between the helical segments, but encompasses more than 80% of the backbone including the distinct kink at residue 29, agrees with that determined by X-ray fiber diffraction with an RMSD value of 2.0 A. The symmetry and distance constraints determined by X-ray fiber and neutron diffraction enable the construction of an accurate model of the bacteriophage particle from the coordinates of the coat protein monomers.
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Affiliation(s)
- David S Thiriot
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093-0307, USA
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82
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Affiliation(s)
- Stanley J Opella
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093, USA
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