Methodological development of solid-state NMR for characterization of membrane proteins

Concepts in Magnetic Resonance Part A: Bridging Education and Research

Volumn 18, Issue 2, 2003, Pages 111-129

  Bjerring, M ^a   Vosegaard, T ^a   Malmendal, A ^a   Nielsen, N C ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

Alamethicin; Aquaporin 1; Computer simulations; Effective Hamiltonian theory; Magic angle spinning; Membrane proteins; Molecular graphics; Oriented samples; SIMMOL; SIMPSON; Solid state NMR

Indexed keywords

MEMBRANE PROTEIN;

ARTICLE; ISOTOPE LABELING; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; PROTEIN ANALYSIS; SOLID STATE;

EID: 0344598683     PISSN: 15466086     EISSN: 15525023     Source Type: Journal    
DOI: 10.1002/cmr.a.10069     Document Type: Article

References (79)

1. Venter JC, et al. 2001. The sequence of the human genome. Science 291:1304-1351.
2. Preusch PC, Norvell JC, Cassatt JC, Cassman M. 1998. Progress away from "no crystals, no grant." Nat Struct Biol 5:13-14.
3. White SH, Wimley WC. 1999. Membrane protein folding and stability: Physical principles. Annu Rev Biophys Biomol Struc 28:319-365.
4. Bernstein FC, Koetzle TF, Williams GJ, Meier EE Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542. Internet address: http://www.rcsb.org/pdb.
5. Russell RB, Eggleston DS. 2000. New roles for structure in biology and drug discovery. Nat Struct Biol 7:928-930.
6. Opella SJ. 1997. NMR and membrane proteins. Nat Struct Biol 4:845-848.
7. Griffin RG. 1998. Dipolar recoupling in MAS spectra of biological solids. Nat Struct Biol 5:508-512.
8. Hohwy M, Nielsen NC. 1998. Systematic design and evaluation of multiple-pulse experiments in nuclear magnetic resonance spectroscopy using a semi-continuous Baker-Campbell-Hausdorff expansion. J Chem Phys 109:3780-3791.
9. Untidt TS, Nielsen NC. 2002. A closed solution to the Baker-Campbell-Hausdorff problem: Exact effective Hamiltonian theory for analysis of nuclear magnetic resonance experiments. Phys Rev E 65:021108-1-021108-17. A Mathematica notebook can be downloaded at: http://nmr.imsb.au.dk.
10. Bak M, Rasmussen JT, Nielsen NC. 2000. SIMPSON: A general simulation program for solid-state NMR spectroscopy. J Magn Reson 147:296-330. Internet address and download site: http://nmr.imsb.au.dk.
11. Bak M, Schultz R, Nielsen NC. 2001. Numerical simulations for experiment design and extraction of structural parameters in biological solid-state NMR spectroscopy. In: Kiihne SR, de Groot HJM, eds. Perspectives on Solid-State NMR in Biology. Dordrecht, Holland: Kluwer Academic Publishers. p 95-109.
12. Bak M, Schultz R, Vosegaard T, Nielsen NC. 2002. Specification and visualization of anisotropic interaction tensors in polypeptides and numerical simulations in biological solid-state NMR. J Magn Reson 154:28-45. Internet address and download site: http://nmr.imsb.au.dk.
13. Vosegaard T, Malmendal A, Nielsen NC. 2002. The flexibility of SIMPSON and SIMMOL for numerical simulations in solid- and liquid-state NMR spectroscopy. Chem Month 133:1555-1574.
14. 15N]-labeled membrane proteins in oriented lipid bilayers. J Biomol NMR 22:225-247.
15. 15N solid-state nuclear magnetic resonance. Biophys J 81:1684-1698.
16. Haeberlen U. 1976. High-Resolution NMR in Solids. Selective Averaging. New York: Academic Press.
17. Mehring M. 1983. Principles of High Resolution NMR in Solids. New York: Springer-Verlag.
18. Schmidt-Rohr K, Spiess HW. 1996. Multidimensional Solid-State NMR and Polymers. London: Academic Press.
19. Bennett AE, Griffin RG, Vega S. 1994. Recoupling of homo- and heteronuclear dipolar interactions in rotating solids. In: Diehl P, Fluck E, Günther H, Kosfeld R, eds. NMR Basic Principles and Progress, Vol. 33. Berlin: Springer-Verlag, p 1-77.
20. Dusold S, Sebald A. 2001. Dipolar recoupling under magic-angle spinning conditions. Annu Rep NMR Spectrosc 41:185-264.
21. Glaubitz C, Watts A. 1998. Magic angle-oriented sample spinning (MAOSS): A new approach toward biomembrane studies. J Magn Reson 130:305-316.
22. Zandomeneghi G, Tomaselli M, van Beek JD, Meier B. 2001. Manipulation of the director in bicellar mesophases by sample spinning: A new tool for NMR spectroscopy. J Am Chem Soc 123:910-913.
23. Maricq MM, Waugh JS. 1979. NMR in rotating solids. J Chem Phys 70:3300-3316.
24. Kraulis P. 1991. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946-950.
25. Vriend G. 1990. WHAT IF: A molecular modelling and drug design program. J Mol Graph 8:52-56. Internet address: http://www.cmbi.kun.nl/whatif.
26. Sattler M, Schleucher J, Griesinger C. 1999. Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog NMR Spectrosc 34:93-158.
27. Haeberlen U, Waugh JS. 1968. Coherent averaging effects in magnetic resonance. Phys Rev 175:453-467.
28. Waugh JS, Huber LM, Haeberlen U. 1968. Approach to high-resolution NMR in solids. Phys Rev Lett 20:180-182.
29. Mansfield P, Orchard MJ, Stalker DC, Richards KHB. 1973. Symmetrized multipulse nuclear-magnetic-resonance experiments in solids: Measurement of the chemical-shift tensor in some compounds. Phys Rev B 7:90-105.
30. Rhim W-K, Elleman DD, Schrieber LB, Vaughan RW. 1973. Analysis of multiple pulse NMR in solids. J Chem Phys 59:3740-3749.
31. Burum DP, Rhim W-K. 1979. Analysis of multiple pulse in solids. III. J Chem Phys 71:944-956.
32. Bielecki A, Kolbert AC, Levitt MH. 1989. Frequency-switched pulse sequences: Homonuclear decoupling and dilute spin NMR in solids. Chem Phys Lett 155:341-346.
33. Shaka AJ, Keeler J, Freeman R. 1983. Evaluation of a new broadband decoupling sequence: WALTZ-16. J Magn Reson 53:313-340.
34. Edén M, Levitt MH. 1999. Pulse sequence symmetries in the nuclear magnetic resonance of spinning solids: Application to heteronuclear decoupling. J Chem Phys 111:1511-1519.
35. Raleigh DP, Levitt MH, Griffin RG. 1988. Rotational resonance in solid state NMR. Chem Phys Lett 146:71-76.
36. Tycko R, Dabbagh G. 1990. Measurement of nuclear magnetic dipole-dipole couplings in magic angle spinning NMR. Chem Phys Lett 173:461-465.
37. Nielsen NC, Bildsøe H, Jakobsen HJ, Levitt MH. 1994. Double-quantum homonuclear rotary resonance: Efficient dipolar recovery in magic-angle spinning nuclear magnetic resonance. J Chem Phys 101:1805-1812.
38. Lee YK, Kurur ND, Helmle M, Johannessen OG, Nielsen NC, Levitt MH. 1995. Efficient dipolar recoupling in the NMR of rotating solids. A sevenfold symmetric radiofrequency pulse sequence. Chem Phys Lett 242:304-309.
39. Hohwy M, Jakobsen HJ, Edén M, Levitt MH, Nielsen NC. 1998. Broadband dipolar recoupling in the nuclear magnetic resonance of rotating solids: A compensated C7 pulse sequence. J Chem Phys 108:2686-2694.
40. 13C-erythromycin A. J Am Chem Soc 120:10602-10612.
41. Hohwy M, Rienstra CM, Jaroniec CP, Griffin RG. 1999. Fivefold symmetric homonuclear dipolar recoupling in rotating solids: Application to double quantum spectroscopy. J Chem Phys 110:7983-7992.
42. Brinkmann A, Edén M, Levitt MH. 2000. Synchronous helical pulse sequences in magic-angle spinning nuclear magnetic resonance: Double quantum recoupling of multiple-spin systems. J Chem Phys 112:8539-8554.
43. Carravetta M, Edén M, Zhao X, Brinkmann A, Levitt MH. 2000. Symmetry principles for the design of radiofrequency pulse sequences in the nuclear magnetic resonance of rotating solids. Chem Phys Lett 321:205-215.
44. Oas TG, Griffin RG, Levitt MH. 1988. Rotary resonance recoupling of dipolar interactions in solid-state nuclear magnetic resonance spectroscopy. J Chem Phys 89:692-695.
45. Gullion T, Schaefer J. 1989. Rotational-echo double-resonance NMR. J Magn Reson 81:196-200.
46. 15N chemical bonds by double cross-polarization NMR. J Magn Reson 59:150-156.
47. Brinkmann A, Levitt MH. 2001. Symmetry priciples in the nuclear magnetic resonance of spinning solids: Heteronuclear recoupling by generalized Hartmann-Hahn sequences. J Chem Phys 115:357-384.
48. Sørensen OW. 1989. Polarization transfer experiments in high-resolution NMR spectroscopy. Progr NMR Spectrosc 21:503-569.
49. Stoustrup J, Schedletzky OJ, Glaser SJ, Griesinger C, Nielsen NC, Sørensen OW. 1995. Generalized bound on quantum dynamics - efficiency of unitary transformations between non-Hermitian states. Phys Rev Lett 74:2921-2924.
50. Glaser SJ, Schulte-Herbrüggen T, Sieveking M, Schedletzky O, Nielsen NC, Sørensen OW, Griesinger C. 1998. Unitary control in quantumn ensembles: Maximizing signal intensity in coherent spectroscopy. Science 280:421-424.
51. Untidt TS, Nielsen NC. 2000. Analytical unitary bounds on quantum dynamics: Design of optimum NMR experiments in two-spin-1/2 systems. J Chem Phys 113:8464-8471.
52. Nielsen NC, Thøgersen H, Sørensen OW. 1996. A systematic strategy for design of optimum coherent experiments applied to efficient interconversion of double- and single-quantum coherences in nuclear magnetic resonance. J Chem Phys 105:135-139.
53. 3S spin systems. Mol Phys 95:787-796.
54. 2S Spin Systems. Phys Chem A 103:8921-8926.
55. Levitt MH. 2002. Symmetry-based pulse sequences in magic-angle spinning solid-state NMR. In: Grant DM, Harris RK, eds. Encyclopedia of Nuclear Magnetic Resonance: Supplementary Volume. Chichester, UK: Wiley. p 165-196.
56. Wolfram A. 1988. Mathematica. A System for Doing Mathematics by Computer. Redwood City, CA: Addison-Wesley.
57. Bennett AE, Ok JH, Griffin RG, Vega S. 1992. Chemical shift correlation spectroscopy in rotating solids: Radio frequency driven dipolar recoupling and longitudinal exchange. J Chem Phys 96:8624-8627.
58. Sun BQ, Costa PR, Griffin RG. 1995. Heteronuclear polarization transfer of radiofrequency driven dipolar recoupling under magic-angle spinning. J Magn Reson A 112:191-198.
59. 15N-labelled polypeptides by solid state NMR. J Biomol NMR 12:39-50.
60. 15N labeled solid proteins by two- and three-dimensional magic-angle-spinning NMR. J Biomol NMR 15:1-14.
61. 15N)-enriched BPTI in the solid state. J Biomol NMR 16:209-219.
62. 15N signal assignments of the a-spectrin SH3 domain by magic angle spinning solid-state NMR at 17.6 Tesla. Chembiochem 2:272-281.
63. Pines A, Gibby M, Waugh JS. 1973. Proton-enhanced NMR of dilute spins in solids. J Chem Phys 59:569-590.
64. Ousterhout JK. 1994. Tcl and the Tk toolkit. Reading, MA: Addison-Wesley.
65. 13C-relaxation studies of randomly fractionally labeled proteins. Biochemistry 35:6116-6125.
66. Wu CH, Ramamoorthy A, Opella SJ. 1994. High-resolution heteronuclear dipolar solid-state NMR spectroscopy. J Magn Reson A 109:270-272.
67. Sui H, Han BG, Lee JK, Walian P, Jap BK. 2001. Structural basis of water-specific transport through the AQP1 water channel. Nature 414:872-878.
68. Ramamoorthy A, Wu CH, Opella SJ. 1999. Experimental aspects of multidimensional solid-state NMR correlation spectroscopy. J Magn Reson 140:131-140.
69. Munowitz M, Bachovchin WW, Herzfeld J, Dobson CM, Griffin RG. 1982. Acid-base and tautomeric equilibriums in the solid state: Nitrogen-15 NMR spectroscopy of histidine and imidazole. J Am Chem Soc 104:1192-1196.
70. Hu W, Lee KC, Cross TA. 1993. Tryptophans in membrane proteins: Indole ring orientations and functional implications in the gramicidin channel. Biochemistry 32:7035-7047.
71. π-histidine side chains determined by three-dimensional solid-state NMR spectroscopy of polycrystalline samples. J Am Chem Soc 119:10479-10486.
72. 15N NMR chemical shift anisotropy of histidines: Experimental and theoretical studies of hydrogen bonding. J Am Chem Soc 121:10389-10394.
73. de Groot BL, Grubmuller H. 2001. Water permeation across biological membranes: Mechanism and dynamics of aquaporin-1 and GlpF. Science 294:2353-2357.
74. Cafiso D. 1994. Alamethicin: A peptid model for voltage gating and protein-membrane interactions. Annu Rev Biophys Biomol Struct 23:141-165.
75. Duclohier D, Wroblewski H. 2001. Voltage-dependent pore formation and antimicrobial activity by alamethicin and analogues. J Membrane Biol 184:1-12.
76. Carpino LA, Beyermann M, Wenschuh H, Bienert M. 1996. Peptide synthesis via amino acid halides. Acc Chem Res 29:268-274.
77. Bechinger B, Opella SJ. 1991. Flat-coil probe for NMR spectroscopy of oriented membrane samples. J Magn Reson 95:585-588.
78. Nielsen NC, Daugaard P, Langer V, Thomsen JK, Nielsen S, Sørensen OW, Jakobsen HJ. 1995. A flat-coil probe with hydration control of oriented phospholipid bilayer samples. J Biomol NMR 5:311-314.
79. Cross TA, Quine JR. 2000. Protein structure in anisotropic environments: Development of orientational constraints. Concepts Magn Reson 12:55-70.