On the combined analysis of 2H and 15N/ 1H solid-state NMR data for determination of transmembrane peptide orientation and dynamics

Biophysical Journal

Volumn 101, Issue 12, 2011, Pages 2939-2947

  Vostrikov, Vitaly V ^a,c   Grant, Christopher V ^b   Opella, Stanley J ^b   Koeppe II, Roger E ^a  

^a UNIVERSITY OF ARKANSAS   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN; MEMBRANE PROTEIN; NITROGEN; PROTON;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; LIPID BILAYER; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; STRUCTURE ACTIVITY RELATION; ULTRASTRUCTURE;

COMPUTER SIMULATION; HYDROGEN; LIPID BILAYERS; MAGNETIC RESONANCE SPECTROSCOPY; MEMBRANE PROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; NITROGEN ISOTOPES; PROTONS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84055211729     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.11.008     Document Type: Article

References (47)

1. A.A. De Angelis, and D.H. Jones S.J. Opella NMR experiments on aligned samples of membrane proteins Methods Enzymol. 394 2005 350 382 (Pubitemid 40460923)
2. 2H NMR Biophys. J. 83 2002 1479 1488 (Pubitemid 34977721)
3. J. Lee, and W. Im Transmembrane helix tilting: insights from calculating the potential of mean force Phys. Rev. Lett. 100 2008 018103
4. 2H-NMR data Biophys. J. 96 2009 3223 3232
5. 15N PISEMA NMR spectra of membrane proteins: a theoretical analysis Biophys. J. 96 2009 3233 3241
6. C.R. Sanders II, and J.P. Schwonek Characterization of magnetically orientable bilayers in mixtures of dihexanoylphosphatidylcholine and dimyristoylphosphatidylcholine by solid-state NMR Biochemistry 31 1992 8898 8905
7. S.H. Park, and A.A. De Angelis S.J. Opella Three-dimensional structure of the transmembrane domain of Vpu from HIV-1 in aligned phospholipid bicelles Biophys. J. 91 2006 3032 3042 (Pubitemid 44526493)
8. R.C. Page, S. Kim, and T.A. Cross Transmembrane helix uniformity examined by spectral mapping of torsion angles Structure 16 2008 787 797 (Pubitemid 351626899)
9. T. Doherty, Y. Su, and M. Hong High-resolution orientation and depth of insertion of the voltage-sensing S4 helix of a potassium channel in lipid bilayers J. Mol. Biol. 401 2010 642 652
10. A. Holt, and L. Rougier A. Milon Order parameters of a transmembrane helix in a fluid bilayer: case study of a WALP peptide Biophys. J. 98 2010 1864 1872
11. K. Bertelsen, and B. Vad N.C. Nielsen Long-term-stable ether-lipid vs conventional ester-lipid bicelles in oriented solid-state NMR: altered structural information in studies of antimicrobial peptides J. Phys. Chem. B 115 2011 1767 1774
12. 5 embedded in bicelles, revealing both structural and dynamical information J. Am. Chem. Soc. 132 2010 5779 5788
13. 2H NMR lineshapes of immobilized uniaxially oriented membrane proteins Solid State Nucl. Magn. Reson. 2 1993 21 36
14. J.M. Froyd-Rankenberg, D.V. Greathouse, and R.E. Koeppe II Half-anchored WALP peptides: effect of anchor position on peptide orientation Biophys. J. 96 2009 455a 456a
15. C.H. Wu, A. Ramamoorthy, and S.J. Opella High-resolution heteronuclear dipolar solid-state NMR spectroscopy J. Magn. Reson. A 109 1994 270 272
16. F.M. Marassi, and S.J. Opella A solid-state NMR index of helical membrane protein structure and topology J. Magn. Reson. 144 2000 150 155
17. J. Wang, and J. Denny T.A. Cross Imaging membrane protein helical wheels J. Magn. Reson. 144 2000 162 167
18. A.A. Nevzorov, and S.J. Opella A "magic sandwich" pulse sequence with reduced offset dependence for high-resolution separated local field spectroscopy J. Magn. Reson. 164 2003 182 186
19. 2H NMR implications for orientation and motion in a bilayer environment Biochemistry 37 1998 16780 16787 (Pubitemid 28543941)
20. J.A. Whiles, and R. Brasseur R.R. Vold Orientation and effects of mastoparan X on phospholipid bicelles Biophys. J. 80 2001 280 293
21. 2H solid-state NMR Biophys. J. 86 2004 3709 3721 (Pubitemid 38780249)
22. R. Verardi, and N.J. Traaseth A. Scaloni Probing membrane topology of the antimicrobial peptide distinctin by solid-state NMR spectroscopy in zwitterionic and charged lipid bilayers Biochim. Biophys. Acta 1808 2011 34 40
23. J.M. Resende, and C.M. Moraes B. Bechinger Membrane structure and conformational changes of the antibiotic heterodimeric peptide distinctin by solid-state NMR spectroscopy Proc. Natl. Acad. Sci. USA 106 2009 16639 16644
24. N.J. Traaseth, and L. Shi G. Veglia Structure and topology of monomeric phospholamban in lipid membranes determined by a hybrid solution and solid-state NMR approach Proc. Natl. Acad. Sci. USA 106 2009 10165 10170
25. R. Verardi, and L. Shi G. Veglia Structural topology of phospholamban pentamer in lipid bilayers by a hybrid solution and solid-state NMR method Proc. Natl. Acad. Sci. USA 108 2011 9101 9106
26. V.V. Vostrikov, and C.V. Grant R.E. Koeppe II Comparison of "polarization inversion with spin exchange at magic angle" and "geometric analysis of labeled alanines" methods for transmembrane helix alignment J. Am. Chem. Soc. 130 2008 12584 12585
27. V.V. Vostrikov, and A.E. Daily R.E. Koeppe II Charged or aromatic anchor residue dependence of transmembrane peptide tilt J. Biol. Chem. 285 2010 31723 31730
28. V.V. Vostrikov, and B.A. Hall M.S. Sansom Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations J. Am. Chem. Soc. 132 2010 5803 5811
29. R.S. Prosser, J.S. Hwang, and R.R. Vold Magnetically aligned phospholipid bilayers with positive ordering: a new model membrane system Biophys. J. 74 1998 2405 2418 (Pubitemid 28225237)
30. A.A. De Angelis, and S.C. Howell S.J. Opella Structure determination of a membrane protein with two trans-membrane helices in aligned phospholipid bicelles by solid-state NMR spectroscopy J. Am. Chem. Soc. 128 2006 12256 12267 (Pubitemid 44413857)
31. R. Mahalakshmi, and F.M. Marassi Orientation of the Escherichia coli outer membrane protein OmpX in phospholipid bilayer membranes determined by solid-State NMR Biochemistry 47 2008 6531 6538 (Pubitemid 351874280)
32. A. Poon, J. Birn, and A. Ramamoorthy How does an amide-N chemical shift tensor vary in peptides? J. Phys. Chem. B 108 2004 16577 16585
33. N.J. Gleason, D.V. Greathouse, and R.E. Koeppe II Using tyrosine to anchor a transmembrane peptide Biophys. J. 100 2011 635a 636a
34. S.K. Kandasamy, and R.G. Larson Molecular dynamics simulations of model trans-membrane peptides in lipid bilayers: a systematic investigation of hydrophobic mismatch Biophys. J. 90 2006 2326 2343
35. S. Ozdirekcan, and C. Etchebest P.F. Fuchs On the orientation of a designed transmembrane peptide: toward the right tilt angle? J. Am. Chem. Soc. 129 2007 15174 15181 (Pubitemid 350247801)
36. T. Kim, and W. Im Revisiting hydrophobic mismatch with free energy simulation studies of transmembrane helix tilt and rotation Biophys. J. 99 2010 175 183
37. V.V. Vostrikov, and R.E. Koeppe II Response of GWALP transmembrane peptides to changes in the tryptophan anchor positions Biochemistry 50 2011 7522 7535
38. Vostrikov, V. V. 2011. Protein-lipid interactions: Influence of anchoring groups and buried arginine on the properties of membrane-spanning peptides. PhD thesis, University of Arkansas, Fayetteville, AR.
39. J.A. Butterwick, and R. MacKinnon Solution structure and phospholipid interactions of the isolated voltage-sensor domain from KvAP J. Mol. Biol. 403 2010 591 606
40. J. Hu, and T. Asbury T.A. Cross Backbone structure of the amantadine-blocked trans-membrane domain M2 proton channel from Influenza A virus Biophys. J. 92 2007 4335 4343 (Pubitemid 46915327)
41. S. Esteban-Martín, and E. Strandberg A.S. Ulrich Solid state NMR analysis of peptides in membranes: influence of dynamics and labeling scheme Biochim. Biophys. Acta 1798 2010 252 257
42. 2H-NMR experiments on the orientation of the transmembrane helix WALP23 by computer simulations Biophys. J. 99 2010 1455 1464
43. R. Thomas, and V.V. Vostrikov R.E. Koeppe II Influence of proline upon the folding and geometry of the WALP19 transmembrane peptide Biochemistry 48 2009 11883 11891
44. J.H. Davis, and K.R. Jeffrey T.P. Higgs Quadrupolar echo deuteron magnetic resonance spectroscopy in ordered hydrocarbon chains Chem. Phys. Lett. 42 1976 390 394
45. A.A. Nevzorov, and S.J. Opella Selective averaging for high-resolution solid-state NMR spectroscopy of aligned samples J. Magn. Reson. 185 2007 59 70 (Pubitemid 46484391)
46. N. Guex, and M.C. Peitsch SWISS-MODEL and the Swiss-PDBViewer: an environment for comparative protein modeling Electrophoresis 18 1997 2714 2723 (Pubitemid 28059943)
47. R. Bertram, and J.R. Quine T.A. Cross Atomic refinement using orientational restraints from solid-state NMR J. Magn. Reson. 147 2000 9 16