Inter- and intramolecular contacts in a membrane protein/surfactant complex observed by heteronuclear dipole-to-dipole cross-relaxation

Journal of Magnetic Resonance

Volumn 197, Issue 1, 2009, Pages 91-95

  Catoire, Laurent J ^a   Zoonens, Manuela ^a   Heijenoort, Carine van ^b   Giusti, Fabrice ^a   Popot, Jean Luc ^a   Guittet, Eric ^b  

^a PSL Research University   (France)

^b INSTITUT DE CHIMIE DES SUBSTANCES NATURELLES   (France)

Author keywords

Amphipol A8 35; Heteronuclear NOE; Membrane protein; Molecular interactions; Surfactants

Indexed keywords

[CARBONYL; AMPHIPOL A8-35; AROMATIC AMINO ACIDS; C ATOMS; CARBONYL CARBONS; CROSS RELAXATIONS; DIPOLAR INTERACTIONS; HETERONUCLEAR NOE; INTER-MOLECULAR INTERACTIONS; INTERMOLECULAR CONTACTS; INTRAMOLECULAR SPATIAL PROXIMITIES; MEMBRANE PROTEIN; NMR SPECTROSCOPIES; POLYMERIC SURFACTANTS; ROTATING FRAMES; STRUCTURAL INFORMATIONS; SUPRAMOLECULAR STRUCTURES; SURFACTANTS;

ACTIVE NETWORKS; AMINES; AMINO ACIDS; AROMATIC COMPOUNDS; CARBONYLATION; MOLECULAR INTERACTIONS; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; ORGANIC ACIDS; PROTEINS; SURFACE ACTIVE AGENTS;

SUPRAMOLECULAR CHEMISTRY;

AMPHIPOL A8 35; AMPHIPOL A8-35; ESCHERICHIA COLI PROTEIN; HYDROLASE; MEMBRANE PROTEIN; OMPX PROTEIN, E COLI; OUTER MEMBRANE PROTEIN; POLYMER; PROPYLAMINE; SURFACTANT;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; PROTEIN BINDING;

ALGORITHMS; BACTERIAL OUTER MEMBRANE PROTEINS; BINDING SITES; COMPUTER SIMULATION; ESCHERICHIA COLI PROTEINS; HYDROLASES; MEMBRANE PROTEINS; MODELS, CHEMICAL; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; POLYMERS; PROPYLAMINES; PROTEIN BINDING; SURFACE-ACTIVE AGENTS;

EID: 60349095580     PISSN: 10907807     EISSN: 10960856     Source Type: Journal    
DOI: 10.1016/j.jmr.2008.11.017     Document Type: Article

References (40)

1. Wüthrich K. NMR of Proteins and Nucleic Acids (1986), Wiley, New York, NY
2. Bauer W. Lithium chemistry: A Theoretical and Experimental Overview (1995), VCH, New York, NY
3. Tribet C., Audebert R., and Popot J.-L. Amphipols: polymers that keep membrane proteins soluble in aqueous solutions. Proc. Natl. Acad. Sci. USA 93 (1996) 15047-15050
4. Popot J.-L., Berry E.A., Charvolin D., Creuzenet C., Ebel C., Engelman D.M., Flötenmeyer M., Giusti F., Gohon Y., Hervé P., Hong Q., Lakey J.H., Leonard K., Shuman H.A., Timmins P., Warschawski D.E., Zito F., Zoonens M., Pucci B., and Tribet C. Amphipols: polymeric surfactants for membrane biology research. Cell. Mol. Life Sci. 60 (2003) 1559-1574
5. Pocanschi C.L., Dahmane T., Gohon Y., Rappaport F., Apell H.-J., Kleinschmidt J.H., and Popot J.-L. Amphipathic polymers: tools to fold integral membrane proteins to their active form. Biochemistry 45 (2006) 13954-13961
6. T. Dahmane, M. Damian, S. Mary, J.-L. Popot, J.-L. Banères, Amphipol-assisted refolding of G protein-coupled receptors, submitted for publication.
7. Fernández C., Hilty C., Wider G., and Wüthrich K. Lipid-protein interactions in DHPC micelles containing the integral membrane protein OmpX investigated by NMR spectroscopy. Proc. Natl. Acad. Sci. USA 99 (2002) 13533-13537
8. Hilty C., Wider G., Fernández C., and Wüthrich K. Membrane protein-lipid interactions in mixed micelles studied by NMR spectroscopy with the use of paramagnetic reagents. Chembiochem 5 (2004) 467-473
9. Zoonens M., Catoire L.J., Giusti F., and Popot J.-L. NMR study of a membrane protein in detergent-free aqueous solution. Proc. Natl. Acad. Sci. USA 102 (2005) 8893-8898
10. Gohon Y., Pavlov G., Timmins P., Tribet C., Popot J.-L., and Ebel C. Partial specific volume and solvent interactions of amphipol A8-35. Anal. Biochem. 334 (2004) 318-334
11. Vogt J., and Schulz G.E. The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence. Structure 7 (1999) 1301-1309
12. Fernández C., Adeishvili K., and Wüthrich K. Transverse relaxation-optimized NMR spectroscopy with the outer membrane protein OmpX in dihexanoyl phosphatidylcholine micelles. Proc. Natl. Acad. Sci. USA 98 (2001) 2358-2363
13. Pervushin K., Riek R., Wider G., and Wüthrich K. Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc. Natl. Acad. Sci. USA 94 (1997) 12366-12371
14. W.L. DeLano. The PyMOL Molecular Graphics System, DeLano Scientific LLC, Palo Alto, CA, USA, 2008. http://www.pymol.org.
15. Rinaldi P.L. Heteronuclear 2D-NOE spectroscopy. J. Am. Chem. Soc. 105 (1983) 5167-5168
16. Yu C., and Levy G.C. Solvent and intramolecular proton dipolar relaxation of the three phosphates of ATP: a heteronuclear 2D NOE study. J. Am. Chem. Soc. 105 (1983) 6994-6996
17. Bull T.E. Selective and heteronuclear ROESY relaxation theory. J. Magn. Reson. 93 (1991) 596-602
18. Delaglio F., Grzesiek S., Vuister G.W., Zhu G., Pfeifer J., and Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6 (1995) 277-293
19. Johnson B.A., and Blevins R.A. NMRView: A computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4 (1994) 603-614
20. Lee B., and Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55 (1971) 379-400
21. Fernández C., Hilty C., Wider G., Güntert P., and Wüthrich K. NMR structure of the integral membrane protein OmpX. J. Mol. Biol. 336 (2004) 1211-1221
22. Collaborative Computational Project, Number 4, The CCP4 suite: programs for protein crystallography, Acta Cryst. D50 (1994) 760-763.
23. Ulrich E.L., Akutsu H., Doreleijers J.F., Harano Y., Ioannidis Y.E., Lin J., Livny M., Mading S., Maziuk D., Miller Z., Nakatani E., Schulte C.F., Tolmie D.E., Kent Wenger R., Yao H., and Markley J.L. BioMagnResBank. Nucl. Acids Res. 36 (2007) D402-D408
24. Hilty C., Fernández C., Wider G., and Wüthrich K. Side chain NMR assignments in the membrane protein OmpX reconstituted in DHPC micelles. J. Biomol. NMR 23 (2002) 289-301
25. Yu L., Hajduk P.J., Mack J., and Olejniczak E.T. Structural studies of Bcl-xL/ligand complexes using 19F NMR. J. Biomol. NMR 34 (2006) 221-227
26. Ernst R.R., Bodenhausen G., and Wokaum A. Principles of Nuclear Magnetic Resonance in One and Two dimensions (1987), Clarendon Press, Oxford
27. 15N multidimensional NMR to study the structure and dynamics of proteins. Annu. Rev. Biophys. Biomol. Struct. 27 (1998) 357-406
28. Tugarinov V., Kanelis V., and Kay L.E. Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy. Nat. Protoc. 1 (2006) 749-754
29. Tugarinov V., and Kay L.E. Side chain assignments of Ile δ1 methyl groups in high molecular weight proteins: an application to a 46 ns tumbling molecule. J. Am. Chem. Soc. 125 (2003) 5701-5706
30. 13C NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes. J. Am. Chem. Soc. 125 (2003) 10420-10428
31. Dayie K.T., and Wagner G. Carbonyl-carbon relaxation rates reveal a dynamic heterogeneity of the polypeptide backbone in villin 14T. J. Magn. Reson. B109 (1995) 105-108
32. 15N-labeled protein. J. Magn. Reson. 126 (1997) 48-57
33. Fischer M.W.F., Zeng L., and Zuiderweg E.R.P. Use of 13C-13C NOE for the assignment of NMR lines of larger labeled proteins at larger magnetic fields. J. Am. Chem. Soc. 118 (1996) 12457-12458
34. Serber Z., Richter C., Moskau D., Böhlen J.-M., Gerfin T., Marek D., Häberli M., Baselgia L., Laukien F., Stern A.S., Hoch J.C., and Dötsch V. New carbon-detected protein NMR experiments using cryoprobes. J. Am. Chem. Soc. 122 (2000) 3554-3555
35. Kovacs H., Moskau D., and Spraul M. Cryogenically cooled probes-a leap in NMR technology. Progr. NMR Spectros. 46 (2005) 131-155
36. 13C-detected protonless NMR spectroscopy of proteins in solution. Progr. NMR Spectros. 48 (2006) 25-45
37. Hoch J.C., and Stern A.S. Encyclopedia of NMR (1996), John Wiley and Sons, Chichester pp. 2980-2988
38. Bermel W., Bertini I., Felli I.C., Matzapetakis M., Pierattelli R., Theil E.C., and Turano P. A method for C(alpha) direct-detection in protonless NMR. J. Magn. Reson. 188 (2007) 301-310
39. Tribet C., Audebert R., and Popot J.-L. Stabilization of hydrophobic colloidal dispersions in water with amphiphilic polymers: application to integral proteins. Langmuir 13 (1997) 5570-5576
40. Zoonens M., Giusti F., Zito F., and Popot J.-L. Dynamics of membrane protein/amphipol association studied by Förster resonance energy transfer: implications for in vitro studies of amphipol-stabilized membrane proteins. Biochemistry 46 (2007) 10392-10404