Journal of Biomolecular NMR

, Volume 21, Issue 4, pp 377–382 | Cite as

A simple apparatus for generating stretched polyacrylamide gels, yielding uniform alignment of proteins and detergent micelles*

  • James J. Chou
  • Sander Gaemers
  • Bernard Howder
  • John M. Louis
  • Ad Bax


Compressed and stretched polyacrylamide hydrogels previously have been shown to offer a robust method for aligning proteins. A simple, funnel-like apparatus is described for generating uniformly stretched hydrogels. For prolate-shaped proteins, gels stretched in the direction of the magnetic field yield two-fold larger alignment than gels compressed to the same aspect ratio in this direction. Empirically, protein alignment is found to be proportional to (c−2.3)2 [(do/dN)3-1], where do and dN are the diameters of the cylindrical gels before and after stretching, respectively, and c is the polyacrylamide weight fraction in percent. Low gel densities, in the 4–7% range, are found to have minimal effects on macromolecular rotational correlation times, τc, and no effect of the compression ratio on τc could be discerned over the range studied (do/dN le1.4). Application is demonstrated for a sample containing the first Ig-binding domain of protein G, and for a detergent-solubilized peptide.

detergent micelle dipolar coupling liquid crystal polyacrylamide gels protein NMR 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Supplementary material

10858_2004_Article_393209_MOESM1_ESM.pdf (505 kb)
Diagram (PDF 509 KB)
10858_2004_Article_393209_MOESM2_ESM.pdf (329 kb)
Diagram (PDF 333 KB)
10858_2004_Article_393209_MOESM3_ESM.rtf (44 kb)
Supplementary Material (RTF 48 KB)


  1. Barrientos, L.G., Dolan, C. and Gronenborn, A.M. (2000) J. Biomol. NMR, 16, 329-337.CrossRefGoogle Scholar
  2. Bastiaan, E.W., Maclean, C., vanZijl, P.C.M. and Bothner-By, A.A. (1987) Ann. Rep. NMR Spectr., 19, 35-77.CrossRefGoogle Scholar
  3. Bax, A. and Tjandra, N. (1997) J. Biomol. NMR, 10, 289-292.CrossRefGoogle Scholar
  4. Chou, J.J., Li, S., Klee, C.B. and Bax, A. (2001) Nat. Struct. Biol., 8, 990-997.CrossRefGoogle Scholar
  5. Clore, G.M., Starich, M.R. and Gronenborn, A.M. (1998) J. Am. Chem. Soc., 120, 10571-10572.CrossRefGoogle Scholar
  6. Emsley, J.W. (1996) In Encyclopedia of Nuclear Magnetic Resonance, D.M. Grant and R.K. Harris (Eds.), Wiley, Chichester, pp. 2788-2799.Google Scholar
  7. Fleming, K., Gray, D., Prasannan, S. and Matthews, S. (2000) J. Am. Chem. Soc., 122, 5224-5225.CrossRefGoogle Scholar
  8. Goto, N.K., Skrynnikov, N.R., Dahlquist, F.W. and Kay, L.E. (2001) J. Mol. Biol., 308, 745-764.CrossRefGoogle Scholar
  9. Hansen, M.R., Mueller, L. and Pardi, A. (1998) Nat. Struct. Biol., 5, 1065-1074.CrossRefGoogle Scholar
  10. Ishii, Y., Markus, M.A. and Tycko, R. (2001) J. Biomol. NMR, in press.Google Scholar
  11. Ottiger, M. and Bax, A. (1998a) J. Biomol. NMR, 12, 361-372.CrossRefGoogle Scholar
  12. Ottiger, M. and Bax, A. (1998b) J. Am. Chem. Soc., 120, 12334-12341.CrossRefGoogle Scholar
  13. Ottiger, M., Delaglio, F. and Bax, A. (1998) J. Magn. Reson., 131, 373-378.CrossRefADSGoogle Scholar
  14. Permi, P., Rosevear, P.R. and Annila, A. (2000) J. Biomol. NMR, 17, 43-54.CrossRefGoogle Scholar
  15. Prosser, R.S., Losonczi, J.A. and Shiyanovskaya, I.V. (1998) J. Am. Chem. Soc., 120, 11010-11011.CrossRefGoogle Scholar
  16. Ruckert, M. and Otting, G. (2000) J. Am. Chem. Soc., 122, 7793-7797.CrossRefGoogle Scholar
  17. Sass, H.J., Musco, G., Stahl, S.J., Wingfield, P.T. and Grzesiek, S. (2000) J. Biomol. NMR, 18, 303-309.CrossRefGoogle Scholar
  18. Saupe, A. and Englert, G. (1963) Phys. Rev. Lett., 11, 462-464.CrossRefADSGoogle Scholar
  19. Shortle, D. and Ackerman, M.S. (2001) Science, 293, 487-489.CrossRefGoogle Scholar
  20. Tjandra, N. and Bax, A. (1997) Science, 278, 1111-1114.CrossRefADSGoogle Scholar
  21. Tjandra, N., Omichinski, J.G., Gronenborn, A.M., Clore, G.M. and Bax, A. (1997) Nat. Struct. Biol., 4, 732-738.CrossRefGoogle Scholar
  22. Tolman, J.R., Flanagan, J.M., Kennedy, M.A. and Prestegard, J.H. (1995) Proc. Natl. Acad. Sci. USA, 92, 9279-9283.CrossRefADSGoogle Scholar
  23. Tycko, R., Blanco, F.J. and Ishii, Y. (2000) J. Am. Chem. Soc., 122, 9340-9341.CrossRefGoogle Scholar
  24. Veglia, G. and Opella, S.J. (2000) J. Am. Chem. Soc., 122, 11733-11734.CrossRefGoogle Scholar
  25. Yang, D.W., Venters, R.A., Mueller, G.A., Choy, W.Y. and Kay, L.E. (1999) J. Biomol. NMR, 14, 333-343.CrossRefGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2001

Authors and Affiliations

  • James J. Chou
    • 1
  • Sander Gaemers
    • 1
  • Bernard Howder
    • 1
  • John M. Louis
    • 1
  • Ad Bax
    • 1
  1. 1.Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney DiseasesNational Institutes of HealthBethesdaU.S.A

Personalised recommendations