Fourier transform coupled to tryptophan-scanning mutagenesis: lessons from its application to the prediction of secondary structure in the acetylcholine receptor lipid-exposed transmembrane domains

Biochim Biophys Acta. 2008 Sep;1784(9):1200-7. doi: 10.1016/j.bbapap.2008.01.020. Epub 2008 Feb 20.


Although Fourier transform (FT) and tryptophan-scanning mutagenesis (TrpScanM) have been extremely useful for predicting secondary structures of membrane proteins, they are deemed to be low-resolution techniques. Herein, we describe the combined use of FT and TrpScanM (FT-TrpScanM) as a more reliable approach for the prediction of secondary structure. Five TrpScanM studies of the acetylcholine receptor lipid-exposed transmembrane domains (LETMDs) were revisited and analyzed by FT-TrpScanM. FT analysis of the raw data from the aforementioned TrpScanM studies supports and validates the conclusions derived from their tryptophan-periodicity profiles. Furthermore, by FT-TrpScanM, we were able to determine the minimum number of consecutive tryptophan substitutions necessary for more robust prediction of alpha-helical secondary structures and evaluate the quality of structure predictions by alpha-helical character curves. Finally, this study encourages future utilization of FT-TrpScanM to more reliably predict secondary structures of the membrane protein LETMDs.

MeSH terms

  • Animals
  • Female
  • Fourier Analysis
  • In Vitro Techniques
  • Membrane Lipids / chemistry
  • Membrane Proteins / chemistry
  • Membrane Proteins / genetics
  • Mice
  • Mutagenesis, Insertional
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Receptors, Cholinergic / chemistry*
  • Receptors, Cholinergic / genetics*
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Torpedo
  • Tryptophan / chemistry
  • Xenopus laevis


  • Membrane Lipids
  • Membrane Proteins
  • Receptors, Cholinergic
  • Recombinant Proteins
  • Tryptophan