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

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.

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Department of Chemistry, University of Puerto Rico, Río Piedras Campus, San Juan, P.R. 00931, Puerto Rico.


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.

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