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

• Published in: Biochimica et biophysica acta 2008-09, Vol.1784 (9), p.1200-1207
• Main Authors: Otero-Cruz, José David, Torres-Núñez, David Abner, Báez-Pagán, Carlos Alberto, Lasalde-Dominicci, José Antonio
• Format: Article
• Language: English
• Subjects: Animals; Female; Fourier Analysis; Fourier transform; In Vitro Techniques; Ligand-gated ion channel; Lipid-exposed transmembrane domain; 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; Secondary structure; Torpedo; Tryptophan - chemistry; Tryptophan-scanning mutagenesis; Two-electrode voltage clamp; Xenopus laevis
• ISSN: 1570-9639; 0006-3002; 1878-1454
• DOI: 10.1016/j.bbapap.2008.01.020

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 α-helical secondary structures and evaluate the quality of structure predictions by α-helical character curves. Finally, this study encourages future utilization of FT-TrpScanM to more reliably predict secondary structures of the membrane protein LETMDs.