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.
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.
Otero-Cruz
José David
JD
Department of Chemistry, University of Puerto Rico, Río Piedras Campus, San Juan, P.R. 00931, Puerto Rico.
Torres-Núñez
David Abner
DA
Báez-Pagán
Carlos Alberto
CA
Lasalde-Dominicci
José Antonio
JA
D000818:Animals; D005260:Female; D005583:Fourier Analysis; D066298:In Vitro Techniques; D008563:Membrane Lipids / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry / Q000235:genetics; D051379:Mice; D016254:Mutagenesis, Insertional; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011950:Receptors, Cholinergic / Q000737:chemistry* / Q000235:genetics*; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics; D014101:Torpedo; D014364:Tryptophan / Q000737:chemistry; D014982:Xenopus laevis
D008563:Membrane Lipids; D008565:Membrane Proteins; D011950:Receptors, Cholinergic; D011994:Recombinant Proteins; D014364:Tryptophan