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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.
Otero-Cruz JD
,
Torres-Núñez DA
,
Báez-Pagán CA
,
Lasalde-Dominicci JA
.
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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.
Blanton,
Identifying the lipid-protein interface of the Torpedo nicotinic acetylcholine receptor: secondary structure implications.
1994, Pubmed
Blanton,
Identifying the lipid-protein interface of the Torpedo nicotinic acetylcholine receptor: secondary structure implications.
1994,
Pubmed
Blanton,
Mapping the lipid-exposed regions in the Torpedo californica nicotinic acetylcholine receptor.
1992,
Pubmed
Blanton,
Probing the structure of the nicotinic acetylcholine receptor ion channel with the uncharged photoactivable compound -3H-diazofluorene.
1998,
Pubmed
Choe,
Three distinct structural environments of a transmembrane domain in the inwardly rectifying potassium channel ROMK1 defined by perturbation.
1995,
Pubmed
,
Xenbase
Collins,
Scanning mutagenesis of the putative transmembrane segments of Kir2.1, an inward rectifier potassium channel.
1997,
Pubmed
,
Xenbase
Cornette,
Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins.
1987,
Pubmed
Cukras,
Structural and functional determinants of conserved lipid interaction domains of inward rectifying Kir6.2 channels.
2002,
Pubmed
Guzmán,
Tryptophan scanning mutagenesis in the alphaM3 transmembrane domain of the Torpedo californica acetylcholine receptor: functional and structural implications.
2003,
Pubmed
,
Xenbase
Hackos,
Scanning the intracellular S6 activation gate in the shaker K+ channel.
2002,
Pubmed
,
Xenbase
Hong,
The lipid-protein interface of a Shaker K(+) channel.
2000,
Pubmed
,
Xenbase
Honse,
Sites in the fourth membrane-associated domain regulate alcohol sensitivity of the NMDA receptor.
2004,
Pubmed
Irizarry,
Opening the KcsA K+ channel: tryptophan scanning and complementation analysis lead to mutants with altered gating.
2002,
Pubmed
Jenkins,
Tryptophan scanning mutagenesis in TM4 of the GABA(A) receptor alpha1 subunit: implications for modulation by inhaled anesthetics and ion channel structure.
2002,
Pubmed
Kashlan,
Distinct structural elements in the first membrane-spanning segment of the epithelial sodium channel.
2006,
Pubmed
Komiya,
Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: symmetry relations and sequence comparisons between different species.
1988,
Pubmed
Li-Smerin,
A localized interaction surface for voltage-sensing domains on the pore domain of a K+ channel.
2000,
Pubmed
,
Xenbase
Li-Smerin,
Helical structure of the COOH terminus of S3 and its contribution to the gating modifier toxin receptor in voltage-gated ion channels.
2001,
Pubmed
Li-Smerin,
alpha-helical structural elements within the voltage-sensing domains of a K(+) channel.
2000,
Pubmed
,
Xenbase
Monks,
Helical structure and packing orientation of the S2 segment in the Shaker K+ channel.
1999,
Pubmed
,
Xenbase
Ortiz-Acevedo,
Tryptophan scanning mutagenesis of the gammaM4 transmembrane domain of the acetylcholine receptor from Torpedo californica.
2004,
Pubmed
,
Xenbase
Otero-Cruz,
Tryptophan-scanning mutagenesis in the alphaM3 transmembrane domain of the muscle-type acetylcholine receptor. A spring model revealed.
2007,
Pubmed
,
Xenbase
Panchenko,
Structural similarities between glutamate receptor channels and K(+) channels examined by scanning mutagenesis.
2001,
Pubmed
,
Xenbase
Powl,
Heterogeneity in the binding of lipid molecules to the surface of a membrane protein: hot spots for anionic lipids on the mechanosensitive channel of large conductance MscL and effects on conformation.
2005,
Pubmed
Powl,
Identification of the hydrophobic thickness of a membrane protein using fluorescence spectroscopy: studies with the mechanosensitive channel MscL.
2005,
Pubmed
Rees,
The bacterial photosynthetic reaction center as a model for membrane proteins.
1989,
Pubmed
Rees,
Hydrophobic organization of membrane proteins.
1989,
Pubmed
Santiago,
Tryptophan scanning mutagenesis in the TM3 domain of the Torpedo californica acetylcholine receptor beta subunit reveals an alpha-helical structure.
2004,
Pubmed
,
Xenbase
Silberberg,
Secondary structure and gating rearrangements of transmembrane segments in rat P2X4 receptor channels.
2005,
Pubmed
,
Xenbase
Subbiah,
Tryptophan scanning mutagenesis of the HERG K+ channel: the S4 domain is loosely packed and likely to be lipid exposed.
2005,
Pubmed
,
Xenbase
Tamamizu,
Functional effects of periodic tryptophan substitutions in the alpha M4 transmembrane domain of the Torpedo californica nicotinic acetylcholine receptor.
2000,
Pubmed
,
Xenbase
Ueno,
Tryptophan scanning mutagenesis in TM2 of the GABA(A) receptor alpha subunit: effects on channel gating and regulation by ethanol.
2000,
Pubmed
,
Xenbase
Unwin,
Nicotinic acetylcholine receptor at 9 A resolution.
1993,
Pubmed
Unwin,
Refined structure of the nicotinic acetylcholine receptor at 4A resolution.
2005,
Pubmed
Wang,
Tryptophan scanning of D1S6 and D4S6 C-termini in voltage-gated sodium channels.
2003,
Pubmed
