title: Topology scanning and putative three-dimensional structure of the extracellular binding domains of the apical sodium-dependent bile acid transporter (SLC10A2).
abstract: The apical sodium-dependent bile acid transporter (ASBT, SLC10A2) facilitates the enterohepatic circulation of bile salts and plays a key role in cholesterol metabolism. The membrane topology of ASBT was initially scanned using a consensus topography analysis that predominantly predicts a seven transmembrane (TM) domain configuration adhering to the "positive inside" rule. Membrane topology was further evaluated and confirmed by N-glycosylation-scanning mutagenesis, as reporter sites inserted in the putative extracellular loops 1 and 3 were glycosylated. On the basis of a 7TM topology, we built a three-dimensional model of ASBT using an approach of homology-modeling and remote-threading techniques for the extramembranous domains using bacteriorhodopsin as a scaffold for membrane attachment points; the model was refined using energy minimizations and molecular dynamics simulations. Ramachandran scores and other geometric indicators show that the model is comparable in quality to the crystal structures of similar proteins. Simulated annealing and docking of cholic acid, a natural substrate, onto the protein surface revealed four distinct binding sites. Subsequent site-directed mutagenesis of the predicted binding domain further validated the model. This model agrees further with available data for a pathological mutation (P290S) because the mutant model after in silico mutagenesis loses the ability to bind bile acids.
authors.affiliation: Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA.
authors.forename: Eric Y
authors.initials: EY
authors.lastname: Zhang
authors.forename: Mitch A
authors.initials: MA
authors.lastname: Phelps
authors.forename: Antara
authors.initials: A
authors.lastname: Banerjee
authors.forename: Chandra M
authors.initials: CM
authors.lastname: Khantwal
authors.forename: Cheng
authors.initials: C
authors.lastname: Chang
authors.forename: Freek
authors.initials: F
authors.lastname: Helsper
authors.forename: Peter W
authors.initials: PW
authors.lastname: Swaan
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics; D002236:Carbohydrate Conformation; D003198:Computer Simulation; D016384:Consensus Sequence; D005110:Extracellular Space / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D018698:Glutamic Acid / Q000235:genetics; D006031:Glycosylation; D006801:Humans; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D029363:Organic Anion Transporters, Sodium-Dependent / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D010446:Peptide Fragments / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011110:Polymorphism, Genetic; D011392:Proline / Q000235:genetics; D011485:Protein Binding / Q000235:genetics; D017510:Protein Folding; D017434:Protein Structure, Tertiary / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D012694:Serine / Q000235:genetics; D027981:Symporters / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D008024:Ligands; D029363:Organic Anion Transporters, Sodium-Dependent; D010446:Peptide Fragments; D027981:Symporters; C071908:sodium-bile acid cotransporter; D018698:Glutamic Acid; D012694:Serine; D011392:Proline