title: Inversion of receptor binding preferences by mutagenesis: free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins.
abstract: The Escherichia coli L-arabinose-binding protein (ABP) participates as a specific receptor in the transport of L-arabinose, D-fucose, and D-galactose through the periplasmic space. The wild-type protein binds L-arabinose about 40 times more strongly than D-fucose. A mutation of the protein at position 108 (Met-->Leu) causes a specificity change. The Met108Leu ABP slightly prefers binding of D-fucose over L-arabinose. Molecular dynamics (MD) and thermodynamic integration (TI) computer simulations were performed to study the mechanism of sugar discrimination and specificity change based on the known high-resolution X-ray structures. The specificity change was evaluated by calculating the difference in free energy of L-arabinose versus D-fucose bound to wild-type and Met108Leu ABP. The calculated free energy differences are consistent with the experimentally observed specificity of wild-type and Met108Leu ABP. The simulations indicate that the specificity change of Met108Leu ABP is accomplished mainly by reduced Lennard-Jones interactions of residue 108 with L-arabinose and improved interactions with D-fucose. In addition to MD/TI calculations on sugar binding, finite difference Poisson-Boltzmann calculations were performed to identify the most stable ionization state of buried ionizable residues in ABP.
authors.affiliation: Department of Chemistry, University of Houston, Texas 77204-5641.
authors.forename: M
authors.initials: M
authors.lastname: Zacharias
authors.forename: T P
authors.initials: TP
authors.lastname: Straatsma
authors.forename: J A
authors.initials: JA
authors.lastname: McCammon
authors.forename: F A
authors.initials: FA
authors.lastname: Quiocho
mesh_terms: D001089:Arabinose / Q000378:metabolism*; D002352:Carrier Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D003198:Computer Simulation; D004563:Electrochemistry; D004926:Escherichia coli / Q000737:chemistry*; D029968:Escherichia coli Proteins; D005643:Fucose / Q000378:metabolism*; D016296:Mutagenesis; D011487:Protein Conformation; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014961:X-Ray Diffraction
chemical_list: C016242:AraF protein, E coli; D002352:Carrier Proteins; D029968:Escherichia coli Proteins; D005643:Fucose; D001089:Arabinose