Inversion of Receptor Binding Preferences by Mutagenesis: Free Energy Thermodynamic Integration Studies on Sugar Binding to l-Arabinose Binding Proteins

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.