File S1 - A Biophysical Study with Carbohydrate Derivatives Explains the Molecular Basis of Monosaccharide Selectivity of the Pseudomonas aeruginosa Lectin LecB

Supporting files. Data S1, 1H- and 13C-NMR spectra of new compounds 3, 4, 6, 7, 18, 19. Data S2, Individual titration curves from competitive binding assay. Data S3, Individual titration curves from isothermal calorimetry experiments. Figure S1, Time series of the root mean square deviation (RMSD) of all ligand atoms in the simulation of three complexes of LecB. Before the RMSD calculations the snapshots were aligned based on the binding site residues. Figure S2, Time series of the root mean square deviation (RMSD) of all ligand atoms in the three independent simulation of three complexes of LecB with α-d-mannose. Before the RMSD calculations the snapshots were aligned based on the binding site residues. Figure S3, Time series of the root mean square deviation (RMSD) of all ligand atoms in the three independent simulation of three complexes of LecB with hybrid 4. Before the RMSD calculations the snapshots were aligned based on the binding site residues. Figure S4, Full hydrogen-bond network of Asp96 with Ser22, Gln26, Asp104, and α-l-fucose. The calcium ions are shown as purple spheres. Figure S5, Orientation of Asp96 in the representative structure of the simulations of four complexes of LecB: (A) α-l-fucose (closed), (B) α-d-mannose (open), (C) 1-deoxy l-fucose (3, closed), (D) hybrid 4 (closed); The hydrogen bonds between Asp96 and Ser22 as well as Asp96 and the ligand are indicated by red dashed lines. The calcium ions are shown as purple spheres. Figure S6, Time series of the shortest distance between HG of Ser22 and OD1/OD2 of Asp96 of simulations of three complex of LecB. Figure S7, Time series of the shortest distance between HG of Ser22 and OD1/OD2 of Asp96 of three independent simulations of the complex of LecB with hybrid 4. Figure S8, Overlays of experimental structures and representative structures from the MD simulations: The first structure is shown as a green ribbon, with green carbon atoms and with Ca(II) ions in magenta. The second structure is color coded in grey with brown Ca(II) ions. Upper left: X-ray structure of the fucose (1oxc) and mannose (1our) complex; Upper right: X-ray (1oxc) and MD structure of the fucose complex; Lower left: X-ray structure (1our) and closed form of the mannose complex; Lower right: X-ray structure (1our) and open form of the mannose complex. Table S1, Relative binding free energy for the transition from 1-deoxy l-fucose (3) to hybrid 4 calculated using thermodynamic integration and its partitioning into the free individual steps. The values for two independent calculations of 5 ns length as well as the averages are given. (PDF)