File S1 - Design of Glycopeptides Used to Investigate Class II MHC Binding and T-Cell Responses Associated with Autoimmune Arthritis

Contents. Amino acid descriptors. Amino acid derivatives incorporated into virtual peptides at positions p260 and p263. Docking software parameter tuning and constraints. Table of amino acids selected for p260 and p263 based on docking scores. Score and loading plots from the PCA based on physicochemical properties of amino acids in p260 and p263. Table with yields. purity and MALDI-TOF data for the synthesized glycopeptides. HPLC chromatograms for the modified glycopeptides. Initial Aq binding affinity assay. Dose-response curves for binding to Aq. Dose-response curves for Aq-restricted T-cell responses. Dose-response curves for binding to DR4. Dose-response curves for DR4-restricted T-cell responses. PLS Permutations experiments. RMSD vs. simulation time plots for the whole complex and the ligand. The distance between the GalHyl264 CA and the Aq Lys11C as a function of the simulation time. References. (PDF)