Modelling and simulation of carbohydrate systems: From solution to protein binding in the gas phase

This thesis presents studies aimed at providing a deeper understanding of protein-carbohydrate recognition and binding process by means of theoretical modelling and computational simulations. This study focuses on the theoretical modelling of furanosides in particular. Furanoside ring systems can exist in a variety of conformers that are separated by low energy barriers. This conformational flexibility renders the modelling of such systems quite challenging. An earlier model had been shown to be reliable for simulation studies of more rigid pyranoside ring systems. Our new model, however, incorporates the effects of ring flexibility for better description of furanosides. It is applied to a monosaccharide, the methyl α-D-arabinofuranoside. The simulations results are compared to the results from NMR experiments in order to assess the validity of the model. For the study of the interactions between proteins and carbohydrates, an antibody single-chain fragment (scFv) and its native ligand, αGal[αAbe]αMan are investigated as a model system. The intermolecular hydrogen bonds within a desolvated protein-ligand complex are characterized. This work is inspired by recent mass spectrometry experiments where some specific interactions are found to be preserved from solution to gas phase. We provide a more complete picture of the nature of the binding interactions between the protein and the ligand through hydrogen bond analysis. This analysis method is also used to probe the interactions between crystallographic water molecules and the complex. Through calculations of free energy profiles of the native complex and its mutants, the contributions of various specific protein-ligand interactions to the stability of the mutant complexes are observed. This study also allows us to quantify the strength of specific interactions.