Protein-carbohydrate and protein-protein interactions: using models to better understand and predict specific molecular recognition

v CHAPTER 1 : GENERAL INTRODUCTION 1 Thesis Organization 5 References 9 CHAPTER 2: DISTINCTIONS MADE IN THE PROTEIN RECOGNITION OF CARBOHYDRATES 14 Abstract 14 Introduction 15 Discussion 19 Conclusion 24 References 26 CHAPTER 3: SPECIFIC EMPIRICAL FREE ENERGY FUNCTION FOR AUTOMATED DOCKING OF CARBOHYDRATES TO PROTEINS 34 Abstract 34 Introduction 35 Methods 37 Results and Discussion 42 Conclusion 48 Acknowledgments 49 References 50 CHAPTER 4: POLYSACCHARIDE RECOGNITION BY SURFACTANT PROTEIN D: NOVEL INTERACTIONS OF A C-TYPE LECTIN WITH NONTERMINAL GLUCOSYL RESIDUES 63 Abstract 63 Introduction 64 Experimental Procedures 65 Results 69 Discussion 74 Acknowledgments 79 References 81 CHAPTER 5: ARG343 IN HUMAN SURFACTANT PROTEIN D GOVERNS DISCRIMINATION BETWEEN GLUCOSE AND N-ACETYLGLUCOSAMINE LIGANDS 98 Abstract 98