This thesis is focused on determining the structures of two anti-carbohydrate antibodies to understand how they achieve their specificity toward antigen. First, the structure of the antigen-binding fragment from the monoclonal antibody S64-4 in complex with a pentasaccharide bisphosphate fragment from chlamydial lipopolysaccharide (LPS) has been determined by x-ray diffraction to 2.6 A resolution. Like the well-characterized antibody S25-2, S64-4 displays a pocket formed by the residues of germline sequence corresponding to the heavy and light chain V gene segments that binds the terminal Kdo (3-deoxy-?-D-manno-oct-2-ulopyranosonic acid) residue of the antigen; however, although S64-4 shares the same heavy chain V gene segment as S25-2, it has a different light chain V gene segment. The new light chain V gene segment codes for a combining site that displays greater avidity, different specificity, and allows a novel antigen conformation that brings a greater number of antigen residues into the combining site than possible in S25-2. Further, while antibodies in the S25-2 family use complementarity determining region (CDR) H3 to discriminate among antigens, S64-4 achieves its specificity via the new light chain V genesegment and resulting change in antigen conformation. These structures reveal an intriguing parallel strategy where two different combinations of germline-coded V gene segments can act as starting points for the generation of germline antibodies against chlamydial antigens and show how anti-carbohydrate antibodies can exploit the conformational flexibility of this class of antigens to achieve high avidity and specificity independently of CDR H3. Second, the structure of a rabbit, single chain variable fragment against terminal mannose-6-phosphate (Man6P) residues, termed scFv M6P-1, has been determined by x-ray diffraction to 2.7 A resolution with Man6P in the binding site. The Man6P pathway is the predominant pathway that transports acid hydrolases from the trans-Golgi to endosomes. Newly synthesized hydrolases first require the generation of Man6P markers before they can be transported. Maintaining a full complement of hydrolases within lysosomes is essential as failure to do so results in a number of different lysosomal storage diseases. Due to its specificity, scFv M6P-1 is able to diagnose lysosomal storage diseases mucolipidosis II and mucolipidosis III. scFv M6P-1 is also able to purify Man6P containing proteins which may be useful for enzyme replacement therapies ...

Many pathogens and aberrant malignant cells express unique carbohydrates on their surface representing attractive targets for vaccine design. Considerable progress has recently been made in the identification of novel carbohydrate based vaccines and a large number has reached clinical phase studies. The success of several licensed carbohydrate based vaccines against bacterial pathogens such as Haemophilus influenzae type b, Neisseria meningitidis or Streptococcus pneumoniae demonstrates their great potential. However, the study of anti-carbohydrate antibodies is technically challenging and partly because of low affinities and promiscuous specificity they have not been medically exploited to full potential. The study of antibody specificities and identification of protective carbohydrate epitopes lies at the heart of successful vaccine design. In addition to therapy, antibodies in general serve as diagnostic tools in medical and scientific laboratories. In this setting high affinity and exquisite specificity are important factors for their successful use. “Anticarbohydrate Antibodies – from molecular basis to clinical application” compiles current knowledge on the immunological recognition of carbohydrates by the adaptive immune system from a molecular perspective providing fundamental insight needed for advancing clinically relevant diagnostics and therapeutic applications. Based on significant progress in the fields of glycoimmunology and structural biology in recent years, the book comprehensively reviews the state-of-the-art in defining the key elements of carbohydrate recognition by antibodies, the molecular mimicry of carbohydrate epitopes as well as the molecular features leading to specific and relaxed binding modes. Backed-up by a combination of modern technologies to elucidate structural details of carbohydrate-antibody interactions, biomedically important carbohydrate antigens from viral, bacterial, parasite, insect and tumor cells have been analyzed in in-depth reviews written by well-known experts in the field. Fundamental knowledge of these molecular mechanisms eventually provides a rational basis to improve efficacy of carbohydrate-based vaccines and to further refine diagnostic tools in detection of pathogens and malignant cells.

Sugar chains (glycans) are often attached to proteins and lipids and have multiple roles in the organization and function of all organisms. "Essentials of Glycobiology" describes their biogenesis and function and offers a useful gateway to the understanding of glycans.