Structure and dynamics of antibody hapten complexes

Antibody molecules are highly antigen-specific receptors of the immune system. In this thesis, structural and functional relationship in antibody molecules are studied.The nature of the $\rm V\sb{L}$-$\rm V\sb{H}$ interface and the role of specific residues that are involved in the conserved packing interactions across the domains are analyzed. Specific residues in the framework and hypervariable regions are identified as key residues that contribute to the stability of the interface. Using the residues involved in conserved contacts across the domain, a list of constraints on C$\alpha$-C$\alpha$ distances are obtained which can be used as additional constraints in computer modeling of antibody Fv structures.The high degree of sequence and structural homology among the antibodies make them good targets for homology modeling. Using computer-aided modeling, the structure of the variable domain fragment of two antibodies, NC6.8 and NC10.14, raised against sweet taste ligand NC174, are predicted and the key residues in the combining site of the antibodies identified. Experimental methods, like spectroscopy and competitive ligand binding have also supported these modeling studies. Molecular dynamics simulations of the uncomplexed antibody NC6.8 are performed to understand the nature of the correlated motions of the antibody, prior to hapten binding. The dynamics simulations show that the CDR loops adopt a variety of conformations and the dynamic structure could play a role in antigen binding. The effect of the mutation of $\rm Tyr\to Phe$ in the antibody NC6.8, is evaluated in terms of free energy. The 'slow growth' method is used to determine the stability of the mutation in the native and the complexed antibody, as compared to the unfolded state of the protein. The net difference in the free energy for the change is 1.26 kcal/mol for the native antibody and 1.42 kcal/mol for the complexed antibody, with the Phe residue being more stable in the folded antibody as compared to its unfolded state.U of I OnlyETDs are only available to UIUC Users without author permissio