The proposed research is directed at understanding the physical and chemical basis of specific antibody-antigen binding. The experimental systems to be studied are three antibody/protein complexes and four antibody/hapten complexes for which high resolution X-ray structures and binding data re available, plus data on binding differences for point amino acid mutations and hapten analogue binding. The focus will be on two key aspects: 1) The role of solvation, which involves both electrostatic and hydrophobic interactions. 2)'Association entropy' effects, meaning the loss of translational/rotational entropy upon association, with the concomitant gain in vibrational entropy of the complex, and the change in conformational mobility of groups involved in the intermolecular contact. A combination of theoretical approaches will be used, the aim being to develop computationally feasible yet quantitative methods for calculating both differences in binding energy, and absolute binding energies. This will enable specific questions of biological importance to be addressed, including identifying the overall driving force for binding, contributions to specificity, the role of electrostatic complementarily, whether induced fitting is important, the intrinsic antigenicity of surface groups, and the effect of amino acids mutations and substitutions on binding energies. Electrostatics will be treated using a continuum treatment of solvent with an atomic detail representation of the molecule, using the Finite Difference Poisson-Boltzmann (FDPB) method. Dynamic aspects will be handled by a method which combines the FDPB method with molecular mechanics (FDPB/MD). Hydrophobic interactions will be treated using surface free energy relationships, modified to account for shape effects, calibrated on small molecule solvent transfer data. Translational and rotational entropies effects will be estimated from changes in the rotational and translational partition function upon binding. %%% The ability of an organism to produce molecules that bind specifically to certain 'target' molecules or parts of 'target' molecules, but not to other molecules, gives rise to the phenomenon of biological recognition at the molecular level. This process of molecular recognition underlies many fundamental biological processes including catalysis, gene transcription and the immune response. The design of drugs also involves creating or modifying molecules to recognize given biological target molecules. In physical terms recognition occurs because a molecule binds more tightly to its 'target' than to other molecules. It is known that the tightness of binding is determined by how much energy is released (the binding energy) when two molecules are brought together. it is also known that contributions to the binding energy come from the interaction of the two molecules with each other, the interaction of each molecule with its surroundings, especially water, and from the change in shape and mobility of each molecule upon binding. However it is not yet possible to calculate the binding energy accurately, even if the structure o the two molecules is known. This impedes both our understanding of what properties of molecules are necessary for recognition and the ability to design molecules to recognize a given target. The recognition of foreign antigens by antibodies is one of the key properties of an immune system, and one of the most studied examples of molecular recognition: The structures of at least seven antigen/antibody complexes are known at the atomic level, and their binding energies have been measured. Therefore these systems have been chosen for a detailed theoretical study of binding. The aim of the proposed research is to apply recently developed methods for simulating the behavior of molecules to the problem of calculating the different contributions to the antibody-antigen binding energy. The goal is to identify the properties of the antibodies important for tight binding and specificity, and to improve the ability to calculate binding energies.
