Assessing HIV-1 Broadly Neutralizing Antibody Association Pathways for Vaccine Immunogen Design

ABSTRACT Macromolecular interactions are often understood from the perspective of the bound state as determined at high-resolution from x-ray crystallography or cryo-electron microscopy with kinetic and thermodynamic parameters used to describe the interaction process. This approach is, however, limited spatially and temporally to a bulk, population level description of the process from the perspective of affinity and kinetics, and the single state perspective of a bound state structure. The process of forming an interaction is, in fact, quite complex, involving random collisions between molecules that transition through a complicated set of pathways to the final bound state. These collisions and the mechanism by which they achieve the bound state determine the association rate but are not well defined by current methods. Here, a combined computational and experimental approach to the interrogation of the process of antibody- antigen binding in HIV-1 N332-glycan targeting broadly neutralizing antibodies is proposed to enable precise enhancement of antibody-immunogen association rate kinetics. Using molecular simulation, full encounter to bound state transition mechanisms will be elucidated at atomic resolution. The goal of this effort is to enable precise selection of antigens with an affinity gradient conducive to the consistent induction of broadly neutralizing antibody responses via vaccination. The definition of design principles by which the kinetics of an interaction may be manipulated in a protein engineering context will have a broad impact on the design of novel therapeutics and macromolecular probes in any biological context.