Antibody microarrays are chip-based biomolecular detection devices that can rapidly screen for hundreds to thousands of molecules in parallel. They have disruptive potential in multiple fields including scientific research, medical diagnosis, and national defense. However, current forms of these highly-multiplexed microarrays have not found wide mainstream use due to reliability problems. Multiple factors—such as production tolerances, signal detection, and target selection—contribute to the poor performance.
One of the most problematic issues with the technology is that the antibody must perform its function in an environment far different than that found in vivo. Specifically, the presence of the surface has been show to drastically affect antibody function due to strong interactions between the antibodies, antigens, and the surface which disrupt the opsonization (antigen-binding) process. One of the impediments to the rational design and optimization of antibody microarrays is that the biophysics of antibody and antigen behavior near solid surfaces is not clearly understood. Part of the reason for the lack of knowledge is that typical experimental techniques used to study surface-bound proteins either do not provide sufficient detail of protein structures or are not transferable to heterogeneous environments.
Due to experimental limitations, simulation has emerged as the primary method to investigate protein-surface interactions. Previous studies of antibody-surface interactions have been limited in scope due to computational constraints or models that cannot capture all the relevant phenomena. Our research group recently developed a coarse-grain, protein-surface model that overcomes many of these limitations. It has been shown to give accurate protein folding mechanisms and to quantitatively reproduce protein adsorption energies as a function of surface chemistry and residue identity. The simplicity of this model makes it possible to capture and adequately sample the complex folding and binding events associated with antibody and antigen behavior on surfaces and to obtain reliable thermodynamic data about the system.
In this presentation we describe how this model has been used to study the stability of antibody-antigen complexes near these surfaces in a way that offers unprecedented insights into the substrate-induced factors that inhibit the opsonization process. Thermodynamic results for the antigen lysozyme will show that the surface decreases the antibody-lysozyme binding strength for both flat and upright antibody orientations on the surface. Analysis will also be presented that demonstrates how the surface impacts the antigen-binding process differently based on antigen size. Finally, work will be shown on how the binding ability of antibody fragments (compared to entire antibodies) are affected by surfaces. Taken as a whole, the results provide a much-improved molecular-level view of the protein-surface and protein-protein interactions at the heart of functional antibody microarrays and offer hope that the rational design of improved microarray technologies is possible.