(291f) Molecular Modeling of Antibody Stability and Function Near Solid Surfaces

Antibody microarrays have the potential to revolutionize how molecular detection is accomplished in scientific research, medical diagnoses, and biosensor applications. Because they can screen of thousands of molecules in parallel, require only small sample volume sizes, need only small amounts of diagnostic antibodies, are easy to use, and provide faster results, they have the potential to displace current techniques.   Unfortunately, antibody microarrays have yet to find wide mainstream use because of reliability problems. These problems result from strong antibody-surface and antigen-surface interactions that disrupt the antibodies from properly recognizing and binding to their targets.

One of the difficulties to optimizing antibody arrays is that little is known about the biophysics involved in antibody-surface interactions.  Traditional experimental techniques used to determine protein structure, NMR and X-ray crystallography, are bulk techniques that are not amenable to surface-bound proteins, so simulation has emerged as the primary method to investigate the relevant phenomena. Previous simulation studies have been done to understand how antibodies interact with specific surfaces, but such have been limited in scope due to computational constraints associated with all-atom simulations or have used coarse-grain models that cannot capture all the relevant phenomena. As such, significant questions remain about how antibodies interact with surfaces and how the surface impacts antibody-antigen recognition and binding.

Our research group has recently developed a coarse-grain, protein-surface model that overcomes many previous 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.  In this presentation, we describe how this model has been extended to antibodies and antibody fragments.  The simplicity of this model makes it possible to capture and adequately sample the complex folding and binding events associated with antibody and antibody-antigen behavior on surfaces and obtain reliable thermodynamic data about the system. Results will be presented that show that the thermal stability of antibodies and antibody fragments is mostly a function of surface type and is less dependent on the orientation of the immobilized molecule on the surface. We will also include results from efforts to investigate antibody-antigen interactions in both bulk solution and near solid surfaces.  The results present an improved molecular-level view of the protein-surface and protein-protein interactions at the heart of functional antibody microarrays and offer hope that rational design of improved microarray technologies is possible.