Keywords

Molecular simulations, X-ray crystallography, Hydrophobic effect, Nuclear magnetic resonance, Amino acid, Antibody, Antigen, Lysozyme, Protein structure, Immune system

Abstract

Antibody microarrays have the potential to revolutionize molecular detection for many applications, but their current use is limited by poor reliability, and efforts to change this have not yielded fruitful results. One difficulty which limits the rational engineering of next-generation devices is that little is known, at the molecular level, about the antibody-antigen binding process near solid surfaces. Atomic-level structural information is scant because typical experimental techniques (X-ray crystallography and NMR) cannot be used to image proteins bound to surfaces. To overcome this limitation, this study uses molecular simulation and an advanced, experimentally validated, coarse-grain, protein-surface model to compare fab-lysozyme binding in bulk solution and when the fab is tethered to hydrophobic and hydrophilic surfaces. The results show that the tether site in the fab, as well as the surface hydrophobicity, significantly impacts the binding process and suggests that the optimal design involves tethering fabs upright on a hydrophilic surface. The results offer an unprecedented, molecular-level picture of the binding process and give hope that the rational design of protein-microarrays is possible.

Original Publication Citation

D. B. Bush and T. A. Knotts IV, Probing the E ects of Surface Hydrophobicity and Tether Orientation on Antibody-Antigen Binding, J. Chem. Phys., 146, 155103 (2017).