Computational analysis of non-covalent polymer-protein interactions governing antibody orientation

The ALYGNSA is an affinity-based antibody orientation system produced through the interaction of the polymer poly(methyl methacrylate) (PMMA) and recombinant protein G (rProG), a streptococcal protein. This improved orientation suggests a specific non-covalent attachment of the rProG to PMMA that leaves the IgG binding region of the rProG more readily available. In this study, a full tertiary structure model of the rProG molecule of 198 amino acid residues containing a signal region, two IgG binding domains, and an anchor region, was computationally generated using the iterative threading assembly refinement (I-Tasser) server. The rProG model having the highest confidence score was subject to docking experiments with varied-length short chains of PMMA polymer via the graphic processing units-based Hex server. A five-residue section of the rProG anchor region, with the sequence TPATP, was identified as a potential interaction site. A complete ternary model (rProG, PMMA, and IgG) was assembled and provides insight into a plausible mechanism for non-covalent antibody orientation by the ALYGNSA system.