title: Computational analysis of non-covalent polymer-protein interactions governing antibody orientation.
abstract: 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.
authors.affiliation: Department of Chemistry, College of Sciences, University of Massachusetts Lowell, Lowell, MA 01854, USA.
authors.forename: Leslie R
authors.initials: LR
authors.lastname: Farris
authors.forename: Melisenda J
authors.initials: MJ
authors.lastname: McDonald
mesh_terms: D000595:Amino Acid Sequence; D055910:Antibodies, Immobilized / Q000737:chemistry* / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D003198:Computer Simulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019904:Polymethyl Methacrylate / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment; D012984:Software; D013291:Streptococcus / Q000737:chemistry* / Q000378:metabolism
chemical_list: D055910:Antibodies, Immobilized; D001426:Bacterial Proteins; C034284:IgG Fc-binding protein, Streptococcus; D011994:Recombinant Proteins; D019904:Polymethyl Methacrylate