title: Mapping the Binding Interface of VEGF and a Monoclonal Antibody Fab-1 Fragment with Fast Photochemical Oxidation of Proteins (FPOP) and Mass Spectrometry.
abstract: We previously analyzed the Fab-1:VEGF (vascular endothelial growth factor) system described in this work, with both native top-down mass spectrometry and bottom-up mass spectrometry (carboxyl-group or GEE footprinting) techniques. This work continues bottom-up mass spectrometry analysis using a fast photochemical oxidation of proteins (FPOP) platform to map the solution binding interface of VEGF and a fragment antigen binding region of an antibody (Fab-1). In this study, we use FPOP to compare the changes in solvent accessibility by quantitating the extent of oxidative modification in the unbound versus bound states. Determining the changes in solvent accessibility enables the inference of the protein binding sites (epitope and paratopes) and a comparison to the previously published Fab-1:VEGF crystal structure, adding to the top-down and bottom-up data. Using this method, we investigated peptide-level and residue-level changes in solvent accessibility between the unbound proteins and bound complex. Mapping these data onto the Fab-1:VEGF crystal structure enabled successful characterization of both the binding region and regions of remote conformation changes. These data, coupled with our previous higher order structure (HOS) studies, demonstrate the value of a comprehensive toolbox of methods for identifying the putative epitopes and paratopes for biotherapeutic antibodies. Graphical abstract ᅟ.
authors.affiliation: Center for Biomedical and Bioorganic Mass Spectrometry, Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA.|Analytical Research and Development, Pfizer Inc., Andover, MA, 01810, USA.
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA, 94080, USA. wecksler.aaron@gene.com.
authors.forename: Aaron T
authors.identifier: 0000-0002-6050-0926
authors.initials: AT
authors.lastname: Wecksler
authors.affiliation: Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA, 94080, USA.
authors.forename: Patricia
authors.initials: P
authors.lastname: Molina
authors.affiliation: Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA, 94080, USA.
authors.forename: Galahad
authors.initials: G
authors.lastname: Deperalta
authors.affiliation: Center for Biomedical and Bioorganic Mass Spectrometry, Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA. mgross@wustl.edu.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Gross
mesh_terms: D000595:Amino Acid Sequence; D001666:Binding Sites, Antibody; D018604:Epitope Mapping / Q000379:methods*; D000939:Epitopes / Q000737:chemistry / Q000276:immunology; D006801:Humans; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry / Q000276:immunology*; D013058:Mass Spectrometry / Q000379:methods*; D062105:Molecular Docking Simulation; D010084:Oxidation-Reduction; D011487:Protein Conformation; D042461:Vascular Endothelial Growth Factor A / Q000737:chemistry / Q000276:immunology*
chemical_list: D000939:Epitopes; D007140:Immunoglobulin Fab Fragments; D042461:Vascular Endothelial Growth Factor A
keywords: Biotherapeutics; Epitope mapping; Fast photochemical oxidation of proteins; Hydroxyl radical footprinting-mass spectrometry