Resolving the geometric structure of trastuzumab by mobility capillary electrophoresis and native mass spectrometry

Available online Immunoglobulins G (IgGs) are Y-shaped globular proteins, however, their high flexibility and heterogeneity pose great challenges to their structure and conformation determinations. Geometric structure of IgG closely correlates to its biofunctions, such as the antibody escape of human immunodeficiency virus (HIV) could attribute to the distance mismatch between the ends of two Fab arms (antigen-binding sites) and envelope glycoprotein spikes on virion surface. Herein, we report the first use of mobility capillary electrophoresis (MCE) and native mass spectrometry (nMS) to resolve the internal geometric structure and conformation of an IgG (trastuzumab) in solution phase. After proteolysis, the ellipsoid dimensions of IgG and its subunits were measured by MCE-nMS experiments. IgG was then reconstructed, in which the sizes and relative positions of these three subunits in three-dimensional space were characterized. It was found that the two Fab arms have an angle of ∼102.1° and a distance of ∼11.0 nm between the two antigen-binding sites under native condition, and the Fc arm was tilted ∼16.0° towards one of the Fab arms. Fc was not on the plane of Fab-Fab, but has an angle of no larger than 103.1°. Under acidic environment (pH 3.0), each subunit of the IgG would unfold into larger dimensions, and the angles between these subunits also change. With great potential for tumor imaging and therapy, the structure of F(ab′)₂ fragments was also measured and validated by molecular dynamic simulation. It was found that the electrostatic force among these three subunits and steric hindrance stemming from Fc help maintaining the angle between two Fab arms.