3 years ago

Coarse-Grained Modeling of Antibodies from Small-Angle Scattering Profiles

Coarse-Grained Modeling of Antibodies from Small-Angle Scattering Profiles
Jai Pathak, Robin A. Curtis, Rose Keeling, Daniel Corbett, Clair Baldock, Prasad Sarangapani, Max Hebditch, Sofia Ekizoglou, Christopher F. Van Der Walle, Peng Ke, Carlos Avendaño, Shahid Uddin
Predicting the concentrated solution behavior for monoclonal antibodies requires developing and using minimal models to describe their shape and interaction potential. Toward this end, the small-angle X-ray scattering (SAXS) profiles for a monoclonal antibody (COE-03) have been measured under solution conditions chosen to produce weak self-association. The experiments are complemented with molecular simulations of a three-bead antibody model with and without interbead attraction. The scattering profile is extracted directly from the molecular simulation to avoid using the decoupling approximation. We examine the ability of the three-bead model to capture features of the scattering profile and the dependence of compressibilty on protein concentration. The three-bead model is able to reproduce generic features of the experimental structure factor as a function of wave vector S(k) including a well-defined shoulder, which is a consequence of the planar structure of the antibody, and a well-defined minimum in S(k) at k ∼ 0.025 Å–1. We also show the decoupling approximation is incapable of accounting for highly anisotropic shapes. The best-fit parameters obtained from matching spherical models to simulated scattering profiles are protein concentration dependent, which limits their applicability for predicting thermodynamic properties. Nevertheless, the experimental compressibility curves can be accurately reproduced by an appropriate parametrization of the Baxter adhesive model, indicating the model provides a semiempirical equation of state for the antibody. The results provide insights into how equations of state can be improved for antibodies by accounting for their anisotropic shapes.

Publisher URL: http://dx.doi.org/10.1021/acs.jpcb.7b04621

DOI: 10.1021/acs.jpcb.7b04621

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