IgG1 and IgG4 antibodies sample initial structure dependent local conformational states and exhibit non-identical Fab dynamics

We have investigated the dynamics of two ?-immunoglobulin molecules, IgG1 and IgG4, using long all atom molecular dynamics simulations. We first show that the de novo structures of IgG1 and IgG4 predicted using AlphaFold, with no interactions between the fragment crystallizable (Fc) domain and the antigen fragment binding domain (Fab), eventually relaxes to a state with persistent Fc-Fab interactions that mirrors experimentally resolved structures. We quantified the conformational space sampled by antibody trajectories spawned from six different initial structures and show that the individual trajectories only sample states bound by a local minimum and display very little mixing in their conformational states. Furthermore, the dynamics of the individual Fab domains are strongly dependent on the initial crystal structure and isotype. In all conditions, we observe nonidentical dynamics between the Fab arms in an antibody. For a six-bead coarse grained model, we show that non-covalent Fc-Fab interactions can modulate the stiffnesses associated with Fc-Fab distances, angles, and dihedral angles by up to three orders of magnitude. Our results clearly illustrate the inherent complexities in studying antibody dynamics and highlight the need to include nonidentical Fab dynamics as an inherent feature in computational models of therapeutic antibodies.

Automated summary

We investigated the dynamics of IgG1 and IgG4 using long all atom molecular dynamics simulations. Our results showed that the de novo structures of IgG1 and IgG4, predicted using AlphaFold, eventually relax to a state with persistent Fc-Fab interactions. The conformational space sampled by antibody trajectories is dependent on the initial crystal structure and isotype.