Much work has been done to study the conformational changes taking place in antibodies, particularly during the event of binding to an antigen. This has been done through comparison of crystal structures, circular dichroism, and recently with high resolution single particle electron microscopy. The ability to resolve domains within an antibody from single particles without any averaging made it possible to show distributions of properties such as the shape of a Fab domain, measured by the ratio of width to length. Some of the variation in structure seen involves very large scale motions, but it is not known how conformational changes may be transmitted from the antigen binding region to the Fc, and therefore influence effector function. Molecular dynamics simulations have been performed on some large antibody systems, however none have been possible on a time scale which would be able to provide information on the converged distributions of large scale properties such as the angle between the Fab and Fc fragments.
In my short project with Peter Minary, I used MOSAICS to investigate the dynamics of an antibody Fab fragment, using the coarse-grained natural move Monte Carlo approach described by Sam a few weeks ago. This makes it possible to split a structure into units which are believed to move in a correlated way, and propose moves for the components of each region together. The rate of sampling is accelerated in degrees of freedom which may have functional significance, for example the movement of the domains in a Fab fragment relative to one another (separate regions shown in the diagram below). I used ABangle to analyse the output of each sampling trajectory and observe any changes in the relative orientations of The VH and VL domains.
Of particular interest would be any correlations between conformational changes in the variable and constant parts of the Fab fragment, as these could be involved in transmitting conformational changes between remote parts of the antibody. We also hoped to see in our model some effect of including the antigen in the simulation, bound to the antibody fragment as seen in the crystal structure. In the time available for the project, we was able to set up a model representing the Fab fragment and run some relatively short simulations to explore favoured conformational states and see how the set up of regions affects distributions seen. In order to draw conclusions about the meaning of the results, a much greater number of simulations will need to be run to ensure sampling of the whole conformational space.