General principles of binding between cell surface receptors and multi-specific ligands: A computational study
Fig 6
The internal flexibility of multi-specific ligands was incorporated in the simulations.
Comparing a simulation in which flexibility was incorporated (red) with a simulation without flexibility (black), we found that flexibility not only leads to more interactions on average, but also causes larger fluctuations in the number of interactions along simulation time (a). We further changed the maximal ranges of translational and rotational perturbations in each simulation step to adjust the spatial variability between different binding sites in a multi-specific ligand. The overall testing results are plotted in (b) as a three-dimensional histogram. The maximal ranges of translational and rotational fluctuations are indexed along the x and y directions. The figure suggests that the overall binding of ligands is promoted by the intramolecular flexibility within an appropriate range. However, binding will be negatively affected when molecules are over flexible.