Unveiling intrinsic dynamics in protein-protein interactions

Binding, fundamental in protein-protein interactions, serves as a gateway to biological function. This PhD thesis explores binding/unbinding phenomena, conformational changes and allosteric interactions, identifying dynamic determinants related to protein function. Elastic Network Models (ENM) are used to analyze protein dynamics in both complex and unbound states, with a focus on conformational changes. The slowest dynamic modes, with hinge sites as key mechanistic points, drive binding/unbinding behavior. Disease-related mutations at these sites reinforce their functional significance. ANM-LD (Anisotropic Network Model-guided Langevin Dynamics) simulations uncover underlying dynamic determinants, revealing specific intermediate steps and latent allosteric pathways, providing ordered sequence of events that elucidate principles controlling functional behavior. We explored its potential as ANM-LD Path webserver with targeted simulations on the GroEL chaperone describing structural changes upon GroES binding alongside Atomic Force Microscopy (AFM) topographic imaging experiments. While being successful on large systems, targeted ANM-LD simulations also capture experimentally observed height increase in the GroEL upper ring while identifying the key residues and correlated domains. These all led to the development of ANM-LD Bind, a platform to tinker and explore the dynamic nature of targeted and untargeted binding/unbinding events, exposing intermediate conformations and allosteric interactions. Finally, intrinsic dynamic behavior of the kinesin-tubulin complex is studied via computational approaches to complement AFM pulling experiments, where disease-related hinge site mutations alter unbinding behavior, increasing binding affinity for D72N and decreasing it for S175A and N332A. These findings collectively enhance our understanding of the dynamic mechanisms governing protein interactions, providing insights for developing therapeutic strategies and designing novel biomolecular functions.