Evaluating Protein - Protein Interactions in Chemokine - Inhibitor Complexes using MD Simulation

Abstract

Chemokines are signaling proteins that play many roles, including the recruitment of immune system cells to infections. Pathogens have evolved chemokine inhibitors that show promise as anti-inflammatory drugs. The poxvirus family produces a viral CC chemokine inhibitor (vCCI) which suppresses immune response by sequestering CC chemokines and thus prevents signaling to immune cells. The herpesvirus family produces a CC chemokine analog, viral macrophage inflammatory protein (vMIP-II), to compete with other CC chemokines at receptors to prevent immune response. In this study, we have used computer modeling to study the binding vCCI to three chemokines, human macrophage inflammatory protein-1β (MIP-1β), vMIP-II, and the human CC chemokine Eotaxin to compare the structural basis for their binding. Molecular Dynamics simulations allow for atomistic level detail of potential interactions between the chemokines and vCCI. Solvent accessible surface area analysis, as well as hydrogen bond count and persistence throughout the length of a simulation, provide a means of comparing the strength and types of interactions between vCCI and each of the chemokines. In addition, evaluating these interactions is key to determining which are critical to binding chemokines. vMIP-II, which has experimentally been shown to bind vCCI more strongly, has more overall hydrogen bonds with vCCI and maintains these hydrogen bonds through more of the simulation. We have also studied the effects of vCCI mutations on chemokine binding. Experimental studies of vCCI have shown that the Y80A mutation, predicted to increase binding strength to chemokines, instead, disables protein function. Simulations of vCCI Y80A reveal that the mutation on the microsecond time scale allows for the flexible loop of vCCI to collapse on the beta sheet docking site for chemokines, blocking key interaction sites for chemokine binding.