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Modeling the stability of non-covalent protein complexes and assemblies

Protein-protein interactions (PPIs) play a pivotal role in all biological processes, including signal transduction, enzymatic catalysis as well as the formation of protein quaternary structures. Elucidating the mechanism of protein complexation/dissociation and finding its kinetics and thermodynamics are therefore important to unveil the fundamental principles underlying biochemical pathways in cells. Specific PPIs in solution rest heavily on non-covalent interactions between constituent protomers, including hydrogen bonding and ionic, hydrophobic, van der Waals and $\pi$-$\pi$ interactions. Polar weak interactions have variable strengths as long-range electrostatic interactions depend largely on the distance between two charge sources and their chemical environment. Electrostatic interactions may be enhanced in a vacuum and in non-polar regions away from bulk solution, but they become weak in a dielectric solvent such as water. These interactions are vital for proteins recognizing their partners in a highly crowded environment.

To dissect PPIs in a vast array of non-covalent protein complexes, a combination of different experimental techniques have been used in structural biology, which include native mass spectrometry (MS), X-ray crystallography, NMR spectroscopy, (cryo-)electron microscopy, and methods of bioinformatics. Native MS usually operates by preceding electrospray ionization (ESI), because ESI is a soft ionization method. ESI transfers analytes directly from the parent solution into the gaseous state via intermediate droplets that carry the analytes, solvent, and other ions. During their journey to the mass spectrometer, the droplets reduce in size via solvent evaporation and release of solvated ions. The analytes then emerge from the droplets following a variety of mechanisms. Because of the unknown role of the droplet chemistry in the stability of PPIs or protein-ligand interactions, the question on whether the gas-phase ensemble of the complexes reflects the chemical equilibria of the species in bulk solution has been debated for over twenty years.

The goal of our research is to establish the principles that govern the stability of a weak transient protein complex in the droplet environment and in bulk solution. In relation to the droplet enviroment, we provided the first computational evidence of a protein complex dissociation in a droplet [M. In Oh and SC, Physical Chemistry Chemical Physics v. 19, pp. 31965--31981 (2017); Journal of Physical Chemistry Letters v. 8, pp 80-85 (2017); Analytical Chemistry v. 89, pp. 8192--8202 (2017)]. We have made significant advances by introducing computational methodologies that allow us to find (i) the mechanism of complex dissociation in droplets and (ii) the correction to the equilibrium constant due to possible protein complex dissociation in a droplet. Our computational methods are based on a multi-scale computational approach. In our studies we address the challenging problem of the constantly changing acidity of the droplet due to its evaporation. In droplets we have use all-atom modelling of the protein complexes and explicit modelling of the solvent. On the other end, in bulk solution we use coarse grained models and advanced sampling techniques to investigate the mechanisms of protein association and dissociation.