Multi-scale Computational Analysis of Structure, Dynamics and Function of Protein E from Corona Viruses

Project Summary: To help develop effective strategies to battle and prevent future breakouts of corona viruses, it is essential to understand the functions of their proteins. In this proposal, we focus on the envelope protein (E) from SARS-CoV-2 and MERS-CoV, which is involved in virus assembly and budding, and the ion channel activity associated with the transmembrane domain in the endoplasmic reticulum Golgi intermediate compartment (ERGIC) leads to Ca2+ and H+ imbalance, which in turn induces ER stress, NLRP3 inflamma- some activation and excessive secretion of inflammatory cytokines. These functions make the E protein an attractive drug target. There are, however, major questions regarding the underlying molecular mechanism for channel activation and ion permeation, as well as factors that drive the clustering of E proteins and its connection to the generation of local membrane curvature, which is essential to viral particle formation. We have the following specific aims: Aim 1: Conduct atomistic and hybrid QM/MM simulations to define the con- duction mechanism of an individual pentameric channel formed by protein E; this includes elucidating the roles of calcium/proton binding and transient ion-pairing in regulating channel opening and catalyzing ion(s) perme- ation, respectively, and establishing contribution from key polar and aromatic residues to the regulation of pore hydration and ion exit. Aim 2: Conduct atomistic and coarse-grained simulations to probe the mechanism of protein E clustering and the coupling with membrane curvature. In particular, the simulations will help better define the roles of cholesterol and phosphoinositides, and establish the causal relationship between protein E clustering and membrane curvature generation, including the structural features (! strand vs. ↵ helical) of the C-terminal cytoplasmic domain. The proposed computational studies take advantage of our recent methodol- ogy advances and expertise established in related studies, and predictions that emerge from the computational analyses will be readily tested experimentally through collaboration with the Hong group. The mechanistic in- sights and computational strategies established in this work are potentially applicable to the analysis of other envelope proteins in viruses.