Structural studies of SARS-CoV-2 spike protein and vesicular coats

Abstract

The first part of this thesis concerns SARS-CoV-2, the causative agent of the coronavirus disease 2019 (COVID-19). The COVID-19 pandemic has raised an immediate need for vaccine and therapeutic development. The SARS-CoV-2 S protein, forming a crown on the surface of the virus envelope, is responsible for the receptor interaction and facilitating entry into host cells. It is one of the main antigens and a promising therapeutic target. In my work, I expressed and purified stabilised constructs of SARS-CoV-2 S ectodomain, used in multiple avenues of research. We produced cysteine stabilised mutants, which exhibit increased stability and are trapped in a closed conformation, hindering receptor engagement. In a collaborative project, I investigated the use of such stabilised construct as an antigen in immunising mice and showed that the protein induced potent neutralising responses. I also investigated structural characteristics of synthetic antibodies binding the S protein, to identify promising therapeutics. Lastly, in another collaboration, I used cryo-electron microscopy and single particle analysis to characterise a series of antiviral peptides and their interaction with the S protein in solution as well as on intact virions. In the second part, I discuss my work on vesicular coat proteins. Protein coated vesicles facilitate transport between multiple cell organelles in the secretory and endocytic pathways. The trafficking is mediated by various protein coats, which select appropriate cargo through recognition of sorting signals, mould, and structurally support a vesicle. The four archetypal protein coats are formed by clathrin and its adaptor proteins, COPI, COPII and retromer. COPI facilitates transport within the Golgi apparatus, as well as from the Golgi towards the Endoplasmic Reticulum (ER). GOLPH3 is a Golgi resident protein acting as a gatekeeper at the late Golgi to retain other Golgi-residents. It is known to interact with the COPI coat to modulate its cargo binding capabilities, but the interaction and cargo recognition by the two proteins remains elusive. In my PhD work I studied the COPI and GOLPH3 complex using an in vitro reconstituted system and cryo-electron tomography. I obtained a 14 A resolution structure of the complex on vesicles by subtomogram averaging, which provides insights into the sites of interaction between GOLPH3 and COPI subunits, as well as their possible cargo interaction.