AN INTEGRATIVE APPROACH TO STUDY VIRAL STRUCTURAL PROTEIN CONFORMATIONAL DYNAMICS AND STRUCTURE

Abstract

Viruses are macromolecular assemblies that can sense physiologically relevant thermodynamic and biochemical cues in order to control their overall architecture. Viral structural proteins are the fundamental units that make up the viral particles, some acting in combination with a lipid membrane in the case of enveloped viruses. These structural proteins can shuttle between multiple conformational states in response to physiochemical perturbations during the viral life cycle. In the current thesis, I have characterized the molecular motions of various viral structural proteins to gain mechanistic insights into their function at (near-)atomic resolution. These include the capsid (C) and envelope (E) proteins from the dengue virus, along with some of their biologically relevant complexes, including C: RNA, C: lipid membrane, and E: IgG antibodies. Likewise, I probed the spike (S) protein from the SARS-CoV-2 and its interaction with the host ACE2 receptor. I employed an integrative approach to combine amide-hydrogen deuterium exchange mass spectrometry with molecular modelling and simulations. This work has shed light on: i) the mechanism of dengue capsid mediated genome assembly; ii) dengue serotype-specific dynamics; iii) IgG subclass-specific antibody dynamics and binding-induced effects on the dengue viral particle; and iv) SARS-CoV-2 S protein intrinsic dynamics and ACE2-induced allostery. Collectively, this work has provided a framework to study viral structural proteins using principles of integrative structural biology, wherein data from medium resolution experimental techniques may be utilized to gain high-resolution information on viral processes, towards the design of better therapeutics.