Yumin LiLindsay, Sam Joseph2024-08-272024-07July 2024July 2024http://hdl.handle.net/10342/13657Computational methods including molecular dynamics and molecular docking were utilized to investigate multiple facets of the peripheral membrane binding protein, Annexin A2 (A2). The combined works are presented here as five independent studies. All atomic molecular dynamics simulations were used to conduct the first two studies on the heterotetrameric A2/p11 complex. The first investigated the impact of Ca2+ on the organization of membrane and F-Actin binding sites found within the heterotetramer. It was shown that Ca2+ modulates the availability of key membrane-binding residues and the stability of F-Actin-binding C-terminal residues of A2. The second study investigated the organization of the heterotetramer on the surface of a membrane model. A model of the heterotetramer consistent with measurements from the literature was generated. Additionally, previously unreported interactions between p11 and the membrane were observed. A2 has been implicated in a variety of pathologies where its inhibition would be desirable. A study was undertaken to identify potential inhibitors of A2-membrane binding activity. The stability of A2-ligand binding and effects of ligand binding on A2-membrane interactions was assessed via molecular dynamics simulation. Multiple ligands were identified that disrupt A2-Ca2+ binding and A2-membrane binding. The final two studies involved modelling A2-induced PIP2 microdomain formation. A novel Python package, called MMAEVe, was developed that facilitates the creation of biological-scale membrane-protein models. For the final study, MMAEVe was used to generate a system of A2 surrounding a vesicle. Coarse-grained molecular dynamics simulations were run for the system and the process of A2-induced PIP2 microdomain formation was observed. It was shown that the process occurs in three steps, A2-membrane association, localized PIP2 clustering, and A2 aggregation causing local PIP2 clusters to merge into microdomains. A novel method was developed to track microdomain formation which utilizes the Fréchet mean to define a system-appropriate variance measurement.application/pdfBiology, BioinformaticsBiology, MolecularDoctoral Dissertation2024-08-27