Biochemistry, Biophysics, and Structural Biology Commons^™

On The Origins Of Life — Modelling The Initial Stages Of Complex Coacervate Droplet Formation, Yixuan Wu

Western Libraries Undergraduate Research Awards (WLURAs)

Coacervate droplets are considered a plausible model for protocells due to their spontaneous formation and ability to compartmentalize macromolecules such as nucleic acid and peptides. Although experimental studies have observed and synthesized coacervates under different laboratory conditions, little is known about their structure. Here we present atomistic molecular dynamic simulations of the interactions between water and oppositely charged proteins that cluster together in a salt-dependent process. Observing such liquid-liquid phase separation on an atomic level would serve as a model for the initial stages of complex coacervate formation. Molecular Dynamics was used to compute diagnostics of the structure at different …

Towards Clinical Microscopic Fractional Anisotropy Imaging, Nico Jj Arezza

Electronic Thesis and Dissertation Repository

Microscopic fractional anisotropy (µFA) is a diffusion-weighted magnetic resonance imaging (dMRI) metric that is sensitive to neuron microstructural features without being confounded by the orientation dispersion of axons and dendrites. µFA may potentially act as a surrogate biomarker for neurodegeneration, demyelination, and other pathological changes to neuron microstructure with greater specificity than other dMRI techniques that are sensitive to orientation dispersion, such as diffusion tensor imaging. As with many advanced imaging techniques, µFA is primarily used in research studies and has not seen use in clinical settings.

The primary goal of this Thesis was to assess the clinical viability of …

A Highly Charged Topic: Intrinsically Disordered Proteins And Protein Pka Values, Carter J. Wilson

Electronic Thesis and Dissertation Repository

Intrinsically disordered proteins (IDPs) are known not only for their roles in disease but also for their conformational flexibility, which makes them elusive for experimentation. We consider the role played by theory and simulation in resolving important questions pertaining to IDP structure and dynamics, as well as the nature of the charged residues (e.g., glutamate, lysine, etc.) that enrich them. Specifically, we investigated how the deep learning trained AlphaFold2 (AF2) predictor estimates disorder content, revealing both strong performance in relation to conventional approaches and an important relationship between the AF2 confidence metric and IDP dynamics. We also assessed how modern …