Allsopp, Robert JamesThe membrane contact site theory is a critical theory to understanding lipid transport. The Osh protein is a yeast lipid transport protein theorized to form membrane contact sites. We investigated the contact site theory by identifying a second binding domain and studying the Osh Amphipathic Lipid Packing Sensor (ALPS) to explain better why each protein might target different organelles. The α6- α7 domain appears more charged and prefers lipids with oppositely charged inositol sugars, making it ideal for binding to the Trans Golgi Network (TGN) and the plasma membrane. The ALPS peptide is another dedicated binding domain bound in several membrane types with varied Phosphatidylcholines (PC) tails to vary the lipid packing. If the force field was valid, the results indicate that Osh4 ALPS prefers the loose packing of POPC, and Osh5 ALPS prefers the tighter packing of DMPC. More input from the wet lab is needed before researchers can make predictions from the force field. Another vital area of research is antimicrobial peptides (AMPs) that disrupt the membrane. Part of the dissertation focused on determining the dual placement of the AMPs on the surface and inserted into the membrane. For the first time, the membrane properties of bilayers with AMPs were studied, using the combination of all-atom simulation informed by x-ray scattering. The surface tension was a critical parameter that enabled us to compare the simulation to the wet lab results and became vital in allowing the peptide to be inserted into the membrane and remain stable. The 5-HT3A project simulated predicted structures of toxins with computational tools. Our work simulated these toxins for the first time, and we observed the unbiased binding of σ-GVIIIA conotoxin to the allosteric binding pocket. In the first trajectories, the ion channel pore remained closed, similar enough to the native apo crystal structure that water could form a partially water-filled channel for a few microseconds. In one example, the 5-HT3A had serotonin in all of the binding pockets for close to 1 µs. The long simulation of the conotoxin showed that the extracellular domain (ECD) was deformed by more than a nanometer compared to a control. This deformation was the first indication that such a conformation is possible and might be related to the presence of the toxin. Finally, traumatic brain injury was studied by identifying new molecules that activate fibroblast growth factor (FGF) and toll-like receptor (TLR) proteins. The focus on FGF resulted in identifying a critical conformational change and potential new binding sites (previously unknown) that activate FGF without activating damaging inflammatory TLR responses.enDissertationChemical engineeringMolecular biologyBiophysics5-HT3AAntimicrobial PeptideConformational ChangeFibroblast Growth FactorMembrane Contact SiteOsh4