Researcher(s)
- Riley McKeon, Biochemistry, University of Delaware
- Joshua Whitehead, Chemical Engineering, University of Delaware
Faculty Mentor(s)
- Jodi Hadden-Perilla, Chemistry and Biochemistry, University of Delaware
Abstract
Viruses are infectious agents that replicate inside the living cells of organisms. They replicate by taking over a host cell and using its components to create copies of themselves. Specifically, the Brome Mosaic Virus (BMV) is a tiny, non-enveloped, positive-strand RNA plant virus. BMV is found in many cereal plants, and it causes mosaic symptoms such as alternating light and dark green areas on the leaves. X-ray crystal structures show that the BMV capsid has an outer protein shell and is composed of three chains: A, B, and C. Recent studies show that when the virus is decorated with the fluorescent dye Oregon Green 488 (ORE) at specific lysine residues (K64, K105, K165), the resulting particle can emit super-fluorescence. Here, all-atom molecular dynamics (MD) simulations of the B chain are used to analyze the motion of the dye-decorated capsid protein in two different water solvent models: TIP3P and TIP4P-Ew. Previous studies suggest that protein-dye interactions are more realistic with the TIP4P-Ew water model.
We report the root mean square deviation, root mean square fluctuation, spatial propensity, orientation factor (2), and frequency of protein-dye interactions to determine if TIP4P-Ew is more suitable for studying the super-fluorescent BMV particle. To test the claim, the results are compared to those originating from a system constructed with a TIP3P solvent model proving the accuracy of the TIP4P-Ew model.