Researcher(s)
- Pohl Moreno, Biochemistry, Universidad Nacional de Colombia
Faculty Mentor(s)
- Jodi Hadden-Perilla, Chemistry and Biochemistry, University of Delaware
Abstract
The Brome Mosaic Virus (BMV), which infects plants, can be transformed into a super-fluorescent particle when decorated with many copies of the dye Oregon Green 488. The dyes bind lysines on the virus capsid, the most important of which only become accessible when BMV undergoes a swelling transition upon changes of pH. Here, we use molecular dynamics (MD) simulations to study lysine accessibility and search for clues leading to a possible model of the swollen capsid at pH 6.5. Particularly, we compute the Dye Accessible Surface Area (DASA) of lysine 105 all around the capsid in order to see whether it can become accessible to the dyes through a conformational change of protein subunits or if it is the displacement between subunits that could lead to this event. Based on studies from the literature on the related Cowpea Chlorotic Mottle Virus (CCMV) and on electrostatic potential calculations for BMV, we survey the quasi threefold interface of its capsid at different pHs. Results indicate that displacement of subunits, which occurs during swelling, is a key contributor to lysine accessibility.