Replica Exchange Molecular Dynamics Studies of RNA Binding by Lambda Bacteriophage N Protein
Henry Dust*, Emily Schepers, and Jessica C. Olson
Dr. Maria Nagan, Faculty Mentor
Lambda bacteriophage is a virus infecting Escherichia coli cells that overtakes the native transcription process in order to overexpress viral proteins. The bacteriophage controls gene expression by a process known as antitermination, which requires viral N protein binding to the viral mRNA box B hairpin loop. Computational studies of N protein recognition of box B were undertaken to learn more about the mechanism of binding. Specifically, the nature of the essential arginine-nucleic acid interactions are examined. Computational models have been built. In order to carry out replica exchange molecular dynamics (REMD) simulations, all of the systems must have the same number of atoms and volume. Over the last year, all the systems have been prepared for REMD, which is better able to sample phase space, and are ready for data collection.
Keywords: computational, biochemistry, RNA
Presentation Type: Poster
Location: Georgian Room - SUB