2010 Student Research Conference:
23rd Annual Student Research Conference

Computational Studies of P22 N Peptide-boxB Complex
Michael Jones
Dr. Maria Nagan, Faculty Mentor

Lambdoid bacteriophage is a type of virus that invades bacterial chromosomes by binding to the active site, changing the conformation, prompting RNA polymerase to ignore the termination signal. This process, known as antitermination, results in an overstock of viral RNA in the cell. P22 N peptide recognition of boxB RNA viral signals E.coli RNA polymerase to go around the termination signal to synthesize more viral RNA. The purpose of this computational study is to better understand the N peptide-boxB structure. The NMR structures were retrieved from the RCSB Protein Data Bank. Each structure was separated into its own file, using Unix and the vi text editor. Perl scripts were modified to transform the NMR files into files compatible with AMBER, a program designed to simulate biomolecules. PDB files were further prepared through the LEAP module of AMBER. The next steps are to calculate the potassium and chloride ions needed for 200 mM potassium chloride systems and randomize the ions into a buffer.

Keywords: 1A4T, lamboid, protein


Presentation Type: Poster

Session: 9-4
Location: SUB-GEO
Time: 4:15

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