2010 Student Research Conference:
23rd Annual Student Research Conference

Computational Studies of Phi21 N peptide-boxB Recognition
Kelsey C. Mohs
Dr. Maria Nagan, Faculty Mentor

Phi21 is a bacteriophage that, during infection, employs a form gene expression that mediates the antiterminationof transcription by forming termination resistant forms of RNA polymerase complexes. The phi21 N peptide forms a complex with boxB RNA, which is what specifically mediates antitermination. The peptide contains five, positively-charged arginines, four of which make contact with the phosphate backbone of the RNA. The NMR structure of this complex has been solved, but the arginine positions are not fully discernible. Computational studies are undertaken to gain atomic-level detail in a time-dependent manner. A file containing the data for crystalline structure of the complex was downloaded from the Protein Data Bank and then modified to fit the parameters for AMBER 10. AMBER was then used to place ions to neutralize the backbone and then to reach ionic physiological concentrations. Positions of the atoms throughout time will be analyzed to better determine arginine positions.

Keywords: computational, antitermination, arginine


Presentation Type: Oral Paper

Session: 34-1
Location: MG 1098
Time: 1:15

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