2012 Student Research Conference:
25th Annual Student Research Conference

Computational Studies of P22 N Peptide-boxB RNA Recognition
Michael R. Jones* and Conor J. Dickens
Dr. Maria Nagan, Faculty Mentor

Lambdoid bacteriophage is a type of virus that invades Escherichia coli and manipulates the cell machinery to self-proliferate. One strategy of replication is to turn viral transcription on through the process known as antitermination. P22 N peptide recognition of boxB RNA signals this process to occur. Computational studies of P22 N peptide-boxB complexes have been undertaken to better understand the roles that arginine-rich motifs and water play in peptide-RNA recognition. NMR structures were retrieved from the Protein Data Bank (1A4T) and made compatible with AMBER. Systems were built under a potassium chloride buffer in the presence of explicit water solvent and simulated for 65 ns. Thermodynamic and structural properties were monitored for simulation convergence. The presence of hydrogen bonds between the RNA and the peptide were compared across multiple models and sites of high water density were examined to determine preferential water binding sites.

Keywords: RNA, Computational, Bacteriophage, Protein, arginine, recognition, virus, Molecular Dynamics

Topic(s):Chemistry

Presentation Type: Poster

Session: 300-2
Location: Georgian Room - SUB
Time: 0:00

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