2011 Student Research Conference:
24th Annual Student Research Conference

Molecular Dynamics of the Phi21 N-Peptide - boxB RNA Complex
Erin L. Farmer
Dr. Maria Nagan, Faculty Mentor

The purpose of this study is to determine the role of arginine and observe hydration patterns in a Phi21 N-Peptide boxB RNA complex. It is thought that the arginine side chains of the peptide may play a significant role in the recognition of RNA. The investigation is carried out through use of the computational chemistry program Amber. Molecular dynamics simulations are conducted using Amber to provide information of the complexs behavior. Currently, there are 12 models of the complex with 10.2 ns of completed simulation time and 3 models that are near the completion time of 70 ns. Analysis has included monitoring thermodynamics and RMSD values thus far. In the future, there will be additional analysis of the hydrogen bonding and role of arginine within the complex.

Keywords: Computational, Biochemistry, RNA, Phi21

Topic(s):Chemistry

Presentation Type: Oral Paper

Session: 43-5
Location: MG 1000
Time: 3:45

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