2004 Student Research Conference:
17th Annual Student Research Conference


Molecular Dynamics Simulation of the tRNALys,3UUU Anticodon Step Loop
Katie L. Schembri
Dr. Maria Nagan, Faculty Mentor

The nuclear magnetic resonance (NMR) structure of the third transfer ribonucleic acid (tRNA) that codes for lysine indicated that the inclusion of threonylcarbamoyladenosine at position 37 (t6A37) changes the anticodon stem loop structure such that uracil 34 flips around, leaving only two remaining uracil bases to interact with the messenger RNA (mRNA) codon. It has been proposed that the unusual C32-A+38 base pair stabilizes t6A37. The NMR structure was obtained at pH 5 but at physiological pH, this base pair should not form. The purpose of this study is to analyze the dynamics of t6A37 in the tRNALys, 3UUU structure at pH 7. Four tRNALys, 3 variants are being analyzed using molecular dynamics simulations. Trajectories for all four systems have been collected. Root mean square displacements from starting and average structures as well as helical parameters, all indicate that the systems are equilibrated.

Keywords: transfer RNA, molecular dynamics, lysine, ribonucleic acid


Presentation Type: Oral Paper

Session: 11-5
Location: VH 1010
Time: 9:30

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