2005 Student Research Conference:
18th Annual Student Research Conference


Molecular Dynamics Simulations of the tRNALys Anticodon Stem Loop
Katie L. Schembri
Dr. Maria Nagan, Faculty Mentor

Transfer ribonucleic acid (tRNA) anticodon recognition of its cognate messenger RNA (mRNA) codon is essential for accurate translation of the genetic code. Incorporation of posttranscriptionally modified bases is common in tRNAs and often is required for tRNA-mRNA recognition. Both the structure for the third human tRNA that codes for lysine (tRNALys,3) and E. coli(tRNALys) contain the modified base threonylcarbamoyladenosine at position 37 (t6A37). Nuclear magnetic resonance (NMR) spectroscopy experiments indicate that an unusual C32-A+38 base pair stabilizes t6A37 at pH 5. Molecular dynamics simulations of tRNALys containing t6A37 at physiological pH were obtained to better understand the role of modified bases in tRNA structure. Root mean square displacements from starting and average structures as well as helical parameters, all indicate that the systems are equilibrated. Correlations between biological activity and the structure of tRNALys under physiological conditions will be presented.

Keywords: ribonucleic acids, tRNA, lysine, molecular dynamics


Presentation Type: Oral Paper

Session: 54-2
Location: VH 1010
Time: 4:00

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