2005 Student Research Conference:
18th Annual Student Research Conference


Molecular Dynamics Simulations of Human tRNALys,3UUU: Determination of the Role of Nonstandard Bases
Nina E. McCrate*, Mychel E. Varner, and Katie L. Schembri
Dr. Maria Nagan, Faculty Mentor

Accuracy in translation of the genetic code into proteins depends upon correct recognition of their cognate messenger RNA (mRNA) codons by transfer RNA (tRNA) anticodons. Within tRNAs, incorporation of posttranscriptionally modified bases is common; however, the roles of these chemical modifications are poorly understood. In human tRNALys,3UUU three modified bases are present—two of which are required to achieve wild-type binding activity of wild-type human tRNALys,3UUU (Yarian et al., Biochemistry, 2000, 39, 13390). To elucidate the function of modified bases in the human tRNALys,3UUU anticodon stem loop, RESP charges for nonstandard bases were derived and molecular dynamics (MD) simulations of seven tRNA anticodon stem loops with different combinations of nonstandard bases were performed. The data generated during MD simulations were analyzed to monitor interbase and water-nucleotide hydrogen bonding interactions in the anticodon loop. From these analyses it was found that two modified bases may play significant roles in determining the tertiary structure of the loop through hydrogen-bonding interactions.

Keywords: chemistry, biochemistry, tRNA, molecular dynamics


Presentation Type: Oral Paper

Session: 10-2
Location: VH 1432
Time: 8:30

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