2006 Student Research Conference:
19th Annual Student Research Conference


Computational simulation of human tRNALys,3UUU with ms2t6A37, mcm5s2U34, and pseudouridine 39 modifications
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 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—2-methylthio-6-threonylcarbamoyladenosine at position 37 (ms2t6A37), 5-methyoxycarbonylmethyl-2-thiouridine at position 34 (mcm5s2U34), and pseudouridine (ψ) at position 39—two of which, ms2t6A37 and mcm5s2U34, are required to achieve wild-type binding activity of human tRNALys,3UUU (Yarian et al., Biochemistry, 2000, 39, 13390). To elucidate the function of each modified base in the human tRNALys,3UUU anticodon stem loop, molecular dynamics simulations of nine tRNA anticodon stem loops with different combinations of nonstandard bases were performed. From these simulations it was found that ms2t6A37 enhances stacking between itself and U36 and also prevents U36, the anticodon reading the first codon, from flipping out into solution.

Keywords: molecular dynamics, tRNALys,3, modified bases


Presentation Type: Oral Paper

Session: 53-5
Location: VH 1432
Time: 3:45

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