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Comp Chem Research Developments | |
| Archive of Comp Chem Research News | |
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Oct 20, 1999 |
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Water density contour of wild-type RNA microhelixAla. The G3:U70 wobble base pair is shown in red. (Arrows: Left=start movie; Right=frame by frame) |
Successful protein synthesis requires transfer-RNA (tRNA) molecules to
be "charged" with their proper amino acids (there are
20 amino acids commonly used in protein synthesis, and each has
its own unique set of tRNAs) with very high fidelity. This charging is
accomplished by enzymes called aminoacyl-tRNA synthetases, and
one of the many questions with respect to their specificity is
how they recognize their substrate tRNA molecules. Graduate student
Maria C. Nagan, working with Professors Karin Musier-Forsyth and
Christopher J. Cramer, is modeling how substitution and/or modification
of specific base pairs affects the structure and dynamics of alanine
tRNA-derived microhelices in an effort to correlate such changes with
alanyl tRNA synthetase activity. The unique G3:U70 wobble base pair in the acceptor stem of tRNAAla is a critical determinant for specific recognition by alanyl-tRNA synthetase. Molecular dynamics simulations of RNA microhelixAla indicate that G3:U70 and other 3:70 purine:pyrimidine wobble pairs induce local deviations from A-form geometry in their respective microhelices; the helix is underwound at the base-pair step above and overwound at the base-pair step below, in each case by about 7 to 9 degrees compared to canonical A-form RNA. Based on analysis of average water densities and residence lifetimes, the wild-type microhelix strongly binds a water molecule in the minor groove of the 3:70 base pair, consistent with crystallographic analyses of an RNA duplex derived from the acceptor stem of Escherichia coli tRNAAla. Other wobble pairs show water binding at this position but to a lesser degree; the strength of water binding correlates directly with the measured aminoacylation activities of the microhelices as substrates for E. coli alanyl-tRNA synthetase (G:U > 2AA:IsoC > G:dU > I:U). Watson-Crick base pairs at the 3:70 position show no tendency towards specific hydration. This tightly bound minor-groove water in the microhelices with 3:70 wobble pairs evidently does not function to stabilize a particular local helical structure, but it may play a role as a specific recognition element or serve as an indicator of interaction specificity between the microhelix and a hydroxylated residue of the aminoacyl-tRNA synthetase. This work has been reported in Nagan, M. C.; Kerimo, S. S.; Musier-Forsyth, K.; Cramer, C. J. "Wild-type RNA MicrohelixAla and 3:70 Variants: Molecular Dynamics Analysis of Tightly Bound Water and Local Helical Structure" J. Am. Chem. Soc. 1999, 121, 7310. |
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