Nucleic Acids Research, 2003, Vol. 31, No. 24 7311-7321
© 2003 Oxford University Press
Article |
Effect of G-1 on histidine tRNA microhelix conformation
1 Department of Chemistry, University of Minnesota, 207 Pleasant Street S.E. and 2 Minnesota Supercomputing Institute, University of Minnesota, 117 Pleasant Street S.E., Minneapolis, MN 55455–0421, USA
*To whom correspondence should be addressed. Tel: +1 612 624 0286; Fax: 612 626 7541; Email: musier{at}chem.umn.edu
Present address:
C. Williams, Chemical Diversity Labs, San Diego, CA 92121, USA
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Histidine tRNAs (tRNAHis) are unique in that they possess an extra 5'-base (G-1) not found in other tRNAs. Deletion of G-1 results in at least a 250-fold reduction in the rate of histidine charging in vitro. To better understand the role of the G-1 nucleotide in defining the structure of tRNAHis, and to correlate structure with cognate amino acid charging, NMR and molecular dynamics (MD) studies were performed on the wild-type and a 
G-1 mutant Escherichia coli histidine tRNA acceptor stem microhelix. Using NMR-derived distance restraints, global structural characteristics are described and interpreted to rationalize experimental observations with respect to aminoacylation activity. The quality of the NMR-derived solution conformations of the wild-type and G-1 histidine microhelices (micro helixHis) is assessed using a variety of MD-based computational protocols. Most of the duplex regions of the acceptor stem and the UUCG tetraloop are well defined and effectively superimposable for the wild-type and G-1 mutant microhelixHis. Differences, however, are observed at the end of the helix and in the single-stranded CCCA-3' tail. The wild-type microhelixHis structure is more well defined than the mutant and folds into a ‘stacked fold-back’ conformation. In contrast, we observe fraying of the first two base pairs and looping back of the single-stranded region in the G-1 mutant resulting in a much less well defined conformation. Thus the role of the extra G-1 base of the unique G-1:C73 base pair in tRNAHis may be to prevent end-fraying and stabilize the stacked fold-back conformation of the CCCA-3' region.