@article{harris_bobay_sarachan_sims_bilbille_deutsch_iwata-reuyl_agris_2015, title={NMR-based structural analysis of threonylcarbamoyl-AMP synthase and Its substrate interactions}, volume={290}, number={33}, journal={Journal of Biological Chemistry}, author={Harris, K. A. and Bobay, B. G. and Sarachan, K. L. and Sims, A. F. and Bilbille, Y. and Deutsch, C. and Iwata-Reuyl, D. and Agris, P. F.}, year={2015}, pages={20032–20043} }
 @article{cantara_bilbille_kim_kaiser_leszczynska_malkiewicz_agris_2012, title={Modifications Modulate Anticodon Loop Dynamics and Codon Recognition of E. coli tRNA (Arg1,2)}, volume={416}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2011.12.054}, abstractNote={Three of six arginine codons are read by two tRNAArg isoacceptors in Escherichia coli. The anticodon stem and loop of these isoacceptors (ASLArg1,2) differs only in that the position 32 cytidine of tRNAArg1 is posttranscriptionally modified to 2-thiocytidine (s2C32). The tRNAArg1,2 are also modified at positions 34 (inosine, I34) and 37 (2-methyladenosine, m2A37). To investigate the roles of modifications in the structure and function, we analyzed six ASLArg1,2 constructs differing in their array of modifications by spectroscopy and codon binding assays. Thermal denaturation and circular dichroism spectroscopy indicated that modifications contribute thermodynamic and base stacking properties, resulting in more order but less stability. NMR-derived structures of the ASLArg1,2 showed that the solution structures of the ASLs were nearly identical. Surprisingly, none possessed the U-turn conformation required for effective codon binding on the ribosome. Yet, all ASLArg1,2 constructs efficiently bound the cognate CGU codon. Three ASLs with I34 were able to decode CGC, whereas only the singly modified ASLArg1,2ICG with I34 was able to decode CGA. The dissociation constants for all codon bindings were physiologically relevant (0.4–1.4 μM). However, with the introduction of s2C32 or m2A37 to ASLArg1,2ICG, the maximum amount of ASL bound to CGU and CGC was significantly reduced. These results suggest that, by allowing loop flexibility, the modifications modulate the conformation of the ASLArg1,2, which takes one structure free in solution and two others when bound to the cognate arginyl-tRNA synthetase or to codons on the ribosome where modifications reduce or restrict binding to specific codons.}, number={4}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Cantara, William A. and Bilbille, Yann and Kim, Jia and Kaiser, Rob and Leszczynska, Grazyna and Malkiewicz, Andrzej and Agris, Paul F.}, year={2012}, month={Mar}, pages={579–597} }
 @article{harris_jones_bilbille_swairjo_agris_2011, title={YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase}, volume={17}, number={9}, journal={RNA}, author={Harris, K. A. and Jones, V. and Bilbille, Y. and Swairjo, M. A. and Agris, P. F.}, year={2011}, pages={1678–1687} }
 @article{bilbille_vendeix_guenther_malkiewicz_ariza_vilarrasa_agris_2009, title={The structure of the human tRNA(Lys3) anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs}, volume={37}, ISSN={["0305-1048"]}, DOI={10.1093/nar/gkp187}, abstractNote={Replication of human immunodeficiency virus (HIV) requires base pairing of the reverse transcriptase primer, human tRNALys3, to the viral RNA. Although the major complementary base pairing occurs between the HIV primer binding sequence (PBS) and the tRNA's 3′-terminus, an important discriminatory, secondary contact occurs between the viral A-rich Loop I, 5′-adjacent to the PBS, and the modified, U-rich anticodon domain of tRNALys3. The importance of individual and combined anticodon modifications to the tRNA/HIV-1 Loop I RNA's interaction was determined. The thermal stabilities of variously modified tRNA anticodon region sequences bound to the Loop I of viral sub(sero)types G and B were analyzed and the structure of one duplex containing two modified nucleosides was determined using NMR spectroscopy and restrained molecular dynamics. The modifications 2-thiouridine, s2U34, and pseudouridine, Ψ39, appreciably stabilized the interaction of the anticodon region with the viral subtype G and B RNAs. The structure of the duplex results in two coaxially stacked A-form RNA stems separated by two mismatched base pairs, U162•Ψ39 and G163•A38, that maintained a reasonable A-form helix diameter. The tRNA's s2U34 stabilized the interaction between the A-rich HIV Loop I sequence and the U-rich anticodon, whereas the tRNA's Ψ39 stabilized the adjacent mismatched pairs.}, number={10}, journal={NUCLEIC ACIDS RESEARCH}, author={Bilbille, Yann and Vendeix, Franck A. P. and Guenther, Richard and Malkiewicz, Andrzej and Ariza, Xavier and Vilarrasa, Jaume and Agris, Paul F.}, year={2009}, month={Jun}, pages={3342–3353} }