@article{graham_barley-maloney_stark_kaur_stolarchuk_sproat_leszczynska_malkiewicz_safwat_mucha_et al._2012, title={Functional Recognition of the Modified Human tRNA (Lys3) (UUU) Anticodon Domain by HIV's Nucleocapsid Protein and a Peptide Mimic (vol 410, pg 698, year 2011)}, volume={420}, number={3}, journal={Journal of Molecular Biology}, author={Graham, W. D. and Barley-Maloney, L. and Stark, C. J. and Kaur, A. and Stolarchuk, C. and Sproat, B. and Leszczynska, G. and Malkiewicz, A. and Safwat, N. and Mucha, P. and et al.}, year={2012}, pages={259–259} }
 @article{graham_barley-maloney_stark_kaur_stolyarchuk_sproat_leszczynska_malkiewicz_safwat_mucha_et al._2011, title={Functional recognition of the modified human tRNA(UUU)(Lys3) anticodon domain by HIV's nucleocapsid protein and a peptide mimic}, volume={410}, number={4}, journal={Journal of Molecular Biology}, author={Graham, W. D. and Barley-Maloney, L. and Stark, C. J. and Kaur, A. and Stolyarchuk, K. and Sproat, B. and Leszczynska, G. and Malkiewicz, A. and Safwat, N. and Mucha, P. and et al.}, year={2011}, pages={698–715} }
 @article{scheunemann_graham_vendeix_agris_2010, title={Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA}, volume={38}, number={9}, journal={Nucleic Acids Research}, author={Scheunemann, A. E. and Graham, W. D. and Vendeix, F. A. P. and Agris, P. F.}, year={2010}, pages={3094–3105} }
 @article{jones_jones_graham_agris_spremulli_2008, title={A Disease-causing Point Mutation in Human Mitochondrial tRNA(Met) Results in tRNA Misfolding Leading to Defects in Translational Initiation and Elongation}, volume={283}, ISSN={["1083-351X"]}, DOI={10.1074/jbc.M806992200}, abstractNote={The mitochondrial tRNA genes are hot spots for mutations that lead to human disease. A single point mutation (T4409C) in the gene for human mitochondrial tRNAMet (hmtRNAMet) has been found to cause mitochondrial myopathy. This mutation results in the replacement of U8 in hmtRNAMet with a C8. The hmtRNAMet serves both in translational initiation and elongation in human mitochondria making this tRNA of particular interest in mitochondrial protein synthesis. Here we show that the single 8U→C mutation leads to a failure of the tRNA to respond conformationally to Mg2+. This mutation results in a drastic disruption of the structure of the hmtRNAMet, which significantly reduces its aminoacylation. The small fraction of hmtRNAMet that can be aminoacylated is not formylated by the mitochondrial Met-tRNA transformylase preventing its function in initiation, and it is unable to form a stable ternary complex with elongation factor EF-Tu preventing any participation in chain elongation. We have used structural probing and molecular reconstitution experiments to examine the structures formed by the normal and mutated tRNAs. In the presence of Mg2+, the normal tRNA displays the structural features expected of a tRNA. However, even in the presence of Mg2+, the mutated tRNA does not form the cloverleaf structure typical of tRNAs. Thus, we believe that this mutation has disrupted a critical Mg2+-binding site on the tRNA required for formation of the biologically active structure. This work establishes a foundation for understanding the physiological consequences of the numerous mitochondrial tRNA mutations that result in disease in humans.}, number={49}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Jones, Christie N. and Jones, Christopher I. and Graham, William D. and Agris, Paul F. and Spremulli, Linda L.}, year={2008}, month={Dec}, pages={34445–34456} }
 @article{vendeix_dziergowska_gustilo_graham_sproat_malkiewicz_agris_2008, title={Anticodon domain modifications contribute order to tRNA for ribosome-mediated codon binding}, volume={47}, ISSN={["0006-2960"]}, DOI={10.1021/bi702356j}, abstractNote={The accuracy and efficiency with which tRNA decodes genomic information into proteins require posttranscriptional modifications in or adjacent to the anticodon. The modification uridine-5-oxyacetic acid (cmo (5)U 34) is found at wobble position 34 in a single isoaccepting tRNA species for six amino acids, alanine, leucine, proline, serine, threonine, and valine, each having 4-fold degenerate codons. cmo (5)U 34 makes possible the decoding of 24 codons by just six tRNAs. The contributions of this important modification to the structures and codon binding affinities of the unmodified and fully modified anticodon stem and loop domains of tRNA (Val3) UAC (ASL (Val3) UAC) were elucidated. The stems of the unmodified ASL (Val3) UAC and that with cmo (5)U 34 and N (6)-methyladenosine, m (6)A 37, adopted an A-form RNA conformation (rmsd approximately 0.6 A) as determined with NMR spectroscopy and torsion-angle molecular dynamics. However, the UV hyperchromicity, circular dichroism ellipticity, and structural analyses indicated that the anticodon modifications enhanced order in the loop. ASL (Val3) UAC-cmo (5)U 34;m (6)A 37 exhibited high affinities for its cognate and wobble codons GUA and GUG, and for GUU in the A-site of the programmed 30S ribosomal subunit, whereas the unmodified ASL (Val3) UAC bound less strongly to GUA and not at all to GUG and GUU. Together with recent crystal structures of ASL (Val3) UAC-cmo (5)U 34;m (6)A 37 bound to all four of the valine codons in the A-site of the ribosome's 30S subunit, these results clearly demonstrate that the xo (5)U 34-type modifications order the anticodon loop prior to A-site codon binding for an expanded codon reading, possibly reducing an entropic energy barrier to codon binding.}, number={23}, journal={BIOCHEMISTRY}, author={Vendeix, Franck A. P. and Dziergowska, Agnieszka and Gustilo, Estella M. and Graham, William D. and Sproat, Brian and Malkiewicz, Andrzej and Agris, Paul F.}, year={2008}, month={Jun}, pages={6117–6129} }
 @article{lusic_gustilo_vendeix_kaiser_delaney_graham_moye_cantara_agris_deiters_2008, title={Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNA(Met)}, volume={36}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkn703}, abstractNote={Human mitochondrial methionine transfer RNA (hmtRNAMetCAU) has a unique post-transcriptional modification, 5-formylcytidine, at the wobble position-34 (f5C34). The role of this modification in (hmtRNAMetCAU) for the decoding of AUA, as well as AUG, in both the peptidyl- and aminoacyl-sites of the ribosome in either chain initiation or chain elongation is still unknown. We report the first synthesis and analyses of the tRNA's anticodon stem and loop domain containing the 5-formylcytidine modification. The modification contributes to the tRNA's anticodon domain structure, thermodynamic properties and its ability to bind codons AUA and AUG in translational initiation and elongation.}, number={20}, journal={NUCLEIC ACIDS RESEARCH}, author={Lusic, Hrvoje and Gustilo, Estella M. and Vendeix, Franck A. P. and Kaiser, Rob and Delaney, Michael O. and Graham, William D. and Moye, Virginia A. and Cantara, William A. and Agris, Paul F. and Deiters, Alexander}, year={2008}, month={Nov}, pages={6548–6557} }
 @misc{agris_vendeix_graham_2007, title={tRNA's wobble decoding of the genome: 40 years of modification}, volume={366}, number={1}, journal={Journal of Molecular Biology}, author={Agris, P. F. and Vendeix, F. A. P. and Graham, W. D.}, year={2007}, pages={1–13} }