@article{vendeix_murphy_cantara_leszczynska_gustilo_sproat_malkiewicz_agris_2012, title={Human tRNA(UUU)(LYs3) Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism}, volume={416}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2011.12.048}, abstractNote={Human tRNA(Lys3)(UUU) (htRNA(Lys3)(UUU)) decodes the lysine codons AAA and AAG during translation and also plays a crucial role as the primer for HIV-1 (human immunodeficiency virus type 1) reverse transcription. The posttranscriptional modifications 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U(34)), 2-methylthio-N(6)-threonylcarbamoyladenosine (ms(2)t(6)A(37)), and pseudouridine (Ψ(39)) in the tRNA's anticodon domain are critical for ribosomal binding and HIV-1 reverse transcription. To understand the importance of modified nucleoside contributions, we determined the structure and function of this tRNA's anticodon stem and loop (ASL) domain with these modifications at positions 34, 37, and 39, respectively (hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39)). Ribosome binding assays in vitro revealed that the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39) bound AAA and AAG codons, whereas binding of the unmodified ASL(Lys3)(UUU) was barely detectable. The UV hyperchromicity, the circular dichroism, and the structural analyses indicated that Ψ(39) enhanced the thermodynamic stability of the ASL through base stacking while ms(2)t(6)A(37) restrained the anticodon to adopt an open loop conformation that is required for ribosomal binding. The NMR-restrained molecular-dynamics-derived solution structure revealed that the modifications provided an open, ordered loop for codon binding. The crystal structures of the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39) bound to the 30S ribosomal subunit with each codon in the A site showed that the modified nucleotides mcm(5)s(2)U(34) and ms(2)t(6)A(37) participate in the stability of the anticodon-codon interaction. Importantly, the mcm(5)s(2)U(34)·G(3) wobble base pair is in the Watson-Crick geometry, requiring unusual hydrogen bonding to G in which mcm(5)s(2)U(34) must shift from the keto to the enol form. The results unambiguously demonstrate that modifications pre-structure the anticodon as a key prerequisite for efficient and accurate recognition of cognate and wobble codons.}, number={4}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Vendeix, Franck A. P. and Murphy, Frank V. and Cantara, William A. and Leszczynska, Grazyna and Gustilo, Estella M. and Sproat, Brian and Malkiewicz, Andrzej and Agris, Paul F.}, year={2012}, month={Mar}, pages={467–485} }
 @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{davis_gracz_vendeix_serrano_somasundaram_decatur_franzen_2009, title={Different Modes of Binding of Mono-, Di-, and Trihalogenated Phenols to the Hemoglobin Dehaloperoxidase from Amphitrite ornata}, volume={48}, ISSN={["0006-2960"]}, DOI={10.1021/bi801568s}, abstractNote={The hemoglobin dehaloperoxidase (DHP), found in the coelom of the terebellid polychaete Amphitrite ornata, is a dual-function protein that has the characteristics of both hemoglobins and peroxidases. In addition to oxygen transport function, DHP readily oxidizes halogenated phenols in the presence of hydrogen peroxide. The peroxidase activity of DHP is high relative to that of wild-type myoglobin or hemoglobin, but the most definitive difference in DHP is a well-defined substrate-binding site in the distal pocket, which was reported for 4-iodophenol in the X-ray crystal structure of DHP. The binding of 2,4,6-trihalogenated phenols is relevant since 2,4,6-tribromophenol is considered to be the native substrate and 2,4,6-trichlorophenol also gives high turnover rates in enzymatic studies. The most soluble trihalogenated phenol, 2,4,6-trifluorophenol, acts as a highly soluble structural analogue to the native substrate 2,4,6-tribromophenol. To improve our understanding of substrate binding, we compared the most soluble substrate analogues, 4-bromophenol, 2,4-dichlorophenol, and 2,4,6-trifluorophenol, using (1)H and (19)F NMR to probe substrate binding interactions in the active site of the low-spin metcyano adduct of DHP. Both mono- and dihalogenated phenols induced changes in resonances of the heme prosthetic group and an internal heme edge side chain, while (1)H NMR, (19)F NMR, and relaxation data for a 2,4,6-trihalogenated substrate indicate a mode of binding on the exterior of DHP. The differences in binding are correlated with differences in enzymatic activity for the substrates studied.}, number={10}, journal={BIOCHEMISTRY}, author={Davis, Michael F. and Gracz, Hanna and Vendeix, Franck A. P. and Serrano, Vesna and Somasundaram, Aswin and Decatur, Sean M. and Franzen, Stefan}, year={2009}, month={Mar}, pages={2164–2172} }
 @article{vendeix_munoz_agris_2009, title={Free energy calculation of modified base-pair formation in explicit solvent: A predictive model}, volume={15}, ISSN={["1469-9001"]}, DOI={10.1261/rna.1734309}, abstractNote={The maturation of RNAs includes site-specific post-transcriptional modifications that contribute significantly to hydrogen bond formation within RNA and between different RNAs, especially in formation of mismatch base pairs. Thus, an understanding of the geometry and strength of the base-pairing of modified ribonucleoside 5′-monophosphates, previously not defined, is applicable to investigations of RNA structure and function and of the design of novel RNAs. The geometry and free energies of base-pairings were calculated in aqueous solution under neutral conditions with AMBER force fields and molecular dynamics simulations (MDSs). For example, unmodified uridines were observed to bind to uridine and cytidine with significant stability, but the ribose C1′–C1′ distances were far short (∼8.9 Å) of distances observed for canonical A-form RNA helices. In contrast, 5-oxyacetic acid uridine, known to bind adenosine, wobble to guanosine, and form mismatch base pairs with uridine and cytidine, bound adenosine and guanosine with geometries and energies comparable to an unmodified uridine. However, the 5-oxyacetic acid uridine base paired to uridine and cytidine with a C1′–C1′ distance comparable to that of an A-form helix, ∼11 Å, when a H2O molecule migrated between and stably hydrogen bonded to both bases. Even in formation of canonical base pairs, intermediate structures with a second energy minimum consisted of transient H2O molecules forming hydrogen bonded bridges between the two bases. Thus, MDS is predictive of the effects of modifications, H2O molecule intervention in the formation of base-pair geometry, and energies that are important for native RNA structure and function.}, number={12}, journal={RNA}, author={Vendeix, Franck A. P. and Munoz, Antonio M. and Agris, Paul F.}, year={2009}, month={Dec}, pages={2278–2287} }
 @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} }
 @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} }
 @article{weixlbaumer_murphy_dziergowska_malkiewicz_vendeix_agris_ramakrishnan_2007, title={Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines}, volume={14}, ISSN={["1545-9985"]}, DOI={10.1038/nsmb1242}, abstractNote={One of the most prevalent base modifications involved in decoding is uridine 5-oxyacetic acid at the wobble position of tRNA. It has been known for several decades that this modification enables a single tRNA to decode all four codons in a degenerate codon box. We have determined structures of an anticodon stem-loop of tRNA(Val) containing the modified uridine with all four valine codons in the decoding site of the 30S ribosomal subunit. An intramolecular hydrogen bond involving the modification helps to prestructure the anticodon loop. We found unusual base pairs with the three noncomplementary codon bases, including a G.U base pair in standard Watson-Crick geometry, which presumably involves an enol form for the uridine. These structures suggest how a modification in the uridine at the wobble position can expand the decoding capability of a tRNA.}, number={6}, journal={NATURE STRUCTURAL & MOLECULAR BIOLOGY}, author={Weixlbaumer, Albert and Murphy, Frank V. and Dziergowska, Agnieszka and Malkiewicz, Andrzej and Vendeix, Franck A. P. and Agris, Paul F. and Ramakrishnan, V.}, year={2007}, month={Jun}, pages={498–502} }
 @article{whang_vendeix_gracz_gadsby_tonelli_2008, title={NMR studies of the inclusion complex of cloprostenol sodium salt with beta-cyclodextrin in aqueous solution}, volume={25}, ISSN={["1573-904X"]}, DOI={10.1007/s11095-007-9493-z}, abstractNote={{"Label"=>"PURPOSE", "NlmCategory"=>"OBJECTIVE"} Cloprostenol sodium salt (referred as cloprostenol) may be used for the synchronization of estrous cycles in farm animal species. Cyclodextrins (CDs) have potential as drug delivery systems through the formation of inclusion complexes between CDs and drugs. This is the first study of the inclusion complex of cloprostenol with beta-cyclodextrin (beta-CD) in aqueous solution using NMR and 3D molecular dynamics simulations. {"Label"=>"METHODS", "NlmCategory"=>"METHODS"} 1D proton NMR spectra of beta-CD, a complex of cloprostenol with beta-CD, and cloprostenol in D(2)O were assigned and confirmed. The cross relaxation interactions from ROESY were used as constraints for 3D molecular modeling studies. {"Label"=>"RESULTS", "NlmCategory"=>"RESULTS"} In the 2D ROESY of the complex, cross-peaks were observed between the aromatic protons of cloprostenol and protons of the beta-CD as well as between aliphatic protons and protons of the beta-CD. The stoichiometry of the complex was found that beta-CD forms a 1:1 inclusion complex with cloprostenol. The association constant K was 968 +/- 120 M(-1) at 298 K. {"Label"=>"CONCLUSIONS", "NlmCategory"=>"CONCLUSIONS"} Aromatic side and/or aliphatic side chains of the cloprostenol is included in the beta-CD while aliphatic side and/or aromatic side chains wraps around beta-CD, respectively. The molecular modeling also confirms that beta-CD forms a 1:1 inclusion complex with cloprostenol.}, number={5}, journal={PHARMACEUTICAL RESEARCH}, author={Whang, Hyun Suk and Vendeix, Franck A. P. and Gracz, Hanna S. and Gadsby, John and Tonelli, Alan}, year={2008}, month={May}, pages={1142–1149} }
 @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} }