Preferences of AAA/AAG codon recognition by modified nucleosides, τm⁵s²U₃₄ and t⁶A₃₇ present in tRNA^Lys

References

• Aduri, R., Psciuk, B. T., Saro, P., Taniga, H., Schlegel, H. B., & SantaLucia, J. (2007). AMBER Force field parameters for the naturally occurring modified nucleosides in RNA. J. Chem. Theory Comput., 3, 1464–1475. doi:10.1021/ct600329w
   PubMed Web of Science ®Google Scholar
• Agris, P. F. (2004). Decoding the genome: A modified view. Nucleic Acids Res., 32, 223–238. doi:10.1093/nar/gkh185
   PubMed Web of Science ®Google Scholar
• Agris, P. F. (2008). Bringing order to translation: The contributions of transfer RNA anticodon-domain modifications. EMBO reports., 9, 629–635. doi:10.1038/embor.2008.104
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., & DiNola, A. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81, 3684–3690. doi:10.1063/1.448118
   Web of Science ®Google Scholar
• Case, D. A. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26, 1668–1688. doi:10.1002/jcc.20290
   PubMed Web of Science ®Google Scholar
• Crick, F. H. C. (1966). Codon-anticodon pairing: The wobble hypothesis. Journal of Molecular Biology, 19, 548–555. doi:10.1016/S0022-2836(66)80022-0
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle Mesh Ewald – an N.Log(N) Method for Ewald sums in large systems. The Journal of Chemical Physics, 98, 10089–10092. doi:10.1002/14651858.CD004426.pub3
   Web of Science ®Google Scholar
• Das, G., & Lyngdoh, R. H. (2008). Can configuration of solitary wobble base pairs determine the specificity and degeneracy of the genetic code? Clues from molecular orbital modelling studies. Journal of Molecular Structure: THEOCHEM, 851(1–3), 319–334. doi:10.1016/j.theochem.2007.11.027.
   Web of Science ®Google Scholar
• Das, G., & Lyngdoh, R. H. (2014). Configuration of wobble base pairs having pyrimidines as anticodon wobble bases: Significance for codon degeneracy. Journal of Biomolecular Structure and Dynamics, 32(9), 1500–1520. doi:10.1080/07391102.2013.824822
   PubMed Web of Science ®Google Scholar
• Das, G., & Lyngdoh, R. H. (2012). Role of wobble base pair geometry for codon degeneracy: Purine-type bases at the anticodon wobble position. Journal of Molecular Modeling, 18(8), 3805–3820. doi:10.1007/s00894-012-1385-4
   PubMed Web of Science ®Google Scholar
• Devi, M., & Lyngdoh, R. H. D. (2017). Favored and less favored codon-anticodon duplexes arising from the GC codon family box encoding for alanine: Some computational perspectives. Journal of Biomolecular Structure and Dynamics 1–21. doi:10.1080/07391102.2017.1308886
   PubMed Web of Science ®Google Scholar
• Enriquez, J. A., Chomyn, A., & Attardi, G. (1995). MtDNA mutation in MERRF syndrome causes defective aminoacylation of tRNALys and premature translation termination. Nature Genetics, 10, 47–55. doi:10.1038/ng0595-47
   PubMed Web of Science ®Google Scholar
• Fandilolu, P., Kamble, A., Sambhare, S., & Sonawane, K. (2017). Conformational preferences and structural analysis of hypermodified nucleoside, peroxywybutosine (o2yW) found at 37th position in anticodon loop of tRNAPhe and its role in modulating UUC codon-anticodon interactions. Gene, 641, 310–325.
   PubMed Web of Science ®Google Scholar
• Florentz, C., Sohm, B., Tryoen-Toth, P., Putz, J., & Sissler, M. (2003). Human mitochondrial tRNAs in health and disease. Cellular and Molecular Life Sciences (CMLS), 60, 1356–1375. doi:10.1007/s00018-003-2343-1
   PubMed Web of Science ®Google Scholar
• Hehre, W. J., Yu, J., Klunzinger, P. E., & Lou, L. (1998). Spartan Software. Irvine, CA: Wavefunction, Inc.
   Google Scholar
• Jacobs, H. T. (2003). Disorders of mitochondrial protein synthesis. Human Molecular Genetics, 12, R293–R301. doi:10.1093/hmg/ddg285
   PubMed Web of Science ®Google Scholar
• Jalkute, C., Barage, S., & Sonawane, K. (2015). Insight into molecular interactions of Aβ peptide and gelatinase from Enterococcus faecalis: A molecular modeling approach. RSC Advances, 5, 10488–10496. doi:10.1039/C4RA09354B
   Web of Science ®Google Scholar
• Kamble, A., Fandilolu, P., Sambhare, S., & Sonawane, K. (2017). Idiosyncratic recognition of UUG/UUA codons by modified nucleoside 5-taurinomethyluridine, τm5U present at ‘wobble’ position in anticodon loop of tRNALeu: A molecular modeling approach. PLoS ONE, 12(4), e0176756. doi:10.1371/journal.pone.0176756
   PubMed Web of Science ®Google Scholar
• Kamble, A., Kumbhar, B., Sambhare, S., Bavi, R., & Sonawane, K. (2015). Conformational Preferences of Modified Nucleoside 5-Taurinomethyluridine, τm5U Occur at ‘wobble’ 34th Position in the Anticodon Loop of tRNA. Cell Biochemistry and Biophysics, 71, 1589–1603. doi:10.1007/s12013-014-0382-x
   PubMed Web of Science ®Google Scholar
• Kamble, A., Sambhare, S., Fandilolu, P., & Sonawane, K. (2016). ) Structural significance of modified nucleoside 5-taurinomethyl-2-thiouridine, τm5s2U occur at ‘wobble’ 34th position in the anticodon loop of Human mitochondrial tRNALys. Structural Chemistry, 27, 839–854. doi:10.1007/s11224-015-0642-4
   Web of Science ®Google Scholar
• Konevega, A. L., Soboleva, N. G., Makhno, V. I., Semenkov, Y. P., Wintermeyer, W., Rodnina, M. V., & Katunin, V. I. (2004). Purine bases at position 37 of tRNA stabilize codon–anticodon interaction in the ribosomal A site by stacking and Mg2+ -dependent interactions. RNA., 10, 90–101. doi:10.1261/rna.5142404
   PubMed Web of Science ®Google Scholar
• Labuda, D., Striker, G., Grosjean, H., & Porschke, D. (1985). Mechanism of codon recognition by transfer RNA studied with oligonucleotides larger than triplets. Nucleic Acids Research, 13, 3667–3683. doi:10.1093/nar/13.10.3667
   PubMed Web of Science ®Google Scholar
• Larsson, N., Tulinius, M., Holme, E., & Oldfors, A. (1995). Pathogenetic aspects of the A8344G mutation of mitochondrial DNA associated with MERRF syndrome and multiple symmetric lipomas. Muscle & Nerve, 3, 102–106. doi:10.1002/mus.880181421
   Google Scholar
• Larsson N., Tulinius M., Holme E., Oldfors A., Andersen O., Wahlstrom J., Aasly J. (1992). Segregation and manifestations of the mtDNA tRNA (Lys) A–>G(8344) mutation of myoclonus epilepsy and ragged-red fibers (MERRF) syndrome. American Journal of Human Genetics, 51, 1201–1212. Retrieved from www.ncbi.nlm.nih.gov/pmc/articles/PMC1682923
   PubMed Web of Science ®Google Scholar
• Mangang, S. U., & Lyngdoh, R. H. (2001). Wobble base-pairing in codon-anticodon interactions: A theoretical modelling study. Indian Journal of Biochemistry & Biophysics, 38(1–2), 115–119 http://nopr.niscair.res.in/handle/123456789/19809
   PubMed Web of Science ®Google Scholar
• Masucci J., Schon E., King M. (1997). Point mutations in the mitochondrial tRNA(Lys) gene: Implications for pathogenesis and mechanism. In F. N. Gellerich, S. Zierz (Eds.), Detection of mitochondrial diseases174 (Vol. 21, pp. 215–219). Developments in molecular and cellular biochemistry. Boston, MA: Springer. doi:10.1007%2F978-1-4615-6111-8_33
   Google Scholar
• Murphy, F. V., Ramakrishnan, V., Malkiewicz, A., & Agris, P. F. (2004). The role of modifications in codon discrimination by tRNALys UUU. Nature Structural & Molecular Biology, 11, 1186–1191. doi:10.1038/nsmb861
   PubMed Web of Science ®Google Scholar
• Oldfors, A., Holme, E., Tulinius, M., & Larsson, N. (1995). Tissue distribution and disease manifestations of the tRNA(Lys) A–>G(8344) mitochondrial DNA mutation in a case of myoclonus epilepsy and ragged red fibres. Acta Neuropathologica, 90, 328–333. doi:10.1007/BF00296519
   PubMed Web of Science ®Google Scholar
• Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T. E., Laughton, C. A., & Orozco, M. (2007). Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers. Biophysical Journal, 92, 3817–3829. doi:10.1529/biophysj.106.097782
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25, 1605–1612. doi:10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Quigley, G. J., & Rich, A. (1976). Structural domains of transfer RNA molecules. Science., 194, 796–806. doi:10.1126/science.790568
   PubMed Web of Science ®Google Scholar
• Rodriguez-Hernandez, A., Spears, J. L., Gaston, K. W., Limbach, P. A., Gamper, H., Hou, Y. M., … Perona, J. J. (2013). Structural and mechanistic basis for enhanced translational efficiency by 2-thiouridine at the tRNA anticodon wobble position. Journal of Molecular Biology, 425, 3888–3906. doi:10.1016/j.jmb.2013.05.018
   PubMed Web of Science ®Google Scholar
• Rozov, A., Demeshkina, N., Khusainov, I., Westhof, E., Yusupov, M., & Yusupova, G. (2015). Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code. Nature Communications, 7, 10457. doi:10.1038/ncomms10457
   Web of Science ®Google Scholar
• Ryckaert, J. P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327–341. doi:10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Sadlej-Sosnowska, N. (2009). Quantum chemical considerations on degeneracy of the genetic code: Anticodon–codon wobble base pairing. Journal of Molecular Structure: THEOCHEM, 913(1–3), 270–276.10.1016/j.theochem.2009.08.006
   Web of Science ®Google Scholar
• Schaffer, S. W., Jong, C. J., Ito, T., & Azuma, J. (2014). Role of taurine in the pathologies of MELAS and MERRF. Amino Acids, 46, 47–56. doi:10.1007/s00726-012-1414-8
   PubMed Web of Science ®Google Scholar
• Shi, H. J., & Moore, P. B. (2000). The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: A classic structure revisited. RNA, 6, 1091–1105. Retrieved from http://rnajournal.cshlp.org/content/6/8/1091.full.pdf+html10.1017/S1355838200000364
   PubMed Web of Science ®Google Scholar
• Sonawane, K., & Barage, S. (2014). Structural analysis of membrane-bound hECE-1 dimer using molecular modelling techniques: Insights into conformational changes and Aβ1–42 peptide binding. Amino Acids, 47, 543–559. doi:10.1007/s00726-014-1887-8. Epub 2014 Dec 16.
   PubMed Web of Science ®Google Scholar
• Sonawane, K., Bavi, R., Sambhare, S., & Fandilolu, P. (2016). Comparative structural dynamics of tRNAPhe with respect to hinge region methylated guanosine: A computational approach. Cell Biochemistry and Biophysics, 74(2), 157–173. doi:10.1007/s12013-016-0731-z
   PubMed Web of Science ®Google Scholar
• Sonawane, K., & Sambhare, S. (2015). The influence of hypermodified nucleosides lysidine and t6A to recognize the AUA codon instead of AUG: A molecular dynamics simulation study. Integrative Biology, 7, 1387–1395. doi:10.1039/C5IB00058 K
   PubMed Web of Science ®Google Scholar
• Sprinzl M., Horn C., Brown M., Loudovitch A., Steinberg S. (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Research, 26, 148–153. Retrieved from www.ncbi.nlm.nih.gov/pmc/articles/PMC14721610.1093/nar/26.1.148
   PubMed Web of Science ®Google Scholar
• Suzuki T. (2005). Biosynthesis and function of tRNA wobble modifications. In H. Grosjean. (Ed.), Fine-tuning of RNA functions by modification and editing. Topics in current genetics (Vol. 12, pp. 23–69). Berlin: Springer. doi:10.1007/b106361
   Google Scholar
• Suzuki, T., Suzuki, T., Wada, T., Saigo, K., & Watanabe, K. (2002). Taurine as a constituent of mitochondrial tRNAs: New insights into the functions of taurine and human mitochondrial diseases. The EMBO Journal, 21, 6581–6589. doi:10.1093/emboj/cdf656
   PubMed Web of Science ®Google Scholar
• SYBYL 7.3. (2006). Tripos international. St. Louis, MO: South Hanley Rd.
   Google Scholar
• Varani, G., & McClain, W. (2000). The G.U wobble base pair. EMBO reports, 1, 18–23. doi:10.1093/embo-reports/kvd001
   PubMed Web of Science ®Google Scholar
• Voorhees, R. M., Mandal, D., Neubauer, C., Kohrer, C., RajBhandary, U. L., & Ramakrishnan, V. (2013). The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome. Nature Structural & Molecular Biology, 20, 641–643. doi:10.1038/nsmb.2545
   PubMed Web of Science ®Google Scholar
• Yasukawa, T., Kirino, Y., Ishii, N., Holt, I. J., Jacobs, H. T., Makifuchi, T., … Watanabe, K. (2005). Wobble modification deficiency in mutant tRNAs in patients with mitochondrial diseases. FEBS Letters, 579(13), 2948–2952. doi:10.1016/j.febslet.2005.04.038
   PubMed Web of Science ®Google Scholar
• Yasukawa, T., Suzuki, T., Ishii, N., Ohta, S., & Watanabe, K. (2001). Wobble modification defect in tRNA disturbs codon anticodon interaction in a mitochondrial disease. The EMBO Journal, 20, 4794–4802. doi:10.1093/emboj/20.17.4794
   PubMed Web of Science ®Google Scholar