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Crystal structure of the extracellular region of human tissue factor

STEM and boys

Miller A, Polikarpov I, Tuddenham EGD.
GSID: 0WQ4t1xyeQgJ
…, I Polikarpov, A Miller, EGD Tuddenham, CWG Boys - Nature, 1994 - nature.com

… tetraloop stem-loop element"" (tetraloop), and another, smaller, stem-… Only the tRNAphe and tRNApro anticodon stem-loop … The failure of the scrambled tRNAphe and other stem – loop …

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Harlos, K., Martin, D. M. A., O'brien, D. P., Jones, E. Y., Stuart, D. I., Polikarpov, I., ... & Boys, C. W. G. (1994). Crystal structure of the extracellular region of human tissue factor. Nature, 370(6491), 662-666.
Harlos, K., et al. "Crystal structure of the extracellular region of human tissue factor." Nature 370.6491 (1994): 662-666.
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Incorporation of nonnatural amino acids into proteins

STEM and diversify

Crécy-Lagard VD.
GSID: X6DlCLKSZswJ
TL Hendrickson, VD Crécy-Lagard… - Annual review of …, 2004 - annualreviews.org

… To diversify further the chemistry of misincorporated analogs, mutations in the amino acid … of the tRNA acceptor stem and anticodon loop. The dual recognition of the acceptor stem and …

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Hendrickson, T. L., Crécy-Lagard, V. D., & Schimmel, P. (2004). Incorporation of nonnatural amino acids into proteins. Annual review of biochemistry, 73(1), 147-176.
Hendrickson, Tamara L., Valérie De Crécy-Lagard, and Paul Schimmel. "Incorporation of nonnatural amino acids into proteins." Annual review of biochemistry 73.1 (2004): 147-176.
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Examining the Gm18 and m(1)G Modification Positions in tRNA Sequences.

Genomics & informatics

Subramanian M, Srinivasan T, Sudarsanam D.
PMID: 25031570
Genomics Inform. 2014 Jun;12(2):71-5. doi: 10.5808/GI.2014.12.2.71. Epub 2014 Jun 30.

The tRNA structure contains conserved modifications that are responsible for its stability and are involved in the initiation and accuracy of the translation process. tRNA modification enzymes are prevalent in bacteria, archaea, and eukaryotes. tRNA Gm18 methyltransferase (TrmH) and...

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Subramanian M, Srinivasan T, Sudarsanam D. Examining the Gm18 and m(1)G Modification Positions in tRNA Sequences. Genomics Inform. 2014;12(2):71-5doi: 10.5808/GI.2014.12.2.71.
Subramanian, M., Srinivasan, T., & Sudarsanam, D. (2014). Examining the Gm18 and m(1)G Modification Positions in tRNA Sequences. Genomics & informatics, 12(2), 71-5. https://doi.org/10.5808/GI.2014.12.2.71
Subramanian, Mayavan, et al. "Examining the Gm18 and m(1)G Modification Positions in tRNA Sequences." Genomics & informatics vol. 12,2 (2014): 71-5. doi: https://doi.org/10.5808/GI.2014.12.2.71
Subramanian M, Srinivasan T, Sudarsanam D. Examining the Gm18 and m(1)G Modification Positions in tRNA Sequences. Genomics Inform. 2014 Jun;12(2):71-5. doi: 10.5808/GI.2014.12.2.71. Epub 2014 Jun 30. PMID: 25031570; PMCID: PMC4099351.
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tRNA Core Hypothesis for the Transition from the RNA World to the Ribonucleoprotein World.

Life (Basel, Switzerland)

de Farias ST, Rêgo TG, José MV.
PMID: 27023615
Life (Basel). 2016 Mar 23;6(2). doi: 10.3390/life6020015.

Herein we present the tRNA core hypothesis, which emphasizes the central role of tRNAs molecules in the origin and evolution of fundamental biological processes. tRNAs gave origin to the first genes (mRNA) and the peptidyl transferase center (rRNA), proto-tRNAs...

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de Farias ST, Rêgo TG, José MV. tRNA Core Hypothesis for the Transition from the RNA World to the Ribonucleoprotein World. Life (Basel). 2016;6(2)doi: 10.3390/life6020015.
de Farias, S. T., Rêgo, T. G., & José, M. V. (2016). tRNA Core Hypothesis for the Transition from the RNA World to the Ribonucleoprotein World. Life (Basel, Switzerland), 6(2), . https://doi.org/10.3390/life6020015
de Farias, Savio T, et al. "tRNA Core Hypothesis for the Transition from the RNA World to the Ribonucleoprotein World." Life (Basel, Switzerland) vol. 6,2 (2016). doi: https://doi.org/10.3390/life6020015
de Farias ST, Rêgo TG, José MV. tRNA Core Hypothesis for the Transition from the RNA World to the Ribonucleoprotein World. Life (Basel). 2016 Mar 23;6(2). doi: 10.3390/life6020015. PMID: 27023615; PMCID: PMC4931452.
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Sequence of histidyl tRNA, present as a chloroplast insert in mtDNA ofZea mays.

Plant molecular biology

Iams KP, Heckman JE, Sinclair JH.
PMID: 24310839
Plant Mol Biol. 1985 Jul;4(4):225-32. doi: 10.1007/BF02418240.

Unfractionated tRNA, isolated from maize mitochondria, has been specifically labeled at the -CCA end and used to recover a tRNA gene-bearing fragment from a clone bank of maize mitochondrial DNA. This gene has been mapped, sequenced and found to...

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Iams KP, Heckman JE, Sinclair JH. Sequence of histidyl tRNA, present as a chloroplast insert in mtDNA ofZea mays. Plant Mol Biol. 1985;4(4):225-32doi: 10.1007/BF02418240.
Iams, K. P., Heckman, J. E., & Sinclair, J. H. (1985). Sequence of histidyl tRNA, present as a chloroplast insert in mtDNA ofZea mays. Plant molecular biology, 4(4), 225-32. https://doi.org/10.1007/BF02418240
Iams, K P, et al. "Sequence of histidyl tRNA, present as a chloroplast insert in mtDNA ofZea mays." Plant molecular biology vol. 4,4 (1985): 225-32. doi: https://doi.org/10.1007/BF02418240
Iams KP, Heckman JE, Sinclair JH. Sequence of histidyl tRNA, present as a chloroplast insert in mtDNA ofZea mays. Plant Mol Biol. 1985 Jul;4(4):225-32. doi: 10.1007/BF02418240. PMID: 24310839.
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Genes for tRNA(Asp), tRNA (Pro), tRNA (Tyr) and two tRNAs (Ser) in wheat mitochondrial DNA.

Plant molecular biology

Joyce PB, Spencer DF, Bonen L, Gray MW.
PMID: 24277519
Plant Mol Biol. 1988 May;10(3):251-62. doi: 10.1007/BF00027402.

We have begun a systematic search for potential tRNA genes in wheat mtDNA, and present here the sequences of regions of the wheat mitochondrial genome that encode genes for tRNA(Asp) (anticodon GUC), tRNA(Pro) (UGG), tRNA(Tyr) (GUA), and two tRNAs(Ser)...

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Joyce PB, Spencer DF, Bonen L, et al. Genes for tRNA(Asp), tRNA (Pro), tRNA (Tyr) and two tRNAs (Ser) in wheat mitochondrial DNA. Plant Mol Biol. 1988;10(3):251-62doi: 10.1007/BF00027402.
Joyce, P. B., Spencer, D. F., Bonen, L., & Gray, M. W. (1988). Genes for tRNA(Asp), tRNA (Pro), tRNA (Tyr) and two tRNAs (Ser) in wheat mitochondrial DNA. Plant molecular biology, 10(3), 251-62. https://doi.org/10.1007/BF00027402
Joyce, P B, et al. "Genes for tRNA(Asp), tRNA (Pro), tRNA (Tyr) and two tRNAs (Ser) in wheat mitochondrial DNA." Plant molecular biology vol. 10,3 (1988): 251-62. doi: https://doi.org/10.1007/BF00027402
Joyce PB, Spencer DF, Bonen L, Gray MW. Genes for tRNA(Asp), tRNA (Pro), tRNA (Tyr) and two tRNAs (Ser) in wheat mitochondrial DNA. Plant Mol Biol. 1988 May;10(3):251-62. doi: 10.1007/BF00027402. PMID: 24277519.
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Particle-Based Implicit Solvent Model for Biosimulations:  Application to Proteins and Nucleic Acids Hydration.

Journal of chemical theory and computation

Basdevant N, Ha-Duong T, Borgis D.
PMID: 26627035
J Chem Theory Comput. 2006 Nov;2(6):1646-56. doi: 10.1021/ct0600417.

In addition to the simulation of two proteins described previously, we report on the application of our recently developed particle-based implicit solvent model to the simulations of four nucleic acid molecules, the 17 bases anticodon hairpin of the Asp-tRNA,...

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Basdevant N, Ha-Duong T, Borgis D. Particle-Based Implicit Solvent Model for Biosimulations:  Application to Proteins and Nucleic Acids Hydration. J Chem Theory Comput. 2006;2(6):1646-56doi: 10.1021/ct0600417.
Basdevant, N., Ha-Duong, T., & Borgis, D. (2006). Particle-Based Implicit Solvent Model for Biosimulations:  Application to Proteins and Nucleic Acids Hydration. Journal of chemical theory and computation, 2(6), 1646-56. https://doi.org/10.1021/ct0600417
Basdevant, Nathalie, et al. "Particle-Based Implicit Solvent Model for Biosimulations:  Application to Proteins and Nucleic Acids Hydration." Journal of chemical theory and computation vol. 2,6 (2006): 1646-56. doi: https://doi.org/10.1021/ct0600417
Basdevant N, Ha-Duong T, Borgis D. Particle-Based Implicit Solvent Model for Biosimulations:  Application to Proteins and Nucleic Acids Hydration. J Chem Theory Comput. 2006 Nov;2(6):1646-56. doi: 10.1021/ct0600417. PMID: 26627035.
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Competition of aminoacyl-tRNA synthetases for tRNA ensures the accuracy of aminoacylation.

Nucleic acids research

Sherman JM, Rogers MJ, Söll D.
PMID: 16617497
Nucleic Acids Res. 1992 Apr 11;20(7):1547-52. doi: 10.1093/nar/20.7.1547.

The accuracy of protein biosynthesis rests on the high fidelity with which aminoacyl-tRNA synthetases discriminate between tRNAs. Correct aminoacylation depends not only on identity elements (nucleotides in certain positions) in tRNA (1), but also on competition between different synthetases...

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Sherman JM, Rogers MJ, Söll D. Competition of aminoacyl-tRNA synthetases for tRNA ensures the accuracy of aminoacylation. Nucleic Acids Res. 1992;20(7):1547-52doi: 10.1093/nar/20.7.1547.
Sherman, J. M., Rogers, M. J., & Söll, D. (1992). Competition of aminoacyl-tRNA synthetases for tRNA ensures the accuracy of aminoacylation. Nucleic acids research, 20(7), 1547-52. https://doi.org/10.1093/nar/20.7.1547
Sherman, J M, et al. "Competition of aminoacyl-tRNA synthetases for tRNA ensures the accuracy of aminoacylation." Nucleic acids research vol. 20,7 (1992): 1547-52. doi: https://doi.org/10.1093/nar/20.7.1547
Sherman JM, Rogers MJ, Söll D. Competition of aminoacyl-tRNA synthetases for tRNA ensures the accuracy of aminoacylation. Nucleic Acids Res. 1992 Apr 11;20(7):1547-52. doi: 10.1093/nar/20.7.1547. PMID: 16617497; PMCID: PMC312236.
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Efficient synthesis of nonnatural mutants in Escherichia coli S30 in vitro protein synthesizing system.

Journal of bioscience and bioengineering

Yamanaka K, Nakata H, Hohsaka T, Sisido M.
PMID: 16233649
J Biosci Bioeng. 2004;97(6):395-9. doi: 10.1016/S1389-1723(04)70225-X.

Factors that affect the efficiency of in vitro synthesis of mutant proteins that contain nonnatural amino acids were investigated. The process of the nonnatural mutagenesis consists of chemical aminoacylation of a tRNA that contains a 4-base anticodon, followed by...

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Yamanaka K, Nakata H, Hohsaka T, et al. Efficient synthesis of nonnatural mutants in Escherichia coli S30 in vitro protein synthesizing system. J Biosci Bioeng. 2004;97(6):395-9doi: 10.1016/S1389-1723(04)70225-X.
Yamanaka, K., Nakata, H., Hohsaka, T., & Sisido, M. (2004). Efficient synthesis of nonnatural mutants in Escherichia coli S30 in vitro protein synthesizing system. Journal of bioscience and bioengineering, 97(6), 395-9. https://doi.org/10.1016/S1389-1723(04)70225-X
Yamanaka, Katsuhiro, et al. "Efficient synthesis of nonnatural mutants in Escherichia coli S30 in vitro protein synthesizing system." Journal of bioscience and bioengineering vol. 97,6 (2004): 395-9. doi: https://doi.org/10.1016/S1389-1723(04)70225-X
Yamanaka K, Nakata H, Hohsaka T, Sisido M. Efficient synthesis of nonnatural mutants in Escherichia coli S30 in vitro protein synthesizing system. J Biosci Bioeng. 2004;97(6):395-9. doi: 10.1016/S1389-1723(04)70225-X. PMID: 16233649.
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tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell.

Frontiers in genetics

Himeno H, Kurita D, Muto A.
PMID: 24778639
Front Genet. 2014 Apr 07;5:66. doi: 10.3389/fgene.2014.00066. eCollection 2014.

Transfer messenger RNA (tmRNA; also known as 10Sa RNA or SsrA RNA) is a small RNA molecule that is conserved among bacteria. It has structural and functional similarities to tRNA: it has an upper half of the tRNA-like structure,...

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Himeno H, Kurita D, Muto A. tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell. Front Genet. 2014;5:66doi: 10.3389/fgene.2014.00066.
Himeno, H., Kurita, D., & Muto, A. (2014). tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell. Frontiers in genetics, 566. https://doi.org/10.3389/fgene.2014.00066
Himeno, Hyouta, et al. "tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell." Frontiers in genetics vol. 5 (2014): 66. doi: https://doi.org/10.3389/fgene.2014.00066
Himeno H, Kurita D, Muto A. tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell. Front Genet. 2014 Apr 07;5:66. doi: 10.3389/fgene.2014.00066. eCollection 2014. PMID: 24778639; PMCID: PMC3985003.
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Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics.

Journal of chemical theory and computation

Zhang X, Walker RC, Phizicky EM, Mathews DH.
PMID: 25136272
J Chem Theory Comput. 2014 Aug 12;10(8):3473-3483. doi: 10.1021/ct500107y. Epub 2014 May 28.

Modified nucleotides are prevalent in tRNA. Experimental studies reveal that these covalent modifications play an important role in tuning tRNA function. In this study, molecular dynamics (MD) simulations were used to investigate how modifications alter tRNA dynamics. The X-ray...

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Zhang X, Walker RC, Phizicky EM, et al. Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics. J Chem Theory Comput. 2014;10(8):3473-3483doi: 10.1021/ct500107y.
Zhang, X., Walker, R. C., Phizicky, E. M., & Mathews, D. H. (2014). Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics. Journal of chemical theory and computation, 10(8), 3473-3483. https://doi.org/10.1021/ct500107y
Zhang, Xiaoju, et al. "Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics." Journal of chemical theory and computation vol. 10,8 (2014): 3473-3483. doi: https://doi.org/10.1021/ct500107y
Zhang X, Walker RC, Phizicky EM, Mathews DH. Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics. J Chem Theory Comput. 2014 Aug 12;10(8):3473-3483. doi: 10.1021/ct500107y. Epub 2014 May 28. PMID: 25136272; PMCID: PMC4132867.
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A novel 8-bp duplication in .

Human genome variation

Salehi Chaleshtori AR, Miyake N, Ahmadvand M, Bashti O, Matsumoto N, Noruzinia M.
PMID: 29796286
Hum Genome Var. 2018 May 21;5:7. doi: 10.1038/s41439-018-0007-9. eCollection 2018.

Inosine is a base located at wobble position 34 of the tRNA anticodon stem-loop, enabling the recognition of more than one codon in the translation process. A heterodimer consists of ADAT3 and ADAT2 and is involved in the adenosine-to-inosine...

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Salehi Chaleshtori AR, Miyake N, Ahmadvand M, et al. A novel 8-bp duplication in . Hum Genome Var. 2018;5:7doi: 10.1038/s41439-018-0007-9.
Salehi Chaleshtori, A. R., Miyake, N., Ahmadvand, M., Bashti, O., Matsumoto, N., & Noruzinia, M. (2018). A novel 8-bp duplication in . Human genome variation, 57. https://doi.org/10.1038/s41439-018-0007-9
Salehi Chaleshtori, Ahmad Reza, et al. "A novel 8-bp duplication in ." Human genome variation vol. 5 (2018): 7. doi: https://doi.org/10.1038/s41439-018-0007-9
Salehi Chaleshtori AR, Miyake N, Ahmadvand M, Bashti O, Matsumoto N, Noruzinia M. A novel 8-bp duplication in . Hum Genome Var. 2018 May 21;5:7. doi: 10.1038/s41439-018-0007-9. eCollection 2018. PMID: 29796286; PMCID: PMC5960644.
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Showing 1 to 12 of 147 entries