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Articles

Mechanism of the activation step of the aminoacylation reaction: a significant difference between class I and class II synthetases

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Pages 701-715 | Received 10 Feb 2012, Accepted 27 Mar 2012, Published online: 26 Jun 2012

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Saheb Dutta & Nilashis Nandi. (2019) Classical molecular dynamics simulation of seryl tRNA synthetase and threonyl tRNA synthetase bound with tRNA and aminoacyl adenylate. Journal of Biomolecular Structure and Dynamics 37:2, pages 336-358.
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Saheb Dutta, Soumya Kundu, Amrita Saha & Nilashis Nandi. (2018) Dynamics of the active site loops in catalyzing aminoacylation reaction in seryl and histidyl tRNA synthetases. Journal of Biomolecular Structure and Dynamics 36:4, pages 878-892.
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Ling-yue Kong, Yi-ze Wu, Run-qi Cheng, Pei-han Wang & Bi-wen Peng. (2023) Role of Mutations of Mitochondrial Aminoacyl-tRNA Synthetases Genes on Epileptogenesis. Molecular Neurobiology 60:9, pages 5482-5492.
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Mohamed M. Aboelnga & James W. Gauld. (2023) Establishing a substrate-assisted mechanism for the pre-transfer editing in SerRS and IleRS: a QM/QM investigation. Structural Chemistry.
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Shilpi Chowdhury, Poulami Ghosh & Nilashis Nandi. (2023) Computational Methods for Molecular Understanding of the Antibiotic‐Aminoacyl tRNA Synthetase Interaction. Current Protocols 3:3.
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Wenjing Hu, Hongjun Fang, Yu Peng, Li Li, Danni Guo, Jingwen Tang, Jurong Yi, Qingqing Liu, Wei Qin, Liwen Wu & Zeshu Ning. (2022) Clinical and genetic analyses of premature mitochondrial encephalopathy with epilepsia partialis continua caused by novel biallelic NARS2 mutations. Frontiers in Neuroscience 16.
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Luping Pang, Vladimir Zanki, Sergei V. Strelkov, Arthur Van Aerschot, Ita Gruic-Sovulj & Stephen D. Weeks. (2022) Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip. Communications Biology 5:1.
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Saheb Dutta & Amalendu Chandra. (2022) Free Energy Landscape of the Adenylation Reaction of the Aminoacylation Process at the Active Site of Aspartyl tRNA Synthetase. The Journal of Physical Chemistry B 126:31, pages 5821-5831.
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Ekaterina S. Vinogradova, Oleg S. Nikonov & Ekaterina Yu. Nikonova. (2021) Associations between Neurological Diseases and Mutations in the Human Glycyl-tRNA Synthetase. Biochemistry (Moscow) 86:S1, pages S12-S23.
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Miguel Angel Rubio Gomez & Michael Ibba. (2020) Aminoacyl-tRNA synthetases. RNA 26:8, pages 910-936.
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Anastas Gospodinov & Dimiter Kunnev. (2020) Universal Codons with Enrichment from GC to AU Nucleotide Composition Reveal a Chronological Assignment from Early to Late Along with LUCA Formation. Life 10:6, pages 81.
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V.S. Subramaniam. 2019. Catalysis from A to Z. Catalysis from A to Z.
Florian Kaiser, Sebastian Bittrich, Sebastian Salentin, Christoph Leberecht, V. Joachim Haupt, Sarah Krautwurst, Michael Schroeder & Dirk Labudde. (2018) Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases. PLOS Computational Biology 14:4, pages e1006101.
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Mohamed M. Aboelnga, John J. Hayward & James W. Gauld. (2017) A water-mediated and substrate-assisted aminoacylation mechanism in the discriminating aminoacyl-tRNA synthetase GlnRS and non-discriminating GluRS. Physical Chemistry Chemical Physics 19:37, pages 25598-25609.
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Satya B. Routh & Rajan Sankaranarayanan. 2017. Structural and Mechanistic Enzymology. Structural and Mechanistic Enzymology 305 353 .
Grant B. Fortowsky, Daniel J. Simard, Mohamed M. Aboelnga & James W. Gauld. (2015) Substrate-Assisted and Enzymatic Pretransfer Editing of Nonstandard Amino Acids by Methionyl-tRNA Synthetase. Biochemistry 54:37, pages 5757-5765.
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Saheb Dutta & Nilashis Nandi. (2015) Dynamics of the Active Sites of Dimeric Seryl t RNA Synthetase from Methanopyrus kandleri . The Journal of Physical Chemistry B 119:34, pages 10832-10848.
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Rui Zeng, Xiao-fei Jiang, Yu-cheng Chen, Yuan-ning Xu, Song-hong Ma, Zhi Zeng, Rui Liu, Ou Qiang & Xian Li. (2013) VEGF, not VEGFR2, is associated with the angiogenesis effect of mini-TyrRS/mini-TrpRS in human umbilical vein endothelial cells in hypoxia. Cytotechnology 66:4, pages 655-665.
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Gaston H. Vondenhoff, Ksenia Pugach, Bharat Gadakh, Laurence Carlier, Jef Rozenski, Mathy Froeyen, Konstantin Severinov & Arthur Van Aerschot. (2013) N-Alkylated Aminoacyl sulfamoyladenosines as Potential Inhibitors of Aminoacylation Reactions and Microcin C Analogues Containing D-Amino Acids. PLoS ONE 8:11, pages e79234.
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Samad Jahandideh. (2013) Diversity in Structural Consequences of MexZ Mutations in Pseudomonas aeruginosa . Chemical Biology & Drug Design 81:5, pages 600-606.
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John J. Perona & Ita Gruic-Sovulj. 2014. Aminoacyl-tRNA Synthetases in Biology and Medicine. Aminoacyl-tRNA Synthetases in Biology and Medicine 1 41 .
Sindrila Dutta Banik & Nilashis Nandi. 2013. Biochirality. Biochirality 255 305 .

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