Nucleotide modifications and tRNA anticodon–mRNA codon interactions on the ribosome
Open accessAbstract
We have carried out molecular dynamics simulations of the tRNA anticodon and mRNA codon, inside the ribosome, to study the effect of the common tRNA modifications cmo 5 U34 and m 6 A37. In tRNA Val, these modifications allow all four nucleotides to be successfully read at the wobble position in a codon. Previous data suggest that entropic effects are mainly responsible for the extended reading capabilities, but detailed mechanisms have remained unknown. We have performed a wide range of simulations to elucidate the details of these mechanisms at the atomic level and quantify their effects: extensive free energy perturbation coupled with umbrella sampling, entropy calculations of tRNA (free and bound to the ribosome), and thorough structural analysis of the ribosomal decoding center. No prestructuring effect on the tRNA anticodon stem–loop from the two modifications could be observed, but we identified two mechanisms that may contribute to the expanded decoding capability by the modifications: The further reach of the cmo 5 U34 allows an alternative outer conformation to be formed for the noncognate base pairs, and the modification results in increased contacts between tRNA, mRNA, and the ribosome.
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Accurate decoding of the codons for the weak amino acids requires an extended anticodon with a modified base in the tRNA molecule, which could be an additional argument for the late arrival of these amino acids in the code.
“Accurate decoding of the codons for the latter group requires an extended anticodon with a modified base in the tRNA molecule (2), which could be an additional argument for the late arrival of these amino acids in the code.”
From Origin and Evolution of the Universal Genetic Code (2017) · cites this paper as [2]
The Introduction (page unavailable) says tRNA modifications affect codon recognition, and the Conclusions (page unavailable) describe how modified bases in valine tRNA expand wobble-position decoding. The paper does not establish that accurate decoding of codons for the cited group of amino acids requires an extended anticodon with a modified base. The late-arrival argument follows the citation and is the citing authors’ inference, not a finding attributed to this source. (LLM, conf=0.84)
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Cites
Comparison of simple potential functions for simulating liquid water
Jorgensen, W. L., Chandrasekhar, J., Madura, J., Impey, R., & Klein, M. (1983) · The Journal of Chemical Physics · doi:10.1063/1.445869 · Cited by 38,335 · see citing works
Ryckaert, J., Ciccotti, G., & Berendsen, H. (1977) · Journal of Computational Physics · doi:10.1016/0021-9991(77)90098-5 · Cited by 19,525 · see citing works
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Brooks, B., Bruccoleri, R., Olafson, B. D., States, D., Swaminathan, S., & Karplus, M. (1983) · Journal of Computational Chemistry · doi:10.1002/jcc.540040211 · Cited by 13,736 · see citing works
CHARMM: The biomolecular simulation program
Brooks, B. R., Brooks, C. L., MacKerell, A. D., Nilsson, L., Petrella, R. J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., et al. (2009) · Journal of Computational Chemistry · doi:10.1002/jcc.21287 · Cited by 8,994 · see citing works
Self-citationTHE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method
Kumar, S., Rosenberg, J. M., Bouzida, D., Swendsen, R. H., & Kollman, P. A. (1992) · Journal of Computational Chemistry · doi:10.1002/jcc.540130812 · Cited by 6,808 · see citing works
Encyclopedia of Computational Chemistry
(2003) · Wiley eBooks · doi:10.1002/0470845015 · Cited by 2,741 · see citing works
Free energy calculations: Applications to chemical and biochemical phenomena
Kollman, P. A. (1993) · Chemical Reviews · doi:10.1021/cr00023a004 · Cited by 2,101 · see citing works
McCammon, J., Gelin, B., & Karplus, M. (1977) · Nature · doi:10.1038/267585a0 · Cited by 1,972 · see citing works
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
Jakalian, A., Bush, B. L., Jack, D. B., & Bayly, C. I. (2000) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(20000130)21:2 · Cited by 1,681 · see citing works
Structure of the 70S Ribosome Complexed with mRNA and tRNA
Selmer, M., Dunham, C., Murphy, F., Weixlbaumer, A., Petry, S., Kelley, A. C., Weir, J., & Ramakrishnan, V. (2006) · Science · doi:10.1126/science.1131127 · Cited by 1,352 · see citing works
A new method for predicting binding affinity in computer-aided drug design
Åqvist, J., Medina, C., & Samuelsson, J.-E. (1994) · Protein Engineering Design and Selection · doi:10.1093/protein/7.3.385 · Cited by 1,187 · see citing works
Beutler, T. C., Mark, A. E., van Schaik, R. C., Gerber, P. R., & A, W. F. V. G. (1994) · Chemical Physics Letters · doi:10.1016/0009-2614(94)00397-1 · Cited by 1,150 · see citing works
Free Energy Via Molecular Simulation: Applications to Chemical and Biomolecular Systems
Beveridge, D. L., & DiCapua, F. M. (1989) · Annual Review of Biophysics and Biophysical Chemistry · doi:10.1146/annurev.bb.18.060189.002243 · Cited by 1,088 · see citing works
Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form
Ogle, J. M., Murphy, F. V., Tarry, M. J., & Ramakrishnan, V. (2002) · Cell · doi:10.1016/s0092-8674(02)01086-3 · Cited by 663 · see citing works
A guide to ions and RNA structure
Draper, D. E. (2004) · RNA · doi:10.1261/rna.5205404 · Cited by 646 · see citing works
STRUCTURAL INSIGHTS INTO TRANSLATIONAL FIDELITY
Ogle, J. M., & Ramakrishnan, V. (2005) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.74.061903.155440 · Cited by 586 · see citing works
tRNA’s Wobble Decoding of the Genome: 40 Years of Modification
Agris, P. F., Vendeix, F. A. P., & Graham, W. D. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.11.046 · Cited by 543 · see citing works
Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
Brünger, A. T., & Karplus, M. (1988) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340040208 · Cited by 504 · see citing works
SHI, H., & Moore, P. B. (2000) · RNA · doi:10.1017/s1355838200000364 · Cited by 486 · see citing works
On the calculation of entropy from covariance matrices of the atomic fluctuations
Andricioaei, I., & Karplus, M. (2001) · The Journal of Chemical Physics · doi:10.1063/1.1401821 · Cited by 478 · see citing works
Deformable stochastic boundaries in molecular dynamics
Brooks, C. L., & Karplus, M. (1983) · The Journal of Chemical Physics · doi:10.1063/1.445724 · Cited by 475 · see citing works
Straatsma, T. P., & McCammon, J. A. (1992) · Annual Review of Physical Chemistry · doi:10.1146/annurev.pc.43.100192.002203 · Cited by 442 · see citing works
Pape, T., Wintermeyer, W., & Rodnina, M. V. (1998) · The EMBO Journal · doi:10.1093/emboj/17.24.7490 · Cited by 386 · see citing works
Denning, E. J., Priyakumar, U., Nilsson, L., & MacKerell, A. D. (2011) · Journal of Computational Chemistry · doi:10.1002/jcc.21777 · Cited by 384 · see citing works
Self-citationFree Energy Simulations Come of Age: Protein−Ligand Recognition
Simonson, T., Archontis, G., & Karplus, M. (2002) · Accounts of Chemical Research · doi:10.1021/ar010030m · Cited by 379 · see citing works
Insights into the decoding mechanism from recent ribosome structures
Ogle, J. M., Carter, A. P., & Ramakrishnan, V. (2003) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(03)00066-5 · Cited by 372 · see citing works
Induced fit in initial selection and proofreading of aminoacyl‐tRNA on the ribosome
Pape, T., Wintermeyer, W., & Rodnina, M. (1999) · EMBO Journal · doi:10.1093/emboj/18.13.3800 · Cited by 341 · see citing works
Agris, P. F. (1996) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(08)60143-9 · Cited by 273 · see citing works
On the Truncation of Long-Range Electrostatic Interactions in DNA
Norberg, J., & Nilsson, L. (2000) · Biophysical Journal · doi:10.1016/s0006-3495(00)76405-8 · Cited by 236 · see citing works
Self-citationBringing order to translation: the contributions of transfer RNA anticodon‐domain modifications
Agris, P. F. (2008) · EMBO Reports · doi:10.1038/embor.2008.104 · Cited by 233 · see citing works
Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines
Weixlbaumer, A., Murphy, F. V., Dziergowska, A., Małkiewicz, A. J., Vendeix, F. A. P., Agris, P. F., & Ramakrishnan, V. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1242 · Cited by 196 · see citing works
Mechanism of peptide bond synthesis on the ribosome
Trobro, S., & Åqvist, J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504043102 · Cited by 193 · see citing works
Ditzler, M. A., Otyepka, M., Šponer, J., & Walter, N. G. (2009) · Accounts of Chemical Research · doi:10.1021/ar900093g · Cited by 165 · see citing works
Constant-temperature free energy surfaces for physical and chemical processes
Boczko, E. M., & Brooks, C. L. (1993) · The Journal of Physical Chemistry · doi:10.1021/j100119a043 · Cited by 161 · see citing works
Tenson, T., & Mankin, A. S. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05063.x · Cited by 155 · see citing works
Molecular dynamics simulation of galanin in aqueous and nonaqueous solution
Loof, H. D., Nilsson, L., & Rigler, R. W. (1992) · Journal of the American Chemical Society · doi:10.1021/ja00037a002 · Cited by 145 · see citing works
Self-citationDurant, P. C., Bajji, A. C., Sundaram, M., Kumar, R. K., & Davis, D. R. (2005) · Biochemistry · doi:10.1021/bi050343f · Cited by 136 · see citing works
Thermodynamics of aqueous solvation: Solution properties of alcohols and alkanes
Fleischman, S. H., & Brooks, C. L. (1987) · The Journal of Chemical Physics · doi:10.1063/1.453039 · Cited by 124 · see citing works
Näsvall, J., Chen, P., & Björk, G. R. (2004) · RNA · doi:10.1261/rna.7106404 · Cited by 121 · see citing works
Olejniczak, M., & Uhlenbeck, O. C. (2006) · Biochimie · doi:10.1016/j.biochi.2006.06.005 · Cited by 98 · see citing works
How Consistent are Molecular Dynamics Simulations?
Elofsson, A., & Nilsson, L. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1551 · Cited by 87 · see citing works
Self-citationVaiana, A. C., Westhof, É., & Auffinger, P. (2006) · Biochimie · doi:10.1016/j.biochi.2006.06.006 · Cited by 76 · see citing works
The ribosome’s response to codon–anticodon mismatches
Daviter, T., Gromadski, K. B., & Rodnina, M. V. (2006) · Biochimie · doi:10.1016/j.biochi.2006.04.013 · Cited by 74 · see citing works
Réblová, K., Lankaš, F., Rázga, F., Krasovska, M. V., Koča, J., & Šponer, J. (2006) · Biopolymers · doi:10.1002/bip.20503 · Cited by 71 · see citing works
Optimized representations and maximal information in proteins
Solis, A. D., & Rackovsky, S. R. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(20000201)38:2 · Cited by 69 · see citing works
Stochastic Gating and Drug–Ribosome Interactions
Vaiana, A. C., & Sanbonmatsu, K. Y. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.12.035 · Cited by 68 · see citing works
Sanbonmatsu, K. Y., & Joseph, S. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00236-5 · Cited by 66 · see citing works
The bacterial ribosome, a promising focus for structure-based drug design
Knowles, D. (2002) · Current Opinion in Pharmacology · doi:10.1016/s1471-4892(02)00205-9 · Cited by 59 · see citing works
Free energy calculation of modified base-pair formation in explicit solvent: A predictive model
Vendeix, F. A. P., Munoz, A., & Agris, P. F. (2009) · RNA · doi:10.1261/rna.1734309 · Cited by 58 · see citing works
Molecular Dynamics Study of the Ribosomal A-Site
Romanowska, J., Setny, P., & Trylska, J. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp806814s · Cited by 51 · see citing works
Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA
Scheunemann, A., Graham, W. D., Vendeix, F. A. P., & Agris, P. F. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1253 · Cited by 49 · see citing works
Energy landscape of the ribosomal decoding center
Sanbonmatsu, K. Y. (2006) · Biochimie · doi:10.1016/j.biochi.2006.06.012 · Cited by 48 · see citing works
Effects of Base Substitutions in an RNA Hairpin from Molecular Dynamics and Free Energy Simulations
Sarzyńska, J., Nilsson, L., & Kuliński, T. (2003) · Biophysical Journal · doi:10.1016/s0006-3495(03)74766-3 · Cited by 41 · see citing works
Self-citationNilsson, L. (2008) · Journal of Computational Chemistry · doi:10.1002/jcc.21169 · Cited by 41 · see citing works
Self-citationAlignment/misalignment hypothesis for tRNA selection by the ribosome
Sanbonmatsu, K. Y. (2006) · Biochimie · doi:10.1016/j.biochi.2006.07.002 · Cited by 41 · see citing works
Energetics of Codon−Anticodon Recognition on the Small Ribosomal Subunit
Almlöf, M., Andér, M., & Åqvist, J. (2007) · Biochemistry · doi:10.1021/bi061713i · Cited by 34 · see citing works
Biochemical characterization of the ribosomal decoding site
Noller, H. F. (2006) · Biochimie · doi:10.1016/j.biochi.2006.04.006 · Cited by 31 · see citing works
Models for mRNA Translation: Theory versus Experiment
von HEIJNE, G., Nilsson, L., & Blomberg, C. (1978) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1978.tb12759.x · Cited by 28 · see citing works
Self-citationMeroueh, S. O., & Mobashery, S. (2007) · Chemical Biology & Drug Design · doi:10.1111/j.1747-0285.2007.00505.x · Cited by 28 · see citing works
Molecular Dynamics of the Anticodon Domain of Yeast tRNAPhe:Codon-Anticodon Interaction
Lahiri, A., & Nilsson, L. (2000) · Biophysical Journal · doi:10.1016/s0006-3495(00)76474-5 · Cited by 24 · see citing works
Self-citationThe discovery of modified nucleosides from the early days to the present: A personal perspective
Nishimura, S., & Watanabe, K. (2006) · Journal of Biosciences · doi:10.1007/bf02705186 · Cited by 13 · see citing works
Hart, K., & Nilsson, L. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22062 · Cited by 9 · see citing works
Self-citation
Flagged first, then by citations
1 of the 63 references couldn’t be matched to a known paper.
Research works printed but not linked: 2
- 10.1002/(sici)1096-987x(20000130)21:2<105::aid-jcc3>3.0.co;2-p · DOI
- 1998, CHARMM: The energy function and its parameterization with an overview of the program, Vol. 1, 271
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RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Šponer, J., Bussi, G., Krepl, M., Banáš, P., Bottaro, S., Cunha, R. A., Gil-Ley, A., Pinamonti, G., Poblete, S., Jurečka, P., et al. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00427 · Cited by 584 · see citing works
Magnesium Ion–Water Coordination and Exchange in Biomolecular Simulations
Allnér, O., Nilsson, L., & Villa, A. (2012) · Journal of Chemical Theory and Computation · doi:10.1021/ct3000734 · Cited by 405 · see citing works
Self-citationOrigin and Evolution of the Universal Genetic Code
Koonin, E. V., & Novozhilov, A. S. (2017) · Annual Review of Genetics · doi:10.1146/annurev-genet-120116-024713 · Cited by 200 · see citing works
Additive CHARMM force field for naturally occurring modified ribonucleotides
Xu, Y., Vanommeslaeghe, K., Aleksandrov, A., MacKerell, A. D., & Nilsson, L. (2016) · Journal of Computational Chemistry · doi:10.1002/jcc.24307 · Cited by 88 · see citing works
Self-citationWang, M., Liu, H., Zheng, J., Chen, B., Zhou, M., Fan, W., Wang, H., Liang, X., Zhou, X.-L., Eriani, G., et al. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.739482 · Cited by 79 · see citing works
Zhou, M., Xue, L., Chen, Y., Li, H., He, Q., Wang, B., Meng, F., Wang, M., & Guan, M. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.ra117.000317 · Cited by 70 · see citing works
The Expansion of Inosine at the Wobble Position of tRNAs, and Its Role in the Evolution of Proteomes
Rafels-Ybern, À., Torres, A. G., Camacho, N., et al. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy245 · Cited by 65 · see citing works
Chawla, M., Chermak, E., Zhang, Q., Bujnicki, J. M., Oliva, R., & Cavallo, L. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx757 · Cited by 60 · see citing works
Meng, F., Cang, X., Peng, Y., Li, R., Zhang, Z., Li, F., Fan, Q., Guan, A. S., Fischel-Ghosian, N., Zhao, X., et al. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.749374 · Cited by 51 · see citing works
“In particular, the mischarged tRNAs may cause the global protein misfolding (32, 59).”
BackgroundOdoi, K. A., Huang, Y. R., Rezenom, Y. H., & Liu, W. R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0057035 · Cited by 47 · see citing works
Brandmayr, C., Wagner, M., Brückl, T., et al. (2012) · Angewandte Chemie International Edition · doi:10.1002/anie.201203769 · Cited by 46 · see citing works
Meng, F., Zhou, M., Xiao, Y., Mao, X., Zheng, J., Lin, J., Lin, T., Ye, Z., Cang, X., Fu, Y., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1225 · Cited by 44 · see citing works
Jia, Z., Meng, F., Chen, H., Zhu, G., Li, X., He, Y., Zhang, L., He, X., Zhan, H., Chen, M., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac698 · Cited by 44 · see citing works
Mitochondrial tRNA mutations in 2070 Chinese Han subjects with hypertension
Xue, L., Wang, M., Li, H., Wang, H., Jiang, F., Hou, L., Geng, J., Lin, Z., Peng, Y., Zhou, H., et al. (2016) · Mitochondrion · doi:10.1016/j.mito.2016.08.008 · Cited by 43 · see citing works
Wang, M., Peng, Y., Zheng, J., Zheng, B., Jin, X., Liu, H., Wang, Y., Tang, X., Huang, T., Jiang, P., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw726 · Cited by 42 · see citing works
tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen Pseudomonas aeruginosa
Krueger, J., Preuße, M., Gomez, N. O., Frommeyer, Y. N., Doberenz, S., Lorenz, A., Kordes, A., Grobe, S., Müsken, M., Depledge, D. P., et al. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2312874121 · Cited by 35 · see citing works
Zhang, Q., Zhang, L., Chen, D., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky758 · Cited by 34 · see citing works
Zhou, W., Karcher, D., & Bock, R. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt013 · Cited by 32 · see citing works
Why base tautomerization does not cause errors in mRNA decoding on the ribosome
Satpati, P., & Åqvist, J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1044 · Cited by 30 · see citing works
“It should also be emphasized here that there are distinct advantages with using the spherical simulation models (19,24,26) for the present type of free energy calculations.”
BackgroundZhang, Q., He, X., Yao, S., Lin, T., Zhang, L., Chen, D., Chen, C., Yang, Q., Li, F., Zhu, Y.-M., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab228 · Cited by 27 · see citing works
“Of these modifications, the nucleotides at position 34 (wobble position of anticodon) of tRNA are more prone to be modified than those at other positions of tRNAs and impact the stabilization of anticodon structure, fidelity and efficiency of translation (22–25).”
Guo, Q., Ng, P. Q., Shi, S., Fan, D., Li, J., Zhao, J., Wang, H., David, R., Mittal, P., Do, T., et al. (2019) · PLOS ONE · doi:10.1371/journal.pone.0225064 · Cited by 25 · see citing works
Prabhakar, P. S., Takyi, N. A., & Wetmore, S. D. (2020) · RNA · doi:10.1261/rna.078097.120 · Cited by 25 · see citing works
“2020) and the conformational preferences and structural significance of hypermodifications (Morris et al. 1999; McCrate et al. 2006; Alexander et al. 2010; Allnér and Nilsson 2011; Kumbhar and Sonawane 2011; Kumbhar et al. 2013; Sambhare et al. 2014; Zhang et al. 2014; Kamble et al. 2015; Sonawane and Sambhare 2015; F…”
BackgroundBridging the gap between ribosome structure and biochemistry by mechanistic computations
Åqvist, J., Lind, C., Sund, J., & Wallin, G. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.07.008 · Cited by 24 · see citing works
Sonawane, K. D., & Sambhare, S. B. (2015) · Integrative Biology · doi:10.1039/c5ib00058k · Cited by 22 · see citing works
Selection of start codon during mRNA scanning in eukaryotic translation initiation
Basu, I., Gorai, B., Chandran, T., Maiti, P. K., & Hussain, T. (2022) · Communications Biology · doi:10.1038/s42003-022-03534-2 · Cited by 19 · see citing works
“Computational simulation studies have been used to bring out the detailed energetics and intermolecular interactions involved in various steps in protein synthesis [46,47,48,49,50,51,52].”
Chawla, M., Kalra, K., Cao, Z. Z., Cavallo, L., & Oliva, R. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1081 · Cited by 16 · see citing works
Amino Acid Misincorporation Propensities Revealed through Systematic Amino Acid Starvation
Wong, H. E., Huang, C., & Zhang, Z. (2018) · Biochemistry · doi:10.1021/acs.biochem.8b00976 · Cited by 16 · see citing works
Twice exploration of tRNA +1 frameshifting in an elongation cycle of protein synthesis
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Structural effects of modified ribonucleotides and magnesium in transfer RNAs
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Deb, I., Pal, R., Sarzyńska, J., et al. (2016) · Journal of Computational Chemistry · doi:10.1002/jcc.24374 · Cited by 13 · see citing works
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Bhattacharya, S., & Satpati, P. (2024) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.3c01515 · Cited by 13 · see citing works
Hartono, Y. D., Ito, M., Villa, A., & Nilsson, L. (2017) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.7b10878 · Cited by 12 · see citing works
Self-citationMortazavi, M., Zarenezhad, M., Alavian, S. M., et al. (2016) · Hepatitis Monthly · doi:10.5812/hepatmon.39196 · Cited by 10 · see citing works
RetractedThe free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid
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Self-citationRNA modifications as a common denominator between tRNA and mRNA
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Motorin, Y. (2015) · Encyclopedia of Life Sciences · doi:10.1002/9780470015902.a0000528.pub3 · Cited by 3 · see citing works
The Association Between Mitochondrial tRNAGlu Variants and Hearing Loss: A Case-Control Study
Yu, X., Li, S., Guo, Q., et al. (2024) · Pharmacogenomics and Personalized Medicine · doi:10.2147/pgpm.s441281 · Cited by 2 · see citing works
“43,44 The destabilization of base-pairing (18A-Ψ55) caused by the m.A14692G variant perturbed the conformation and stability of mt-tRNA Glu .”
BackgroundDeb, I., Sarzyńska, J., Nilsson, L., et al. (2019) · ACS Omega · doi:10.1021/acsomega.8b02383 · Cited by 2 · see citing works
Self-citationBhattacharjee, C., Nandy, S. K., Das, P., et al. (2019) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2019.01.008 · Cited by 2 · see citing works
Modeling and Simulation of Oligonucleotide Hybrids: Outlining a Strategy
Nilsson, L., & Villa, A. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9670-4_6 · Cited by 1 · see citing works
Self-citationMierke, C. T. (2020) · Biological and medical physics, biomedical engineering · doi:10.1007/978-3-030-58532-7_11 · Cited by 1 · see citing works
A Unified Mechanism of +1 Ribosomal FrameshiftingPreprint
Sorokin, I. I., & Korostelev, A. A. (2026) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a041968
Nonadditive Conformational Effects of tRNA Core Modifications
Amissah, T. E., Levintov, L., & Vashisth, H. (2026) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.6c02045
Frommeyer, Y. N., Sun, J., Wu, J., Kennepohl, B., Witte, J., Gomez, N. O., Battermann, J., Becker, L., Cetraro, P., Verstraten, R., et al. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2615985123
- Authors
- Allnér, O., & Nilsson, L.
- Affiliations
- Karolinska Institutet (SE)
- ORCID
- Nilsson, Lennart
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-10-25
- Volume
- 17
- Issue
- 12
- Pages
- 2177-2188
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- PMC
- PMC3222130
- OpenAlex
- W2122260546
- Semantic Scholar
- 0a830b6dba7be6bfe5d82c01eea7d70d894175ef
- Cited by
- 50
- References
- 63
- Citations by year
- 2026: 3 · 2024: 4 · 2022: 4 · 2021: 3 · 2020: 3 · 2019: 5 · 2018: 4 · 2017: 8 · 2016: 7 · 2015: 2 · 2014: 1 · 2013: 2 · 2012: 4
- FWCI
- 0.91
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- RNA (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Vetenskapsrådet
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- tRNA anticodon, ribosome, wobble pairing, tRNA modification, 5-methyluridine, N6-methyladenosine, tRNAVal, entropic effects, free energy perturbation, umbrella sampling
- MeSH terms
- Anticodon, Binding Sites, Codon, Hydrogen Bonding, Models, Molecular, Nucleic Acid Conformation, Nucleotides, Ribosomes, RNA, Messenger, RNA, Transfer, Base Pairing, Molecular Dynamics Simulation
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