Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions

Features and development of Coot

Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. D. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910007493 · Cited by 27,510 · see citing works

<i>PHENIX</i> : a comprehensive Python-based system for macromolecular structure solution

Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716 · see citing works

The PyMOL Molecular Graphics System

DeLano, W. L. (2002) · Medical Entomology and Zoology · Cited by 18,147 · see citing works

<i>XDS</i>

Kabsch, W. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909047337 · Cited by 16,463 · see citing works

PHENIX: a comprehensive Python-based system for macromolecular structure solution

Adams, P. D., Afonine, P. V., Bunkòczi, G., Chen, V. B., Davis, I., Echols, N., Headd, J. J., Hung, L., Kapral, G. J., Grosse‐Kunstleve, R. W., et al. (2012) · International Tables for Crystallography · doi:10.1107/97809553602060000865 · Cited by 7,334 · see citing works

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009) · Science · doi:10.1126/science.1168978 · Cited by 3,853 · see citing works

Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics

Carter, A. P., Clemons, W. M., Brodersen, D. E., Morgan-Warren, R. J., Wimberly, B. T., & Ramakrishnan, V. (2000) · Nature · doi:10.1038/35030019 · Cited by 1,615 · 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

Interaction of antibiotics with functional sites in 16S ribosomal RNA

Moazed, D., & Noller, H. F. (1987) · Nature · doi:10.1038/327389a0 · Cited by 1,150 · see citing works

The Structure of the Eukaryotic Ribosome at 3.0 Å Resolution

Shem, A. B., de Loubresse, N. G., Melnikov, S. V., Jenner, L. B., Yusupova, G. Z., & Yusupov, M. (2011) · Science · doi:10.1126/science.1212642 · Cited by 1,114 · see citing works

An Oxygen Scavenging System for Improvement of Dye Stability in Single-Molecule Fluorescence Experiments

Aitken, C. E., Marshall, R. A., & Puglisi, J. D. (2007) · Biophysical Journal · doi:10.1529/biophysj.107.117689 · Cited by 846 · see citing works

Analysis of Single-Molecule FRET Trajectories Using Hidden Markov Modeling

McKinney, S., Joo, C., & Ha, T. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.082487 · Cited by 760 · 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

Locking and Unlocking of Ribosomal Motions

Valle, M., Zavialov, A. V., Sengupta, J., Rawat, U. B. S., Ehrenberg, M., & Frank, J. (2003) · Cell · doi:10.1016/s0092-8674(03)00476-8 · Cited by 590 · 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

Mechanism of bactericidal action of aminoglycosides

Davis, B. D. (1987) · Microbiological Reviews · doi:10.1128/mr.51.3.341-350.1987 · Cited by 511 · see citing works

tRNA dynamics on the ribosome during translation

Blanchard, S. C., Kim, H. D., Gonzalez, R. L., Puglisi, J. D., & Chu, S. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0403884101 · Cited by 469 · see citing works

Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy

Fischer, N., Konevega, A. L., Wintermeyer, W., Rodnina, M. V., & Stark, H. (2010) · Nature · doi:10.1038/nature09206 · Cited by 434 · see citing works

Aminoglycoside Antibiotics in the 21st Century

Becker, B., & Cooper, M. A. (2012) · ACS Chemical Biology · doi:10.1021/cb3005116 · Cited by 420 · see citing works

Ultra-stable organic fluorophores for single-molecule research

Zheng, Q., Juette, M. F., Jockusch, S., Wasserman, M. R., Zhou, Z., Altman, R. B., & Blanchard, S. C. (2013) · Chemical Society Reviews · doi:10.1039/c3cs60237k · Cited by 402 · see citing works

Misreading of RNA Codewords Induced by Aminoglycoside Antibiotics

DAVIES, J. E., Gorini, L., & Davis, B. D. (1965) · Molecular Pharmacology · doi:10.1016/s0026-895x(25)14722-6 · Cited by 402 · see citing works

Spontaneous Intersubunit Rotation in Single Ribosomes

Cornish, P. V., Ermolenko, D. N., Noller, H. F., & Ha, T. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.05.004 · Cited by 393 · see citing works

Structures of the Bacterial Ribosome in Classical and Hybrid States of tRNA Binding

Dunkle, J. A., Wang, L., Feldman, M. B., Pulk, A., Chen, V. B., Kapral, G. J., Noeske, J., Richardson, J. S., Blanchard, S. C., & Cate, J. H. D. (2011) · Science · doi:10.1126/science.1202692 · Cited by 373 · see citing works

Structural basis for aminoglycoside inhibition of bacterial ribosome recycling

Borovinskaya, M. A., Pai, R., Zhang, W., Schuwirth, B., Holton, J., Hirokawa, G., Kaji, H., Kaji, A., & Cate, J. H. D. (2007) · Nature Structural &Molecular Biology · doi:10.1038/nsmb1271 · Cited by 366 · see citing works

The puromycin reaction and its relation to protein synthesis

Traut, R. R., & Monro, R. E. (1964) · Journal of Molecular Biology · doi:10.1016/s0022-2836(64)80028-0 · Cited by 363 · see citing works

Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

Ratje, A. H., Loerke, J., Mikolajka, A., Brunner, M. J., Hildebrand, P. W., Starosta, A. L., Dönhöfer, A., Connell, S. R., Fucini, P., Mielke, T., et al. (2010) · Nature · doi:10.1038/nature09547 · Cited by 358 · see citing works

Fidelity of Aminoacyl-tRNA Selection on the Ribosome: Kinetic and Structural Mechanisms

Rodnina, M. V., & Wintermeyer, W. (2001) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.70.1.415 · Cited by 334 · see citing works

The Ribosome, Structure, Function, Antibiotics, and Cellular Interactions

Garrett, R. A. (2000) · Research at the University of Copenhagen (University of Copenhagen) · Cited by 325 · see citing works

Coupling of Ribosomal L1 Stalk and tRNA Dynamics during Translation Elongation

Fei, J., Kosuri, P., MacDougall, D. D., & Gonzalez, R. L. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.03.012 · Cited by 316 · see citing works

Identification of Two Distinct Hybrid State Intermediates on the Ribosome

Munro, J. B., Altman, R. B., O’Connor, N., & Blanchard, S. C. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.01.022 · Cited by 262 · see citing works

Genetically Encoded Short Peptide Tags for Orthogonal Protein Labeling by Sfp and AcpS Phosphopantetheinyl Transferases

Zhou, Z., Cironi, P., Lin, A. J., Xu, Y., Hrvatin, S., Golan, D. E., Silver, P. A., Walsh, C. T., & Yin, J. (2007) · ACS Chemical Biology · doi:10.1021/cb700054k · Cited by 228 · see citing works

Design and Synthesis of New Aminoglycoside Antibiotics Containing Neamine as an Optimal Core Structure: Correlation of Antibiotic Activity with in Vitro Inhibition of Translation

Greenberg, W. A., Priestley, E. S., Sears, P. S., Alper, P. B., Rosenbohm, C., Hendrix, M., Hung, S., & Wong, C. (1999) · Journal of the American Chemical Society · doi:10.1021/ja9910356 · Cited by 218 · see citing works

Suppression of a nonsense mutation in mammalian cells in vivo by the aminoglycoside anthiotics G–418 and paromomycin

Burke, J. F., & Mogg, A. E. (1985) · Nucleic Acids Research · doi:10.1093/nar/13.17.6265 · Cited by 218 · see citing works

[19] Preparation of functional ribosomal complexes and effect of buffer conditions on tRNA positions observed by cryoelectron microscopy

Blaha, G. M., Stelzl, U., Spahn, C. M. T., Agrawal, R. K., Frank, J., & Nierhaus, K. H. (2000) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(00)17021-1 · Cited by 215 · see citing works

Mitigating Unwanted Photophysical Processes for Improved Single-Molecule Fluorescence Imaging

Dave, R., Terry, D. S., Munro, J. B., & Blanchard, S. C. (2009) · Biophysical Journal · doi:10.1016/j.bpj.2008.11.061 · Cited by 210 · see citing works

Basis for prokaryotic specificity of action of aminoglycoside antibiotics

Recht, M. I., Douthwaite, S. R., & Puglisi, J. D. (1999) · The EMBO Journal · doi:10.1093/emboj/18.11.3133 · Cited by 201 · see citing works

Following movement of the L1 stalk between three functional states in single ribosomes

Cornish, P. V., Ermolenko, D. N., Staple, D. W., Hoang, L., Hickerson, R. P., Noller, H. F., & Ha, T. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0813180106 · Cited by 186 · see citing works

Conformational Changes of the Small Ribosomal Subunit During Elongation Factor G-dependent tRNA–mRNA Translocation

Peske, F., Savelsbergh, A., Katunin, V. I., Rodnina, M. V., & Wintermeyer, W. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.08.097 · Cited by 185 · see citing works

The structure of the eukaryotic ribosome at 3.0 A resolution.

Shem, A. B., de Loubresse, N. G., Melnikov, S. V., Jenner, L. B., Yusupova, G. Z., & Yusupov, M. (2011) · Worldwide Protein Data Bank · doi:10.2210/pdb4v88/pdb · Cited by 182 · see citing works

How the ribosome hands the A-site tRNA to the P site during EF-G–catalyzed translocation

Zhou, J., Lancaster, L., Donohue, J. P., & Noller, H. F. (2014) · Science · doi:10.1126/science.1255030 · Cited by 174 · see citing works

FEM: feature-enhanced map

Afonine, P. V., Moriarty, N. W., Mustyakimov, M., Sobolev, O. V., Terwilliger, T. C., Türk, V., Urzhumtsev, A., & Adams, P. D. (2015) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s1399004714028132 · Cited by 170 · see citing works

Structural rearrangements of the ribosome at the tRNA proofreading step

Jenner, L. B., Demeshkina, N., Yusupova, G. Z., & Yusupov, M. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1880 · Cited by 151 · see citing works

Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: Functional implications

Agrawal, R. K., Sharma, M. R., Kiel, M. C., Hirokawa, G., Booth, T. M., Spahn, C. M. T., Grassucci, R. A., Kaji, A., & Frank, J. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401904101 · Cited by 147 · see citing works

Thermodynamics of Aminoglycoside−rRNA Recognition: The Binding of Neomycin-Class Aminoglycosides to the A Site of 16S rRNA

Kaul, M., & Pilch, D. S. (2002) · Biochemistry · doi:10.1021/bi020130f · Cited by 144 · see citing works

Intersubunit movement is required for ribosomal translocation

Horan, L. H., & Noller, H. F. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700762104 · Cited by 141 · see citing works

Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation

Fei, J., Bronson, J. E., Hofman, J. M., Srinivas, R. L., Wiggins, C. H., & Gonzalez, R. L. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0908077106 · Cited by 140 · see citing works

Allosteric control of the ribosome by small-molecule antibiotics

Wang, L., Pulk, A., Wasserman, M. R., Feldman, M. B., Altman, R. B., Cate, J. H. D., & Blanchard, S. C. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2360 · Cited by 136 · see citing works

Rotation of the head of the 30S ribosomal subunit during mRNA translocation

Guo, Z., & Noller, H. F. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1218999109 · Cited by 127 · see citing works

Irreversible chemical steps control intersubunit dynamics during translation

Marshall, R. A., Dorywalska, M., & Puglisi, J. D. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0805299105 · Cited by 119 · see citing works

Structure and Dynamics of the Mammalian Ribosomal Pretranslocation Complex

Budkevich, T. V., Giesebrecht, J., Altman, R. B., Munro, J. B., Mielke, T., Nierhaus, K. H., Blanchard, S. C., & Spahn, C. M. T. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.07.040 · Cited by 115 · see citing works

Inhibition of ribosomal translocation by aminoglycoside antibiotics

Cabañas, M. J., Vázquez, D., & Modolell, J. (1978) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(78)91493-6 · Cited by 114 · see citing works

Aminoglycoside activity observed on single pre-translocation ribosome complexes

Feldman, M. B., Terry, D. S., Altman, R. B., & Blanchard, S. C. (2009) · Nature Chemical Biology · doi:10.1038/nchembio.274 · Cited by 109 · see citing works

Systematic Chromosomal Deletion of Bacterial Ribosomal Protein Genes

Shoji, S., Dambacher, C. M., Shajani, Z., Williamson, J. R., & Schultz, P. G. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.09.004 · Cited by 109 · see citing works

Structure-Activity Relationships Among the Aminoglycoside Antibiotics: Role of Hydroxyl and Amino Groups

Benveniste, R. Ė., & Davies, J. (1973) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.4.4.402 · Cited by 107 · see citing works

Interaction of kanamycin and related antibiotics with the large subunit of ribosomes and the inhibition of translocation

Misumi, M., Nishimura, T., Komai, T., & Tanaka, N. (1978) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(78)90178-x · Cited by 95 · see citing works

A ribosomal ambiguity mulation in the 530 loop ofE.coli16S rRNA

O'Connor, M., Göringer, H. U., & Dahiberg, A. E. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.16.4221 · Cited by 88 · see citing works

A fast dynamic mode of the EF‐G‐bound ribosome

Munro, J. B., Altman, R. B., Tung, C., Sanbonmatsu, K. Y., & Blanchard, S. C. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.384 · Cited by 85 · see citing works

Affinity purification of in vivo-assembled ribosomes for in vitro biochemical analysis

Youngman, E. M., & Green, R. (2005) · Methods · doi:10.1016/j.ymeth.2005.04.007 · Cited by 79 · see citing works

Exploring the Substrate Promiscuity of Drug‐Modifying Enzymes for the Chemoenzymatic Generation of N‐Acylated Aminoglycosides

Green, K. D., Chen, W., Houghton, J. L., Fridman, M., & Garneau‐Tsodikova, S. (2009) · ChemBioChem · doi:10.1002/cbic.200900584 · Cited by 79 · see citing works

4′-O-substitutions determine selectivity of aminoglycoside antibiotics

Perez‐Fernandez, D., Shcherbakov, D., Matt, T., Ng, C. L., Kudyba, I., Duscha, S., Boukari, H., Patak, R., Dubbaka, S. R., Lang, K., et al. (2014) · Nature Communications · doi:10.1038/ncomms4112 · Cited by 75 · see citing works

Binding of Neomycin-Class Aminoglycoside Antibiotics to Mutant Ribosomes with Alterations in the A Site of 16S rRNA

Hobbie, S. N., Pfister, P., Bruell, C. M., Sander, P., François, B., Westhof, É., & Böttger, E. C. (2006) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.50.4.1489-1496.2006 · Cited by 72 · 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

Mutagenesis of 16S rRNA C1409-G1491 Base-pair Differentiates Between 6′OH and 6′NH3+ Aminoglycosides

Pfister, P., Hobbie, S. N., Bruell, C. M., Corti, N., Vasella, A. T., Westhof, É., & Böttger, E. C. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.11.073 · Cited by 65 · see citing works

Effects of Apramycin, a Novel Aminoglycoside Antibiotic on Bacterial Protein Synthesis

Perzyński, S., Cannon, M., Cundliffe, E., Chahwala, S. B., & DAVIES, J. E. (1979) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1979.tb13295.x · Cited by 56 · see citing works

Conformational Changes in the Ribosome Induced by Translational Miscoding Agents

Jerinic, O., & Joseph, S. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4269 · Cited by 52 · 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

Enzymatic Modification of Aminoglycoside Antibiotics: a New 3- N -Acetylating Enzyme from a Pseudomonas aeruginosa Isolate

Biddlecome, S., Haas, M. J., DAVIES, J. E., Miller, G. H., Rane, D. F., & Daniels, P. J. L. (1976) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.9.6.951 · Cited by 49 · see citing works

Definition of bases in 23S rRNA essential for ribosomal subunit association

Maiväli, Ü., & Rèmme, J. (2004) · RNA · doi:10.1261/rna.5220504 · Cited by 48 · see citing works

Macromolecular arrangement in the aminoacyl-tRNA.cntdot.elongation factor Tu.cntdot.GTP ternary complex. A fluorescence energy transfer study

Watson, B. S., Hazlett, T. L., Eccleston, J. F., Davis, C. T., Jameson, D. M., & Johnson, A. E. (1995) · Biochemistry · doi:10.1021/bi00024a015 · Cited by 43 · see citing works

Insights into the molecular determinants of EF-G catalyzed translocation

Wang, L., Altman, R. B., & Blanchard, S. C. (2011) · RNA · doi:10.1261/rna.029033.111 · Cited by 35 · see citing works

Design and Synthesis of Aminoglycoside Antibiotics to Selectively Target 16S Ribosomal RNA Position 1408

Pathak, R., Böttger, E. C., & Vasella, A. T. (2005) · Helvetica Chimica Acta · doi:10.1002/hlca.200590240 · Cited by 19 · see citing works

Death rates of bacterial mutants

Jörgensen, F., & Kurland, C. G. (1987) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1987.tb01979.x · Cited by 13 · see citing works

Mechanisms of resistance to aminoglycoside antibiotics: overview and perspectives

Garneau‐Tsodikova, S., & Labby, K. J. (2015) · MedChemComm · doi:10.1039/c5md00344j · Cited by 582 · see citing works

A clock network for geodesy and fundamental science

Lisdat, C., Grosche, G., Quintin, N., Shi, C., Raupach, S. M. F., Grebing, C., Nicolodi, D., Stefani, F., Al-Masoudi, A., Dörscher, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms12443 · Cited by 460 · see citing works

Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond timescale

Juette, M. F., Terry, D. S., Wasserman, M. R., Altman, R. B., Zhou, Z., Zhao, H. C., & Blanchard, S. C. (2016) · Nature Methods · doi:10.1038/nmeth.3769 · Cited by 268 · see citing works

Structure of the bacterial ribosome at 2 Å resolution

Watson, Z. L., Ward, F. R., Méheust, R., Ad, O., Schepartz, A., Banfield, J. F., & Cate, J. H. (2020) · eLife · doi:10.7554/elife.60482 · Cited by 263 · see citing works

Aminoglycoside interactions and impacts on the eukaryotic ribosome

Prokhorova, I., Altman, R. B., Djumagulov, M., Shrestha, J. P., Urzhumtsev, A., Ferguson, A., Chang, C. T., Yusupov, M., Blanchard, S. C., & Yusupova, G. Z. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1715501114 · Cited by 210 · see citing works

A smart aminoglycoside hydrogel with tunable gel degradation, on-demand drug release, and high antibacterial activity

Hu, J., Quan, Y., Lai, Y., Zheng, Z., Hu, Z., Wang, X., Dai, T., Zhang, Q., & Cheng, Y. (2017) · Journal of Controlled Release · doi:10.1016/j.jconrel.2017.01.003 · Cited by 203 · see citing works

Antibiotic Combination Therapy: A Strategy to Overcome Bacterial Resistance to Aminoglycoside Antibiotics

Wang, N., Luo, J., Deng, F., Huang, Y.-S., & Zhou, H. (2022) · Frontiers in Pharmacology · doi:10.3389/fphar.2022.839808 · Cited by 156 · see citing works

Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation

Wasserman, M. R., Alejo, J. L. P., Altman, R. B., & Blanchard, S. C. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3177 · Cited by 117 · see citing works

tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis

Flis, J., Holm, M., Rundlet, E. J., Loerke, J., Hilal, T., Dabrowski, M., Bürger, J., Mielke, T., Blanchard, S. C., Spahn, C. M. T., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.11.040 · Cited by 95 · see citing works

Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin

Shalev-Benami, M., Zhang, Y., Rozenberg, H., Nobe, Y., Taoka, M., Matzov, D., Zimmerman, E., Bashan, A., Isobe, T., Jaffe, C. L., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01664-4 · Cited by 94 · see citing works

Destination of aminoglycoside antibiotics in the ‘post-antibiotic era’

Takahashi, Y., & Igarashi, M. (2017) · The Journal of Antibiotics · doi:10.1038/ja.2017.117 · Cited by 90 · see citing works

Structural basis of early translocation events on the ribosome

Rundlet, E. J., Holm, M., Schacherl, M., Natchiar, S. K., Altman, R. B., Spahn, C. M. T., Myasnikov, A. G., & Blanchard, S. C. (2021) · Nature · doi:10.1038/s41586-021-03713-x · Cited by 89 · see citing works

Aminoglycoside Resistance

Wachino, J.-I., Doi, Y., & Arakawa, Y. (2020) · Infectious Disease Clinics of North America · doi:10.1016/j.idc.2020.06.002 · Cited by 82 · see citing works

Translation error clusters induced by aminoglycoside antibiotics

Wohlgemuth, I., Garofalo, R., Samatova, E., Günenç, A. N., Lenz, C., Urlaub, H., & Rodnina, M. V. (2021) · Nature Communications · doi:10.1038/s41467-021-21942-6 · Cited by 82 · see citing works

Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities

Chandrika, N. T., & Garneau‐Tsodikova, S. (2018) · Chemical Society Reviews · doi:10.1039/c7cs00407a · Cited by 73 · see citing works

Virulence and Antibiotic Resistance Characteristics of Vibrio Isolates From Rustic Environmental Freshwaters

Gxalo, O., Digban, T. O., Igere, B. E., Olapade, O. A., Okoh, A. I., & Nwodo, U. U. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.732001 · Cited by 66 · see citing works

A photo-cleavable polyprodrug-loaded wound dressing with UV-responsive antibacterial property

Pang, Q., Zheng, X., Luo, Y., Ma, L., & Gao, C. (2017) · Journal of Materials Chemistry B · doi:10.1039/c7tb01696d · Cited by 60 · see citing works

A review of patents (2011–2015) towards combating resistance to and toxicity of aminoglycosides

Chandrika, N. T., & Garneau‐Tsodikova, S. (2015) · MedChemComm · doi:10.1039/c5md00453e · Cited by 54 · see citing works

Composite laser-pulses spectroscopy for high-accuracy optical clocks: a review of recent progress and perspectives

Zanon-Willette, T., Lefèvre, R., Metzdorff, R., Sillitoe, N., Almonacil, S., Minissale, M., de Clercq, E., Тайченачев, А. В., Yudin, V. I., & Arimondo, E. (2018) · Reports on Progress in Physics · doi:10.1088/1361-6633/aac9e9 · Cited by 54 · see citing works

A simple approach to fabricate the rose petal-like hierarchical surfaces for droplet transportation

Yuan, C., Huang, M., Yu, X., Ma, Y., & Luo, X. (2016) · Applied Surface Science · doi:10.1016/j.apsusc.2016.05.128 · Cited by 40 · see citing works

Real-time measurements of aminoglycoside effects on protein synthesis in live cells

Rivera, J. A., Larsson, J., Volkov, I. L., Seefeldt, A. C., Sanyal, S., & Johansson, M. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2013315118 · Cited by 38 · see citing works

Structure of Pseudomonas aeruginosa ribosomes from an aminoglycoside-resistant clinical isolate

Halfon, Y., Jiménez‐Fernández, A., Rosa, R. L., Espinosa, R., Johansen, H. K., Matzov, D., Eyal, Z., Bashan, A., Zimmerman, E., Belousoff, M. J., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1909831116 · Cited by 37 · see citing works

Modification at the 2′-Position of the 4,5-Series of 2-Deoxystreptamine Aminoglycoside Antibiotics To Resist Aminoglycoside Modifying Enzymes and Increase Ribosomal Target Selectivity

Sati, G. C., Sarpe, V. A., Furukawa, T., Mondal, S., Mantovani, M., Hobbie, S. N., Vasella, A. T., Böttger, E. C., & Crich, D. (2019) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.9b00128 · Cited by 36 · see citing works

Identifying targets to prevent aminoglycoside ototoxicity

Kim, J., Hemachandran, S., Cheng, A. G.-L., & Ricci, A. J. (2022) · Molecular and Cellular Neuroscience · doi:10.1016/j.mcn.2022.103722 · Cited by 34 · see citing works

Probe light-shift elimination in generalized hyper-Ramsey quantum clocks

Zanon-Willette, T., de Clercq, E., & Arimondo, E. (2016) · Physical Review A · doi:10.1103/physreva.93.042506 · Cited by 32 · see citing works

Miscoding-induced stalling of substrate translocation on the bacterial ribosome

Alejo, J. L., & Blanchard, S. C. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1707539114 · Cited by 32 · see citing works

Multifunctional gelatin nanoparticle stabilized-Pickering emulsion hydrogel based on dextran and amikacin with controlled drug release and enhanced antibacterial capability for promoting infected wound healing

Zhang, R., Huang, X., Wu, Q., Chu, S., Bai, X., Zhou, Y., You, J., Yang, C., & Tan, H. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.130172 · Cited by 29 · see citing works

Inhibitors of Eukaryotic Translational Machinery as Therapeutic Agents

Fan, A. P., & Sharp, P. P. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.0c01746 · Cited by 29 · see citing works

Antibiotic resistance, virulence and genetic characteristics of Vibrio alginolyticus isolates from aquatic environment in costal mariculture areas in China

Yu, Y., Li, H., Wang, Y., Zhang, Z., Liao, M., Rong, X., Li, B., Wang, C., Ge, J., & Zhang, X. (2022) · Marine Pollution Bulletin · doi:10.1016/j.marpolbul.2022.114219 · Cited by 29 · see citing works

Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome

Seely, S. M., Parajuli, N. P., Tarafder, A. D., Ge, X., Sanyal, S., & Gagnon, M. G. (2023) · Nature Communications · doi:10.1038/s41467-023-40416-5 · Cited by 28 · see citing works

Chemical Modifications Reduce Auditory Cell Damage Induced by Aminoglycoside Antibiotics

Zada, S. L., Baruch, B. B., Simhaev, L., Engel, H., & Fridman, M. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.9b12420 · Cited by 28 · see citing works

Mechanistic insights into translation inhibition by aminoglycoside antibiotic arbekacin

Parajuli, N. P., Mandava, C. S., Pavlov, M. Y., & Sanyal, S. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab495 · Cited by 20 · see citing works

Universal interrogation protocol with zero probe-field-induced frequency shift for quantum clocks and high-accuracy spectroscopy

Zanon-Willette, T., Lefèvre, R., Taǐchenachev, A. V., & Yudin, V. I. (2017) · Physical Review A · doi:10.1103/physreva.96.023408 · Cited by 18 · see citing works

Chemical probing for examining the structure of modified RNAs and ligand binding to RNA

Waduge, P., Sakakibara, Y., & Chow, C. S. (2018) · Methods · doi:10.1016/j.ymeth.2018.10.015 · Cited by 18 · see citing works

Inhibition of the Eukaryotic 80S Ribosome as a Potential Anticancer Therapy: A Structural Perspective

Pellegrino, S., Terrosu, S., Yusupova, G. Z., & Yusupov, M. (2021) · Cancers · doi:10.3390/cancers13174392 · Cited by 18 · see citing works

N6′, N6′′′, and O4′ Modifications to Neomycin Affect Ribosomal Selectivity without Compromising Antibacterial Activity

Sati, G. C., Shcherbakov, D., Hobbie, S. N., Vasella, A. T., Böttger, E. C., & Crich, D. (2017) · ACS Infectious Diseases · doi:10.1021/acsinfecdis.6b00214 · Cited by 17 · see citing works

Optical Atomic Clocks for Redefining SI Units of Time and Frequency

Sharma, L., Rathore, H. K., Utreja, S., Neelam, N., Roy, A., De, S., & Panja, S. (2020) · MAPAN · doi:10.1007/s12647-020-00397-y · Cited by 16 · see citing works

Perturbation of ribosomal subunit dynamics by inhibitors of tRNA translocation

Belardinelli, R., Sharma, H., Peske, F., & Rodnina, M. V. (2021) · RNA · doi:10.1261/rna.078758.121 · Cited by 16 · see citing works

Interactions of aminoglycoside antibiotics with rRNA

Trylska, J., & Kulik, M. (2016) · Biochemical Society Transactions · doi:10.1042/bst20160087 · Cited by 16 · see citing works

New focus on ecological risks of pesticides: The effect of pesticides on the development of bacterial antibiotic resistance

Zhao, Y., Wu, J., Wei, C., Li, L., Liang, F., Man, Y., Zhang, H., Han, L., Fang, H., Zheng, Y., et al. (2026) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2026.141062 · Cited by 14 · see citing works

Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting

Nishima, W., Girodat, D. J., Holm, M., Rundlet, E. J., Alejo, J. L., Fischer, K., Blanchard, S. C., & Sanbonmatsu, K. Y. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac597 · Cited by 14 · see citing works

Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding

Girodat, D. J., Wieden, H., Blanchard, S. C., & Sanbonmatsu, K. Y. (2023) · Nature Communications · doi:10.1038/s41467-023-40404-9 · Cited by 13 · see citing works

A Single Folded Beam Magneto-Optical Trap System for Neutral Mercury Atoms

Liu, K., Zhao, R.-C., Gou, W., Fu, X., Liu, H., Yin, S.-Q., Sun, J., Xu, Z., & Wang, Y. (2016) · Chinese Physics Letters · doi:10.1088/0256-307x/33/7/070602 · Cited by 12 · see citing works

Morphological Entanglement in Living Systems

Day, T. C., Zamani-Dahaj, S. A., Bozdag, G. O., Burnetti, A., Bingham, E. P., Conlin, P. L., Ratcliff, W. C., & Yunker, P. J. (2024) · Physical Review X · doi:10.1103/physrevx.14.011008 · Cited by 11 · see citing works

Dioclea violacea lectin increases the effect of neomycin against multidrug-resistant strains and promotes the purification of the antibiotic in immobilized lectin column

Santos, M. H. C., Santos, V. F., Freitas, P. R., Silva, R. R. D. S., Roma, R. R., Santos, A. L. E., Ribeiro, D. A., Coutinho, H. D. M., Rocha, B. A. M., Oliveira, M. M. E., et al. (2023) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2023.123941 · Cited by 11 · see citing works

A computational workflow to determine drug candidates alternative to aminoglycosides targeting the decoding center of E. coli ribosome

Yuce, M., Ates, B., Yasar, N. İ., Sungur, F. A., & Kürkçüoğlu, Ö. (2024) · Journal of Molecular Graphics and Modelling · doi:10.1016/j.jmgm.2024.108817 · Cited by 10 · see citing works

Mechanism of read-through enhancement by aminoglycosides and mefloquine

Kolosova, O., Zgadzay, Y., Stetsenko, A., Sukhinina, A. P., Atamas, A., Validov, S. Z., Rogachev, A. V., Usachev, K. S., Jenner, L. B., Dmitriev, S. E., et al. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2420261122 · Cited by 9 · see citing works

Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides

Dastidar, N. G., Freyer, N. S., Petrychenko, V., Schwarzer, A. C. D. A. P., Peng, B., Samatova, E., Kothe, C., Schmidt, M., Peske, F., Politi, A. Z., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65298-7 · Cited by 8 · see citing works

Antibiotic thermorubin tethers ribosomal subunits and impedes A-site interactions to perturb protein synthesis in bacteria

Parajuli, N. P., Emmerich, A., Mandava, C. S., Pavlov, M. Y., & Sanyal, S. (2023) · Nature Communications · doi:10.1038/s41467-023-36528-7 · Cited by 8 · see citing works

Detection and Quantification of Ribosome Inhibition by Aminoglycoside Antibiotics in Living Bacteria Using an Orthogonal Ribosome-Controlled Fluorescent Reporter

Huang, S., Zhu, X., & Melançon, C. E. (2015) · ACS Chemical Biology · doi:10.1021/acschembio.5b00779 · Cited by 8 · see citing works

Human ribosomes interactions reveal the binding landscape of neomycinPreprint

Wu, M., Zhu, L., Wu, M., Jia, C., Zhang, X., Zhao, Z., Liu, H., Yi, C., Sun, S., Liu, K., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.22.666027 · Cited by 8 · see citing works

Operative Binding of Class I Release Factors and YaeJ Stabilizes the Ribosome in the Nonrotated State

Casy, W., Prater, A. R., & Cornish, P. V. (2018) · Biochemistry · doi:10.1021/acs.biochem.7b00824 · Cited by 7 · see citing works

Preparation of ribosomes for smFRET studies: A simplified approach

Shebl, B., Menke, D. E., Pennella, M., Poudyal, R. R., Burke, D. H., & Cornish, P. V. (2016) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2016.05.010 · Cited by 6 · see citing works

Substrate Recognition and Modification by a Pathogen-Associated Aminoglycoside Resistance 16S rRNA Methyltransferase

Vinal, K., & Conn, G. L. (2017) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00077-17 · Cited by 6 · see citing works

A fitness landscape instability governs the morphological diversity of tip-growing cells

Ohairwe, M. E., Živanović, B. D., & Rojas, E. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113961 · Cited by 6 · see citing works

Engineering of Streptoalloteichus tenebrarius 2444 for Sustainable Production of Tobramycin

Mitousis, L., Maier, H., Martinovic, L., Kulik, A., Stockert, S., Wohlleben, W., Stiefel, A., & Musiol-Kroll, E. M. (2021) · Molecules · doi:10.3390/molecules26144343 · Cited by 6 · see citing works

Structure–function comparison of Arbekacin with other aminoglycosides elucidates its higher potency as bacterial translation inhibitor

Majumdar, S., Parajuli, N. P., Ge, X., & Sanyal, S. (2025) · Scientific Reports · doi:10.1038/s41598-025-02391-3 · Cited by 4 · see citing works

Improving the production of carbamoyltobramycin by an industrial Streptoalloteichus tenebrarius through metabolic engineering

Feng, Y., Jiang, Y., Chen, X., Zhu, L., Xue, H., Wu, M., Yang, L., Yu, H., & Lin, J. (2024) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-024-13141-2 · Cited by 4 · see citing works

Characterization of ribostamycin and its impurities using a nano-quantity analyte detector: Systematic comparison of performance among three different aerosol detectors

Meng, F., Zhou, X., Hou, Y., Zhao, H., Zhang, J., Huang, Q. B., Zhang, M., Adams, E., Yuan, Y., & Shi, H. C. (2024) · Talanta · doi:10.1016/j.talanta.2024.126359 · Cited by 3 · see citing works

Aminoglycoside Susceptibility among Extensive Drug Resistant Pseudomonas aeruginosa from Hospitalized Patients in Al-Diwaniyah, Iraq

Jawad, S. S., & Al-Azawi, I. H. (2024) · Medical Journal of Babylon · doi:10.4103/mjbl.mjbl_694_23 · Cited by 3 · see citing works

Influence of ring size in conformationally restricted ring I analogs of paromomycin on antiribosomal and antibacterial activity

Pirrone, M. G., Hobbie, S. N., Vasella, A. T., Böttger, E. C., & Crich, D. (2021) · RSC Medicinal Chemistry · doi:10.1039/d1md00214g · Cited by 3 · see citing works

TB-annotator: a scalable web application that allows in-depth analysis of very large sets of publicly available Mycobacterium tuberculosis complex genomesPreprint

Senelle, G., Guyeux, C., Refrégier, G., & Sola, C. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.12.526393 · Cited by 3 · see citing works

How Medically Important Antimicrobials Bind to the 30S Ribosomal Subunit in a Bacterial Pathogen

(2026) · doi:10.1021/acs.biochem.6c00008 · Cited by 1 · see citing works

Structural basis for hygromycin B inhibition of yeast pseudouridine-deficient ribosomes

Zhao, Y., Xu, C., Chen, X., Jin, H., & Li, H. (2025) · Science Advances · doi:10.1126/sciadv.adu0151 · Cited by 1 · see citing works

Plat: A Web Based Protein Local Alignment Tool

Jaegle, S. (2017) · doi:10.23860/thesis-jaegle-stephen-2017 · Cited by 1 · see citing works

Detuning of the Ribosome Conformational Landscape Promotes Antibiotic Resistance and Collateral SensitivityPreprint

Mesa, P., Jiménez‐Fernández, A., Rosa, R. L., Espinosa, R., Johansen, H. K., Molin, S., & Montoya, G. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.13.544509 · Cited by 1 · see citing works

Synthetic Receptors for RNA Recognition

Bhaduri, S., Spano, M. N., & Arya, D. P. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-409547-2.12550-8

Kinetics of subunit rotation of the ribosome during tRNA-mRNA translocation

Sharma, H. (2017) · doi:10.53846/goediss-6407

Bacterial ribosome conformational dynamics during translation termination and rescue

Casy, W. (2017) · doi:10.32469/10355/66770

Zero ac Stark frequency shift of an atom trapped in pulsed laser light*

Afanasiev, A. E., & Balykin, V. I. (2021) · Quantum Electronics · doi:10.1070/qel17500

Analysis of translational fidelity in cellular proteins

Garofalo, R. (2019) · doi:10.53846/goediss-7371

Faculty Opinions recommendation of tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.

Kovalevsky, A. Y., & Armbruster, E. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.734549733.793557363

Ribosome inhibition : cryo-EM and advancements in X-ray crystallography

Kolosova, O. A. (2023) · theses.fr (ABES) · doi:10.70675/fac7636bz91a9z4dbazb803z20817e06b018

Antitumor effect of the AP5Z1 small-molecule inhibitor PGG in hepatocellular carcinoma

Quan, Z., Hu, Q., Liu, M. R., Ma, G., He, Z., Liu, Y., Wei, Y., Wei, Y., Zheng, X., Qin, C., et al. (2026) · Medical Oncology · doi:10.1007/s12032-026-03322-6

Binding properties of chiral ruthenium(II) polypyridyl complexes Λ- and Δ-[Ru(bpy)2(bipp)]2+ with double-stranded RNA

Wan, K., Ling, X., & Tan, L. (2026) · Inorganica Chimica Acta · doi:10.1016/j.ica.2026.123412

BindingDB Entry 50018392: Inhibitors of Eukaryotic Translational Machinery as Therapeutic Agents.

BindingDB (2024) · UC San Diego · doi:10.7270/q2t43z96

Allosteric control of the ribosome by small-molecule antibiotics

Wang, L., Pulk, A., Wasserman, M. R., Feldman, M. B., Altman, R. B., Cate, J. H. D., & Blanchard, S. C. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2360 · Cited by 136 · see citing works

Pseudouridine modifications influence binding of aminoglycosides to helix 69 of bacterial ribosomes

Sakakibara, Y., & Chow, C. S. (2017) · Organic & Biomolecular Chemistry · doi:10.1039/c7ob02147j · Cited by 4 · 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

Aminoglycoside Association Pathways with the 30S Ribosomal Subunit

Długosz, M., & Trylska, J. (2009) · The Journal of Physical Chemistry B · doi:10.1021/jp8112914 · Cited by 34 · see citing works

A minimum structure of aminoglycosides that causes an initiation shift of trans-translation

Konno, T. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh750 · Cited by 20 · see citing works