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Publications

2024

Soni, C.; Prywes, N.; Hall, M.; Nair, M. A.; Savage, D. F.; Schepartz, A.; Chatterjee, A. A Translation-Independent Directed Evolution Strategy to Engineer Aminoacyl-tRNA Synthetases. ACS Cent. Sci. 2024. https://doi.org/10.1021/acscentsci.3c01557.

— Data: SI | Sequencing Data | PAC Bio NGS script | NGS analysis for selection

Hamlish, N. X.; Abramyan, A. M.; Shah, B.; Zhang, Z.; Schepartz, A. Incorporation of Multiple Β2-Hydroxy Acids into a Protein In Vivo Using an Orthogonal Aminoacyl-tRNA Synthetase. ACS Cent. Sci. 2024. https://doi.org/10.1021/acscentsci.3c01366.

— Data: SI

Shulgina, Y.; Trinidad, M. I.; Langeberg, C. J.; Nisonoff, H.; Chithrananda, S.; Skopintsev, P.; Nissley, A. J.; Patel, J.; Boger, R. S.; Shi, H.; Yoon, P. H.; Doherty, E. E.; Pande, T.; Iyer, A. M.; Doudna, J. A.; Cate, J. H. D. RNA Language Models Predict Mutations That Improve RNA Function. bioRxiv. 2024. p 2024.04.05.588317. https://doi.org/10.1101/2024.04.05.588317.

— Press: Innovative Genomics Institute

Navarrete, F. A. C.; Griffin, W. C.; Chan, Y.-C.; Martin, M. I.; Alejo, J. L.; Natchiar, S. K.; Knudson, I.; Altman, R. B.; Schepartz, A.; Miller, S. J.; Blanchard, S. C. β-Amino Acids Reduce Ternary Complex Stability and Alter the Translation Elongation Mechanism. bioRxiv. 2024, p 2024.02.24.581891. https://doi.org/10.1101/2024.02.24.581891.

Tangpradabkul, T.; Palo, M.; Townley, J.; Hsu, K. B.; participants, E.; Smaga, S.; Das, R.; Schepartz, A. Minimization of the E. Coli Ribosome, Aided and Optimized by Community Science. Nucleic Acids Research. 2024, 52 (3), 1027–1042. https://doi.org/10.1093/nar/gkad1254.

— Data: SI | Code: Zenodo, Github

2023

Soni, C.; Prywes, N.; Hall, M.; Savage, D. F.; Schepartz, A.; Chatterjee, A. A Translation-Independent Directed Evolution Strategy to Engineer Aminoacyl-tRNA Synthetases. bioRxiv. 2023, p 2023.12.13.571473. https://doi.org/10.1101/2023.12.13.571473.

Davisson, J.; Alejo, J.; Blank, M.; Kalb, E.; Prasad, A.; Knudson, I.; Schepartz, A.; Engelhart, A. E.; Adamala, K. P. High Yield, Low Magnesium Flexizyme Reactions in a Water-Ice Eutectic Phase. bioRxiv. 2023. https://doi.org/10.1101/2023.12.03.569792.

Roe, L.; Schissel, C. K.; Dover, T. L.; Shah, B.; Hamlish, N. X.; Zheng, S.; Dilworth, D. A.; Wong, N.; Zhang, Z.; Chatterjee, A.; Francis, M. B.; Miller, S. J.; Schepartz, A. Backbone Extension Acyl Rearrangements Enable Cellular Synthesis of Proteins with Internal Β2-Peptide Linkages. bioRxiv. 2023. https://doi.org/10.1101/2023.10.03.560714.

Fricke, R.; Knudson, I.; Schepartz, A. Direct, Quantitative, and Comprehensive Analysis of tRNA Acylation Using Intact tRNA Liquid-Chromatography Mass-Spectrometry. bioRxiv. 2023. https://doi.org/10.1101/2023.07.14.549096.

Nissley, A. J.; Kamal, T. S.; Cate, J. H. D. Interactions between Terminal Ribosomal RNA Helices Stabilize the Escherichia Coli Large Ribosomal Subunit. RNA. 2023, rna.079690.123. https://doi.org/10.1261/rna.079690.123.

— Data: SI | EM maps (50S, 30S, 70S, composite) | Structure: 8FTO

Watson, Z. L.; Knudson, I. J.; Ward, F. R.; Miller, S. J.; Cate, J. H. D.; Schepartz, A.; Abramyan, A. M. Atomistic Simulations of the Escherichia Coli Ribosome Provide Selection Criteria for Translationally Active Substrates. Nature Chemistry. 2023, 1–9. https://doi.org/10.1038/s41557-023-01226-w.

— Data: SI | MetaD minima | EM maps (50S, 30S, 70S, composite) | Structure: 8EMM

— Press: Nature News | Nat. Chem. News and Views | Berkeley News

Fricke, R.; Swenson, C. V.; Roe, L. T.; Hamlish, N. X.; Shah, B.; Zhang, Z.; Ficaretta, E.; Ad, O.; Smaga, S.; Gee, C. L.; Chatterjee, A.; Schepartz, A. Expanding the Substrate Scope of Pyrrolysyl-Transfer RNA Synthetase Enzymes to Include Non-α-Amino Acids in Vitro and in Vivo. Nature Chemistry. 2023, 1–12. https://doi.org/10.1038/s41557-023-01224-y.

— Data: SI | Raw Data (Zenodo)| Plasmids (Addgene) |  Structure: 7U0R

— Press: Nature News | Nature Chem. Bio. Highlight | Berkeley News

Majumdar, C.; Walker, J. A.; Francis, M. B.; Schepartz, A.; Cate, J. H. D. Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome. ACS Central Science. 2023. https://doi.org/10.1021/acscentsci.3c00153.

— Data: SI (PDF) | Structures: 8G6W (oABZ), 8G6X (mABZ), and 8G6Y (Apy)

— Press: Berkeley News

Westhof, E.; Watson, Z. L.; Zirbel, C. L.; Cate, J. H. D. Anionic G•U Pairs in Bacterial Ribosomal rRNAs. RNA. 2023, rna.079583.123. https://doi.org/10.1261/rna.079583.123.

— Data: Supplemental Material

Holm, M.; Natchiar, S. K.; Rundlet, E. J.; Myasnikov, A. G.; Watson, Z. L.; Altman, R. B.; Wang, H.-Y.; Taunton, J.; Blanchard, S. C. mRNA Decoding in Human Is Kinetically and Structurally Distinct from BacteriaNature. 2023, 1–8. https://doi.org/10.1038/s41586-023-05908-w.

— Data: SI | Maps and models

— Press: Nature Research Briefing St Jude press release

Nissley, A. J.; Penev, P. I.; Watson, Z. L.; Banfield, J. F.; Cate, J. H. D. Rare ribosomal RNA sequences from Archaea stabilize the bacterial ribosomeNucleic Acids Research. 2023, https://doi.org/10.1093/nar/gkac1273.
— Data: A loop sequence analysis | PDB 8EIU | EMDB 28165 28218 28229 28230

2022

Dias-Fields, L.; Adamala, K. P. Engineering Ribosomes to Alleviate Abiotic Stress in Plants: A PerspectivePlants202211 (16), 2097. https://doi.org/10.3390/plants11162097.

Walker, J. A.; Hamlish, N.; Tytla, A.; Brauer, D. D.; Francis, M. B.; Schepartz, A. Redirecting RiPP biosynthetic enzymes to proteins and backbone-modified substrates. ACS Central Science. 2022, https://doi.org/10.1021/acscentsci.1c01577.
— Data: SI PDF | Conformers (MAE format)

Radford, F.; Elliott, S. D.; Schepartz, A.; Isaacs, F. J. Targeted editing and evolution of engineered ribosomes in vivo by filtered editingNature Communications. 202213 (1), 180. https://doi.org/10.1038/s41467-021-27836-x.
— Data: Raw NGS data (GSA ID: CRA005526)

2021

Santiago, S.; Ad, O.; Shah, B.; Zhang, Z.; Zhang, X.; Chatterjee, A.; Schepartz, A. Genetic code expansion in the engineered organism Vmax X2: High yield and exceptional fidelityACS Central Science2021. https://doi.org/10.1021/acscentsci.1c00499.
— Data: SI PDF

Gaffney, S. G.; Smaga, S.; Schepartz, A.; Townsend, J. P. Chemsearch: Collaborative compound libraries with structure-aware browsingBioinformatics Advances. 2021, vbab008. https://doi.org/10.1093/bioadv/vbab008.
— Data: Chemsearch github repository

Tharp, J. M.*; Walker, J. A.*; Söll, D.; Schepartz, A. Initiating protein synthesis with noncanonical monomers in vitro and in vivo. In Methods in Enzymology; Academic Press, 2021. https://doi.org/10.1016/bs.mie.2021.05.002.

Tharp, J. M.; Vargas-Rodriguez, O.; Schepartz, A.; Söll, D. Genetic encoding of three distinct noncanonical amino acids using reprogrammed initiator and nonsense codonsACS Chemical Biology. 202116 (4), 766–774. https://doi.org/10.1021/acschembio.1c00120.
— Data: SI PDF

2020

Krahn, N.; Tharp, J. M.; Crnković, A.; Söll, D. Engineering aminoacyl-tRNA synthetases for use in synthetic biology. In The Enzymes; Academic Press, 2020. doi:10.1016/bs.enz.2020.06.004.

Watson, Z. L.; Ward, F. R.; Méheust, R.; Ad, O.; Schepartz, A.; Banfield, J. F.; Cate, J. H. D., Structure of the bacterial ribosome at 2 Å resolutioneLife. 2020. doi:10.7554/eLife.60482.
— Data: PDB (7K00) | EMDR (22586) | EMPIAR-10509

Walker, A. S.; Russ, W. P.; Ranganathan, R.; Schepartz, A. RNA sectors and allosteric function within the ribosomeProceedings of the National Academy of Sciences. 2020117 (33). 19879-19887.
— Data: Supplementary Materials | SCA6 script | Ribosomal SCA analysis

Tharp, J. M.; Krahn, N.; Varshney, U.; Söll, D., Hijacking translation initiation for synthetic biologyChemBioChem202021 (10). 1387-1396.

Tharp, J. M.; Ad, O.; Amikura, K.; Ward, F. R.; Garcia, E. M.; Cate, J. H. D.; Schepartz, A.; Söll, D., Initiation of protein synthesis with non-canonical amino acids in vivoAngewandte Chemie202059 (8). 3122-3126.
— Data: SI PDF

2019

Ward, F. R.*; Watson, Z. L.*; Ad, O.; Schepartz, A.; Cate, J. H. D., Defects in the assembly of ribosomes selected for β-amino acid incorporationBiochemistry201958, 4494-4504.
— Data: WT 50S (EMD 20853) | P7A7 50S (EMD 20854)

Ad, O.; Hoffman, K. S.; Cairns, A. G.; Featherston, A. L.; Miller, S. J.; Söll, D.; Schepartz, A., Translation of diverse aramid- and 1,3-dicarbonyl-peptides by wild type ribosomes in vitroACS Central Science. 20195, 1289–1294.
— Data: SI PDF

Schepartz, A.; Townsend, J. P., GEM-NET: Lessons in multi-institution teamwork using collaboration softwareACS Central Science. 20195, 1159–1169.
— Data: SI PDF | github - strains | portal | podcast-rss

2018

Hoffman, K. S.; Crnković, A.; Söll, D., Versatility of synthetic tRNAs in genetic code expansionGenes20189, epub.

Vargas-Rodriguez, O.; Sevostyanova, A.; Söll, D.; Crnković, A., Upgrading aminoacyl-tRNA synthetases for genetic code expansionCurrent Opinion in Chemical Biology201846, 115-122. 

Arranz-Gibert, P.; Vanderschuren, K.; Isaacs, F. J., Next-generation genetic code expansionCurrent Opinion in Chemical Biology. 201846, 203-211.

Barber, K. W.; Muir, P.; Szeligowski, R. V.; Rogulina, S.; Gerstein, M.; Sampson, J. R.; Isaacs, F. J.;
Rinehart, J., Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactionsNature Biotechnology201836, 638-644.
— Data: Supplementary Materials

Schepartz, A., Foldamers wave to the ribosomeNature Chemistry201810, 377.