Publications
2024
Nissley, A. J.; Shulgina, Y.; Kivimae, R. W.; Downing, B. E.; Penev, P. I.; Banfield, J. F.; Nayak, D. D.; Cate, J. H. D. Structure of an Archaeal Ribosome with a Divergent Active Site. bioRxiv 2024, p 2024.11.12.623245. https://doi.org/10.1101/2024.11.12.623245.
Boyko, K. V.; Bernstein, R. A.; Kim, M.; Cate, J. H. D. Role of Ribosomal Protein bS1 in Orthogonal mRNA Start Codon Selection. bioRxiv 2024. https://doi.org/10.1101/2024.10.14.618353.
Kent, A.; Robins, J.; Knudson, I.; Vance, J.; Solivan, A.; Hamlish, N.; Fitzgerald, K.; Schepartz, A.; Miller, S.; Cate, J. Thioesters Support Efficient Protein Biosynthesis by the Ribosome. ChemRxiv 2024. https://doi.org/10.26434/chemrxiv-2024-6hxv7.
Kivenson, V.; Peters, S. L.; Borrel, G.; Kivenson, A.; Roe, L. T.; Hamlish, N. X.; Fadhlaoui, K.; Schepartz, A.; Gribaldo, S.; Hettich, R.; Banfield, J. Sporadic Distribution of a New Archaeal Genetic Code with All TAG Codons as Pyrrolysine. bioRxiv 2024. https://doi.org/10.1101/2024.09.30.615893.
Schissel, C.; Roberts-Mataric, H.; Garcia, I.; Kang, H.; Francis, M.; Schepartz, A. Ribosomal Synthesis of Ketone-Containing Peptide Backbone via O to C Acyl Shift. ChemRxiv 2024. https://doi.org/10.26434/chemrxiv-2024-bkzp3.
Davisson, J. A.; Kalb, E. M.; Knudson, I. J.; Schepartz, A.; Engelhart, A. E.; Adamala, K. Nonenzymatic, Prebiotic Aminoacylation Couples Chirality of RNA and Protein. bioRxiv 2024. https://doi.org/10.1101/2024.07.29.605638.
Stone, E.; Whitten, A.; Angelisanti, N.; Kissman, E.; Millar, D.; Vargas-Figueroa, A.; Chang, M. Discovery and Application of a Lysine 5-Hydroxylase for Bioorthogonal Chemistry. ChemRxiv 2024. https://doi.org/10.26434/chemrxiv-2024-xj5bw.
Knudson, I. J.; Dover, T. L.; Dilworth, D. A.; Paloutzian, C.; Cho, H.; Schepartz, A.; Miller, S. J. Chemo-Ribosomal Synthesis of Atropisomeric and Macrocyclic Peptides with Embedded Quinolines. ChemRxiv 2024. https://doi.org/10.26434/chemrxiv-2024-kvdpq.
Cruz-Navarrete, F. A.✝; Griffin, W. C.✝; Chan, Y.-C.✝; Martin, M. I.; Alejo, J. L.; Brady, R. A.; Natchiar, S. K.; Knudson, I. J.; Altman, R. B.; Schepartz, A.; Miller, S. J.; Blanchard, S. C. β-Amino Acids Reduce Ternary Complex Stability and Alter the Translation Elongation Mechanism. ACS Cent. Sci. 2024. https://doi.org/10.1021/acscentsci.4c00314.
— Data: SI
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
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
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 Bacteria. Nature. 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 ribosome. Nucleic 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 Perspective. Plants. 2022, 11 (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 editing. Nature Communications. 2022, 13 (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 fidelity. ACS Central Science. 2021. 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 browsing. Bioinformatics 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 codons. ACS Chemical Biology. 2021, 16 (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 resolution. eLife. 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 ribosome. Proceedings of the National Academy of Sciences. 2020. 117 (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 biology, ChemBioChem. 2020, 21 (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 vivo. Angewandte Chemie. 2020, 59 (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 incorporation, Biochemistry. 2019, 58, 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 vitro, ACS Central Science. 2019, 5, 1289–1294.
— Data: SI PDF
Gaffney, S. G.; Ad, O.; Smaga, S.; Schepartz, A.; Townsend, J. P., GEM-NET: Lessons in multi-institution teamwork using collaboration software. ACS Central Science. 2019, 5, 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 expansion, Genes. 2018, 9, epub.
Vargas-Rodriguez, O.; Sevostyanova, A.; Söll, D.; Crnković, A., Upgrading aminoacyl-tRNA synthetases for genetic code expansion, Current Opinion in Chemical Biology. 2018, 46, 115-122.
Arranz-Gibert, P.; Vanderschuren, K.; Isaacs, F. J., Next-generation genetic code expansion, Current Opinion in Chemical Biology. 2018, 46, 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 interactions, Nature Biotechnology. 2018, 36, 638-644.
— Data: Supplementary Materials
Schepartz, A., Foldamers wave to the ribosome, Nature Chemistry. 2018, 10, 377.