Publications

2022 Publications

  1. Akkineni, S., C. Zhu, J. Chen, M. Song, S.E. Hoff, J. Bonde, J. Tao, H. Heinz, S. Habelitz, and J.J. De Yoreo, “Amyloid-like amelogenin nanoribbons template mineralization via a low-energy interface of ion binding sites,” Proceedings of the National Academy of Sciences of the United States of America 119(19), e2106965119 (2022). (doi:10.1073/pnas.2106965119)

  2. Anderson, B.W., M.A. Schumacher, J. Yang, A. Turdiev, H. Turdiev, J.W. Schroeder, Q. He, V.T. Lee, R.G. Brennan, and J.D. Wang, “The nucleotide messenger (p)ppGpp is an anti-inducer of the purine synthesis transcription regulator PurR in Bacillus,” Nucleic Acids Research 50(2), 847-866 (2022). (doi:10.1093/nar/gkab1281)

  3. Arrigoni, C., M. Lolicato, D. Shaya, A. Rohaim, F. Findeisen, L.-K. Fong, C.M. Colleran, P. Dominik, S.S. Kim, J.P. Schuermann, W.F. DeGrado, M. Grabe, A.A. Kossiakoff, and D.L. Minor, “Quaternary structure independent folding of voltage-gated ion channel pore domain subunits,” Nature Structural & Molecular Biology 29(6), 537-548 (2022). (doi:10.1038/s41594-022-00775-x)

  4. Azimova, D., N. Herrera, L. Duvenage, M. Voorhies, R.A. Rodriguez, B.C. English, J.C. Hoving, O. Rosenberg, and A. Sil, “Cbp1, a fungal virulence factor under positive selection, forms an effector complex that drives macrophage lysis,” PLoS Pathogens 18(6), e1010417 (2022). (doi:10.1371/journal.ppat.1010417)

  5. Barbosa Da Silva, E., V. Sharma, L. Hernandez-Alvarez, A.H. Tang, A. Stoye, A.J. O’Donoghue, W.H. Gerwick, R.J. Payne, J.H. McKerrow, and L.M. Podust, “Intramolecular Interactions Enhance the Potency of Gallinamide A Analogues against Trypanosoma cruzi,” Journal of Medicinal Chemistry 65(5), 4255-4269 (2022). (doi:10.1021/acs.jmedchem.1c02063)

  6. Bednarczyk, M., J.K. Peters, R. Kasprzyk, J. Starek, M. Warminski, T. Spiewla, J.S. Mugridge, J.D. Gross, J. Jemielity, and J. Kowalska, “Fluorescence-Based Activity Screening Assay Reveals Small Molecule Inhibitors of Vaccinia Virus mRNA Decapping Enzyme D9,” ACS Chemical Biology 17(6), 1460-1471 (2022). (doi:10.1021/acschembio.2c00049)

  7. Bratkowski, M., T.C. Burdett, J. Danao, X. Wang, P. Mathur, W. Gu, J.A. Beckstead, S. Talreja, Y.-S. Yang, G. Danko, J.H. Park, M. Walton, S.P. Brown, C.M. Tegley, P.B. Joseph, C.H. Reynolds, and S. Sambashivan, “Uncompetitive, adduct-forming SARM1 inhibitors are neuroprotective in preclinical models of nerve injury and disease,” Neuron 110(22), 3711-3726.e16 (2022). (doi:10.1016/j.neuron.2022.08.017)

  8. Campbell, M.R., A. Ruiz-Saenz, E. Peterson, C. Agnew, P. Ayaz, S. Garfinkle, P. Littlefield, V. Steri, J. Oeffinger, M. Sampang, Y. Shan, D.E. Shaw, N. Jura, and M.M. Moasser, “Targetable HER3 functions driving tumorigenic signaling in HER2-amplified cancers,” Cell Reports 38(5), 110291 (2022). (doi:10.1016/j.celrep.2021.110291)

  9. Cofsky, J.C., G.J. Knott, C.L. Gee, and J.A. Doudna, “Crystal structure of an RNA/DNA strand exchange junction,” PLoS ONE 17(4), e0263547 (2022). (doi:10.1371/journal.pone.0263547)

  10. Correy, G.J., D.W. Kneller, G. Phillips, S. Pant, S. Russi, A.E. Cohen, G. Meigs, J.M. Holton, S. Gahbauer, M.C. Thompson, A. Ashworth, L. Coates, A. Kovalevsky, F. Meilleur, and J.S. Fraser, “The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature,” Science Advances 8(21), eabo5083 (2022). (doi:10.1126/sciadv.abo5083)

  11. Faust, B.T., “Antibody control of protein conformation in pathology and for therapeutic pharmacology,” Doctoral Dissertation, University of California, San Francisco, San Francisco, CA, 2022, advisor Y. Cheng. Hulce, K.R., P. Jaishankar, G.M. Lee, M.-F. Bohn, E.J. Connelly, K. Wucherer, C. Ongpipattanakul, R.F. Volk, S.-W. Chuo, M.R. Arkin, A.R. Renslo, and C.S. Craik, “Inhibiting a dynamic viral protease by targeting a non-catalytic cysteine,” Cell Chemical Biology 29(5), 785-798.e19 (2022). (doi:10.1016/j.chembiol.2022.03.007)

  12. Jian, T., Y. Zhou, P. Wang, W. Yang, P. Mu, X. Zhang, X. Zhang, and C.-L. Chen, “Highly stable and tunable peptoid/hemin enzymatic mimetics with natural peroxidase-like activities,” Nature Communications 13(1), 3025 (2022). (doi:10.1038/s41467-022-30285-9)

  13. Krivacic, C., K. Kundert, X. Pan, R.A. Pache, L. Liu, S. O Conchúir, J.R. Jeliazkov, J.J. Gray, M.C. Thompson, J.S. Fraser, and T. Kortemme, “Accurate positioning of functional residues with robotics-inspired computational protein design,” Proceedings of the National Academy of Sciences of the United States of America 119(11), e2115480119 (2022). (doi:10.1073/pnas.2115480119)

  14. Krivacic, C., “Positioning residues for function in designed proteins,” Doctoral Dissertation, University of California, San Francisco, San Francisco, CA, 2022, advisor T. Kortemme. Legault, S., D.P. Fraser-Halberg, R.L. McAnelly, M.G. Eason, M.C. Thompson, and R.A. Chica, “Generation of bright monomeric red fluorescent proteins via computational design of enhanced chromophore packing,” Chemical Science 13(5), 1408-1418 (2022). (doi:10.1039/D1SC05088E)

  15. Li, Z., D.K. Tran, M. Nguyen, T. Jian, F. Yan, S.A. Jenekhe, and C. Chen, “Amphiphilic Peptoid-Directed Assembly of Oligoanilines into Highly Crystalline Conducting Nanotubes,” Macromolecular Rapid Communications 43(4), 2100639 (2022). (doi:10.1002/marc.202100639)

  16. Neugebauer, M.E., E.N. Kissman, J.A. Marchand, J.G. Pelton, N.A. Sambold, D.C. Millar, and M.Y. Chang, “Reaction pathway engineering converts a radical hydroxylase into a halogenase,” Nature Chemical Biology 18(2), 171-179 (2022). (doi:10.1038/s41589-021-00944-x)

  17. Nienhaus, K., V. Sharma, G.U. Nienhaus, and L.M. Podust, “Homodimerization Counteracts the Detrimental Effect of Nitrogenous Heme Ligands on the Enzymatic Activity of Acanthamoeba castellanii CYP51,” Biochemistry 61(13), 1363-1377 (2022). (doi:10.1021/acs.biochem.2c00198)

  18. Ohmer, C.J., M. Dasgupta, A. Patwardhan, I. Bogacz, C. Kaminsky, M.D. Doyle, P.-T. Chen, S.M. Keable, H. Makita, P.S. Simon, R. Massad, T. Fransson, R. Chatterjee, A. Bhowmick, D.W. Paley, N.W. Moriarty, A.S. Brewster, L.B. Gee, R. Alonso-Mori, F. Moss, F.D. Fuller, A. Batyuk, N.K. Sauter, U. Bergmann, C.L. Drennan, V.K. Yachandra, J. Yano, J.F. Kern, and S.W. Ragsdale, “XFEL serial crystallography reveals the room temperature structure of methyl-coenzyme M reductase,” Journal of Inorganic Biochemistry 230, 111768 (2022). (doi:10.1016/j.jinorgbio.2022.111768)

  19. Pellegrino, J., “DMS-Guided Structural Biology Approaches to Durable Streptogramin A Antibiotics,” Doctoral Dissertation, University of California, San Francisco, San Francisco, CA, 2022, advisor J. Fraser. Peters, J.K., R.W. Tibble, M. Warminski, J. Jemielity, and J.D. Gross, “Structure of the poxvirus decapping enzyme D9 reveals its mechanism of cap recognition and catalysis,” Structure 30(5), 721-732.e4 (2022). (doi:10.1016/j.str.2022.02.012)

  20. Pugliese, R., and F. Gelain, “Programmable stiffness and stress-relaxation of cross-linked self-assembling peptide hydrogels,” Journal of Applied Polymer Science 139(9), 51759 (2022). (doi:10.1002/app.51759)

  21. Ricemeyer, L., N. Aguilar-Hernández, T. López, R. Espinosa, S. Lanning, S. Mukherjee, C. Cuellar, S. López, C.F. Arias, and R.M. DuBois, “Structures of Two Human Astrovirus Capsid/Neutralizing Antibody Complexes Reveal Distinct Epitopes and Inhibition of Virus Attachment to Cells,” Journal of Virology 96(1), e01415-21 (2022). (doi:10.1128/JVI.01415-21)

  22. Schoof, M., “A Unifying Mechanism for Activation and Inhibition of the Integrated Stress Response and Aerosolized Nanobodies for the Treatment of Sars-CoV-2,” Doctoral Dissertation, University of California, San Francisco, San Francisco, CA, 2022, advisor M. Kampmann. Travis, B.A., “Transcriptional control of virulence in Francisella tularensis,” Doctoral Dissertation, Duke University, Durham, NC, 2022, advisor M.A. Schumacher. Yang, T., A. Cuesta, X. Wan, G.B. Craven, B. Hirakawa, P. Khamphavong, J.R. May, J.C. Kath, J.D. Lapek, S. Niessen, A.L. Burlingame, J.D. Carelli, and J. Taunton, “Reversible lysine-targeted probes reveal residence time-based kinase selectivity,” Nature Chemical Biology 18(9), 934-941 (2022). (doi:10.1038/s41589-022-01019-1)

  23. Zhao, M., K.J. Lachowski, S. Zhang, S. Alamdari, J. Sampath, P. Mu, C.J. Mundy, J. Pfaendtner, J.J. De Yoreo, C.-L. Chen, L.D. Pozzo, and A.L. Ferguson, “Hierarchical Self-Assembly Pathways of Peptoid Helices and Sheets,” Biomacromolecules 23(3), 992-1008 (2022). (doi:10.1021/acs.biomac.1c01385)