Publications

2024 Publications

  1. Ali, B.A., R.M. Judy, S. Chowdhury, N.K. Jacobsen, D.T. Castanzo, K.L. Carr, C.D. Richardson, G.C. Lander, A. Martin, and B.M. Gardner, “The N1 domain of the peroxisomal AAA-ATPase Pex6 is required for Pex15 binding and proper assembly with Pex1,” Journal of Biological Chemistry 300(1), 105504 (2024). (doi:10.1016/j.jbc.2023.105504) 8.3.1

  2. Beernink, P.T., C. Di Carluccio, R. Marchetti, L. Cerofolini, S. Carillo, A. Cangiano, N. Cowieson, J. Bones, A. Molinaro, L. Paduano, M. Fragai, B.P. Beernink, S. Gulati, J. Shaughnessy, P.A. Rice, S. Ram, and A. Silipo, “Gonococcal Mimitope Vaccine Candidate Forms a Beta-Hairpin Turn and Binds Hydrophobically to a Therapeutic Monoclonal Antibody,” JACS Au 4(7), 2617-2629 (2024). (doi:10.1021/jacsau.4c00359) 8.3.1

  3. Bragagnolo, N., and G.F. Audette, “The 1.3?Å resolution structure of the truncated group Ia type IV pilin from Pseudomonas aeruginosa strain P1,” Acta Crystallographica, Section D: Structural Biology 80(12), 834-849 (2024). (doi:10.1107/S205979832401132X) 8.3.1

  4. Brosey, C.A., T.M. Link, R. Shen, D. Moiani, K. Burnett, G.L. Hura, D.E. Jones, and J.A. Tainer, “Chemical screening by time-resolved X-ray scattering to discover allosteric probes,” Nature Chemical Biology 20(9), 1199-1209 (2024). (doi:10.1038/s41589-024-01609-1) 8.3.1,12.3.1

  5. Goldberg, K.A., M.P. Kota, G.D. Cutler, and J.M. Holton, “Specification of monochromator crystals for diffraction-limited x-ray optical performance,” Proceedings of SPIE 13150, 131500A (2024). [Proceedings of Advances in X-Ray/EUV Optics and Components XIX, (San Diego, CA, 2024)]. (doi:10.1117/12.3028642) 8.3.1,Instrumentation

  6. Hooks, G.M., J.C. Ayala, C.L. Holley, V. Dhulipala, G.A. Beggs, J.R. Perfect, M.A. Schumacher, W.M. Shafer, and R.G. Brennan, “Hormonal steroids induce multidrug resistance and stress response genes in Neisseria gonorrhoeae by binding to MtrR,” Nature Communications 15(1), 1153 (2024). (doi:10.1038/s41467-024-45195-1) 5.0.2,8.3.1

  7. Lu, L., X. Gou, S.K. Tan, S.I. Mann, H. Yang, X. Zhong, D. Gazgalis, J. Valdiviezo, H. Jo, Y. Wu, M.E. Diolaiti, A. Ashworth, N. Polizzi, and W. DeGrado, “De novo design of drug-binding proteins with predictable binding energy and specificity,” Science 384(6691), 106-112 (2024). (doi:10.1126/science.adl5364) 8.3.1

  8. Nadel, C.M., S. Pokhrel, K. Wucherer, A. Oehler, A.C. Thwin, K. Basu, M. Callahan, D.R. Southworth, D.A. Mordes, C. Craik, and J.E. Gestwicki, “Phosphorylation of tau at a single residue inhibits binding to the E3 ubiquitin ligase, CHIP,” Nature Communications 15(1), 7972 (2024). (doi:10.1038/s41467-024-52075-1) 8.3.1

  9. Parkins, A., A.V. Pilien, A.M. Wolff, C. Argueta, J. Vargas, S. Sadeghi, A.H. Franz, M.C. Thompson, and G. Pantouris, “The C-terminal Region of D-DT Regulates Molecular Recognition for Protein-Ligand Complexes,” Journal of Medicinal Chemistry 67(9), 7359-7372 (2024). (doi:10.1021/acs.jmedchem.4c00177) 8.3.1

  10. Parkins, A., “Structural and Functional Studies of the Human Members of the Macrophage Migration Inhibitory Factor Family,” Doctoral Dissertation, University of the Pacific, Stockton, CA, 2024, advisor G. Pantouris. 8.2.1,8.3.1

  11. Rakotoharisoa, R.V., B. Seifinoferest, N. Zarifi, J.M. Miller, J. Rodriguez, M.C. Thompson, and R.A. Chica, “Design of Efficient Artificial Enzymes Using Crystallographically Enhanced Conformational Sampling,” Journal of the American Chemical Society 146(14), 10001-10013 (2024). (doi:10.1021/jacs.4c00677) 8.3.1

  12. Schönherr, H., P. Ayaz, A.M. Taylor, J.B. Casaletto, B.B. Touré, D.T. Moustakas, B.M. Hudson, R. Valverde, S. Zhao, P.J. O’Hearn, L. Foster, D.A. Sharon, S. Garfinkle, F. Giordanetto, A. Lescarbeau, R. Kurukulasuriya, N. Gerami-Moayed, D. Maglic, K. Bruderek, G. Naik, H. Gunaydin, M.M. Mader, A.A. Boezio, T.H. McLean, R. Chen, Y. Wang, D.E. Shaw, J. Watters, and D.A. Bergstrom, “Discovery of lirafugratinib (RLY-4008), a highly selective irreversible small-molecule inhibitor of FGFR2,” Proceedings of the National Academy of Sciences of the United States of America 121(6), e2317756121 (2024). (doi:10.1073/pnas.2317756121) 8.3.1

  13. Shao, L., D. Hu, S. Zheng, T.K. Trinh, W. Zhou, H. Wang, Y. Zong, C. Li, and C.-L. Chen, “Hierarchical Self-Assembly of Multidimensional Functional Materials from Sequence-Defined Peptoids,” Angewandte Chemie International Edition 63(24), e202403263 (2024). (doi:10.1002/anie.202403263) 8.3.1

  14. Song, Y., X. Cai, M. Wang, D. Du, Y. Lin, and C.-L. Chen, “Assembly of highly efficient aqueous light-harvesting system from sequence-defined peptoids for cytosolic microRNA detection,” Nano Research 17, 788-796 (2024). (doi:10.1007/s12274-023-6008-0) 8.3.1

  15. Velagapudi, U.K., E. Rouleau-Turcotte, R. Billur, X. Shao, M. Patil, B.E. Black, J. Pascal, and T.T. Talele, “Novel modifications of PARP inhibitor veliparib increase PARP1 binding to DNA breaks,” Biochemical Journal 481(6), 437-460 (2024). (doi:10.1042/BCJ20230406) 8.3.1

  16. Weaver, J., G.B. Craven, L. Tram, H. Chen, and J. Taunton, “Aminomethyl Salicylaldehydes Lock onto a Surface Lysine by Forming an Extended Intramolecular Hydrogen Bond Network,” Journal of the American Chemical Society 146(35), 24233-24237 (2024). (doi:10.1021/jacs.4c04314) 8.3.1

  17. Zheng, R., M. Zhao, J.S. Du, T.R. Sudarshan, Y. Zhou, A.K. Paravastu, J.J. De Yoreo, A.L. Ferguson, and C.-L. Chen, “Assembly of short amphiphilic peptoids into nanohelices with controllable supramolecular chirality,” Nature Communications 15(1), 3264 (2024). (doi:10.1038/s41467-024-46839-y) 8.3.1

2023 Publications

  1. Allert, M.J., S. Kumar, Y. Wang, L.S. Beese, and H.W. Hellinga, “Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching,” Communications Chemistry 6(1), 168 (2023). (doi:10.1038/s42004-023-00982-7)

  2. Bhowmick, A., R. Hussein, I. Bogacz, P.S. Simon, M. Ibrahim, R. Chatterjee, M.D. Doyle, M.H. Cheah, T. Fransson, P. Chernev, I.-S. Kim, H. Makita, M. Dasgupta, C.J. Kaminsky, M. Zhang, J. Gätcke, S. Haupt, I. Nangca, S.M. Keable, A.O. Aydin, K. Tono, S. Owada, L.B. Gee, F.D. Fuller, A. Batyuk, R. Alonso-Mori, J.M. Holton, D.W. Paley, N.W. Moriarty, F. Mamedov, P.D. Adams, A.S. Brewster, H. Dobbek, N.K. Sauter, U. Bergmann, A. Zouni, J. Messinger, J. Kern, J. Yano, and V.K. Yachandra, “Structural evidence for intermediates during O 2 formation in photosystem II,” Nature 617(7961), 629-636 (2023). (doi:10.1038/s41586-023-06038-z)

  3. Chen, P.-Y., B.J. Huang, M. Harris, C. Boone, W. Wang, H. Carias, B. Mesiona, D. Mavrici, A.C. Kohler, G. Bollag, C. Zhang, Y. Zhang, and K. Shannon, “Structural and functional analyses of a germline KRAS T50I mutation provide insights into Raf activation,” JCI Insight 8(17), e168445 (2023). (doi:10.1172/jci.insight.168445)

  4. Demir, M., L.P. Russelburg, W.-J. Lin, C.H. Trasviña-Arenas, B. Huang, P.K. Yuen, M.P. Horvath, and S.S. David, “Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism,” Nucleic Acids Research 51(3), 1034-1049 (2023). (doi:10.1093/nar/gkac1246)

  5. Fink, E., C. Bardine, S. Gahbauer, I. Singh, T.C. Detomasi, K. White, S. Gu, X. Wan, J. Chen, B. Ary, I. Glenn, J. O’Connell, H. O’Donnell, P. Fajtová, J. Lyu, S. Vigneron, N.J. Young, I.S. Kondratov, A. Alisoltani, L.M. Simons, R. Lorenzo?Redondo, E.A. Ozer, J.F. Hultquist, A.J. O’Donoghue, Y.S. Moroz, J. Taunton, A.R. Renslo, J.J. Irwin, A. García?Sastre, B.K. Shoichet, and C.S. Craik, “Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors,” Protein Science 32(8), e4712 (2023). (doi:10.1002/pro.4712)

  6. Fricke, R., C.V. Swenson, L.T. Roe, N.X. Hamlish, B. Shah, Z. Zhang, E. Ficaretta, O. Ad, S. Smaga, C.L. Gee, A. Chatterjee, and A. Schepartz, “Expanding the substrate scope of pyrrolysyl-transfer RNA synthetase enzymes to include non-?-amino acids in vitro and in vivo,” Nature Chemistry 15(7), 960-971 (2023). (doi:10.1038/s41557-023-01224-y)

  7. Frigon, L., and J. Pascal, “Structural and biochemical analysis of the PARP1-homology region of PARP4/vault PARP,” Nucleic Acids Research 51(22), 12492-12507 (2023). (doi:10.1093/nar/gkad1064)

  8. Han, K., Z. Zhang, and F.A. Tezcan, “Spatially Patterned, Porous Protein Crystals as Multifunctional Materials,” Journal of the American Chemical Society 145(36), 19932-19944 (2023). (doi:10.1021/jacs.3c06348)

  9. Hing, Z.A., J.S. Walker, E.C. Whipp, L. Brinton, M. Cannon, P. Zhang, S. Sher, C.B. Cempre, F. Brown, P.L. Smith, C. Agostinelli, S.A. Pileri, J.N. Skinner, K. Williams, H. Phillips, J. Shaffer, L.P. Beaver, A. Pan, K. Shin, C.T. Gregory, G.H. Ozer, S.A. Yilmaz, B.K. Harrington, A.M. Lehman, L. Yu, V. Coppola, P. Yan, P. Scherle, M. Wang, P. Pitis, C. Xu, K. Vaddi, S. Chen-Kiang, J. Woyach, J.S. Blachly, L. Alinari, Y. Yang, J.C. Byrd, R.A. Baiocchi, B.W. Blaser, and R. Lapalombella, “Dysregulation of PRMT5 in chronic lymphocytic leukemia promotes progression with high risk of Richter’s transformation,” Nature Communications 14(1), 97 (2023). (doi:10.1038/s41467-022-35778-1)

  10. Hoffnagle, A.M., and F.A. Tezcan, “Atomically Accurate Design of Metalloproteins with Predefined Coordination Geometries,” Journal of the American Chemical Society 145(26), 14208-14214 (2023). (doi:10.1021/jacs.3c04047)

  11. Kissman, E.N., M.E. Neugebauer, K.H. Sumida, C.V. Swenson, N.A. Sambold, J.A. Marchand, D.C. Millar, and M.C. Chang, “Biocatalytic control of site-selectivity and chain length-selectivity in radical amino acid halogenases,” Proceedings of the National Academy of Sciences of the United States of America 120(12), e2214512120 (2023). (doi:10.1073/pnas.2214512120)

  12. Kratochvil, H.T., L.C. Watkins, M. Mravic, J.L. Thomaston, J.M. Nicoludis, N.H. Somberg, L. Liu, M. Hong, G.A. Voth, and W. DeGrado, “Transient water wires mediate selective proton transport in designed channel proteins,” Nature Chemistry 15(7), 1012-1021 (2023). (doi:10.1038/s41557-023-01210-4)

  13. Lin, C.-C., L. Wieteska, G. Poncet-Montange, K.M. Suen, S.T. Arold, Z. Ahmed, and J. Ladbury, “The combined action of the intracellular regions regulates FGFR2 kinase activity,” Communications Biology 6(1), 728 (2023). (doi:10.1038/s42003-023-05112-6)

  14. Longo, M.A., S. Roy, Y. Chen, K.-H. Tomaszowski, A.S. Arvai, J.T. Pepper, R.A. Boisvert, S. Kunnimalaiyaan, C. Keshvani, D. Schild, A. Bacolla, G.J. Williams, J.A. Tainer, and K. Schlacher, “RAD51C-XRCC3 structure and cancer patient mutations define DNA replication roles,” Nature Communications 14(1), 4445 (2023). (doi:10.1038/s41467-023-40096-1)

  15. Madani, A., B. Krause, E.R. Greene, S. Subramanian, B.P. Mohr, J.M. Holton, J.L. Olmos, C. Xiong, Z.Z. Sun, R. Socher, J.S. Fraser, and N. Naik, “Large language models generate functional protein sequences across diverse families,” Nature Biotechnology 41(8), 1099-1106 (2023). (doi:10.1038/s41587-022-01618-2)

  16. O’Herin, C.B., Y.W. Moriuchi, T.A. Bemis, A.J. Kohlbrand, M.D. Burkart, and S.M. Cohen, “Development of Human Carbonic Anhydrase II Heterobifunctional Degraders,” Journal of Medicinal Chemistry 66(4), 2789-2803 (2023). (doi:10.1021/acs.jmedchem.2c01843)

  17. Ogbu, C.P., S. Kapoor, and A.J. Vecchio, “Structural Basis of Clostridium perfringens Enterotoxin Activation and Oligomerization by Trypsin,” Toxins 15(11), 637 (2023). (doi:10.3390/toxins15110637)

  18. Russo, A.E., S. Giacopazzi, A. Deshong, M. Menon, V. Ortiz, K.M. Ego, K.D. Corbett, and N. Bhalla, “The conserved AAA ATPase PCH-2 distributes its regulation of meiotic prophase events through multiple meiotic HORMADs in C. elegans,” PLoS Genetics 19(4), e1010708 (2023). (doi:10.1371/journal.pgen.1010708)

  19. Sharma, V., V.N. Madia, V. Tudino, J.V. Nguyen, A. Debnath, A. Messore, D. Ialongo, E. Patacchini, I. Palenca, S. Basili Franzin, L. Seguella, G. Esposito, R. Petrucci, P. Di Matteo, M. Bortolami, F. Saccoliti, R. Di Santo, L. Scipione, R. Costi, and L.M. Podust, “Miconazole-like Scaffold is a Promising Lead for Naegleria fowleri-Specific CYP51 Inhibitors,” Journal of Medicinal Chemistry 66(24), 17059-17073 (2023). (doi:10.1021/acs.jmedchem.3c01898)

  20. St-Jacques, A.D., J.M. Rodriguez, M.G. Eason, S.M. Foster, S.T. Khan, A.M. Damry, N.K. Goto, M.C. Thompson, and R.A. Chica, “Computational remodeling of an enzyme conformational landscape for altered substrate selectivity,” Nature Communications 14(1), 6058 (2023). (doi:10.1038/s41467-023-41762-0)

  21. Taha, T.Y., R.K. Suryawanshi, I.P. Chen, G.J. Correy, M. McCavitt-Malvido, P.C. O’Leary, M.P. Jogalekar, M.E. Diolaiti, G.R. Kimmerly, C.-L. Tsou, R. Gascon, M. Montano, L. Martinez-Sobrido, N.J. Krogan, A. Ashworth, J.S. Fraser, and M. Ott, “A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo,” PLoS Pathogens 19(8), e1011614 (2023). (doi:10.1371/journal.ppat.1011614)

  22. Taylor, A.M., B.R. Williams, F. Giordanetto, E.H. Kelley, A. Lescarbeau, K. Shortsleeves, Y. Tang, W.P. Walters, A. Arrazate, C. Bowman, E. Brophy, E.W. Chan, G. Deshmukh, J.B. Greisman, T.L. Hunsaker, D.R. Kipp, P. Saenz Lopez-Larrocha, D. Maddalo, I.J. Martin, P. Maragakis, M. Merchant, M. Murcko, H. Nisonoff, V. Nguyen, V. Nguyen, O. Orozco, C. Owen, L. Pierce, M. Schmidt, D.E. Shaw, S. Smith, E. Therrien, J.C. Tran, J. Watters, N.J. Waters, J. Wilbur, and L. Willmore, “Identification of GDC-1971 (RLY-1971), a SHP2 Inhibitor Designed for the Treatment of Solid Tumors,” Journal of Medicinal Chemistry 66(19), 13384-13399 (2023). (doi:10.1021/acs.jmedchem.3c00483)

  23. Trinh, T.K., T. Jian, B. Jin, D.-T. Nguyen, R. Zuckermann, and C.-L. Chen, “Designed Metal-Containing Peptoid Membranes as Enzyme Mimetics for Catalytic Organophosphate Degradation,” ACS Applied Materials & Interfaces 15(44), 51191–51203 (2023). (doi:10.1021/acsami.3c11816)

  24. Wych, D.C., P.C. Aoto, L. Vu, A.M. Wolff, D.L. Mobley, J.S. Fraser, S.S. Taylor, and M.E. Wall, “Molecular-dynamics simulation methods for macromolecular crystallography,” Acta Crystallographica, Section D: Structural Biology 79(1), 50-65 (2023). (doi:10.1107/S2059798322011871)

  25. Yarmarkovich, M., Q.F. Marshall, J.M. Warrington, R. Premaratne, A. Farrel, D. Groff, W. Li, M. di Marco, E. Runbeck, H. Truong, J.S. Toor, S.M. Tripathi, S. Nguyen, H. Shen, T. Noel, N.L. Church, A. Weiner, N. Kendsersky, D. Martinez, R. Weisberg, M. Christie, L. Eisenlohr, K.R. Bosse, D.S. Dimitrov, S. Stevanovic, N.G. Sgourakis, B.R. Kiefel, and J.M. Maris, “Targeting of intracellular oncoproteins with peptide-centric CARs,” Nature 623(7988), 820-827 (2023). (doi:10.1038/s41586-023-06706-0)

  26. Yu, T., X. Luo, D. Prendergast, G.L. Butterfoss, B. Rad, N.P. Balsara, R.N. Zuckermann, and X. Jiang, “Structural Elucidation of a Polypeptoid Chain in a Crystalline Lattice Reveals Key Morphology-Directing Role of the N-Terminus,” ACS Nano 17(5), 4958-4970 (2023). (doi:10.1021/acsnano.2c12503)

  27. Zhang, S., J.J. Hettige, Y. Li, T. Jian, W. Yang, Y. Yao, R. Zheng, Z. Lin, J. Tao, J.J. De Yoreo, M. Baer, A. Noy, and C. Chen, “Co-Assembly of Carbon Nanotube Porins into Biomimetic Peptoid Membranes,” Small 19(21), 2206810 (2023). (doi:10.1002/smll.202206810)

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)