Publications 2023

Crystal structure of afRubisco

Crystal structure of afRubisco. Proteins, doi: 10.1002/prot.26431

  1. Chen P-C., Chen C., Yang Y., Maulana A.L., Jin J., Feijoo J., and Yang P. "Chemical and Structural Evolution of AgCu Catalysts in Electrochemical CO2 Reduction". J. Am. Chem. Soc., 145, 18, 10116–10125, 2023. doi: 10.1021/jacs.3c00467. Instrument: ID2A (PIPOXS)

  2. Chia J.C., Woll A.R., Smieska L., Vatamaniuk O.K. "Visualizing Metal Distribution in Plants Using Synchrotron X-R ay Fluorescence Microscopy Techniques". Methods Mol. Biol., 2665:177-189, 2023. doi: 10.1007/978-1-0716-3183-6_14. Instrument: F3 and ID3B/FMB

  3. Chia J.C., Yan J., Rahmati Ishka M., Faulkner M.M., Simons E., Huang R., Smieska L., Woll A., Tappero R., Kiss A., Jiao C., Fei Z., Kochian L.V., Walker E., Piñeros M., Vatamaniuk O.K. "Loss of OPT3 function decreases phloem copper levels and impairs crosstalk between copper and iron homeostasis and shoot-to-root signaling in Arabidopsis thaliana". Plant Cell. 2023. doi: 10.1093/plcell/koad053. Instrument:F3

  4. Chowdhury A., Manohar N., Guruprasad G., Chen A.T., Lanzaro A.,  Blanco M., Johnston K.P., Truskett T.M. "Characterizing Experimental Monoclonal Antibody Interactions and Clustering Using a Coarse-Grained Simulation Library and a Viscosity Model." J. Phys. Chem., B, 127, 5, 1120–1137, 2023. doi: 10.1021/acs.jpcb.2c07616. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  5. Chowdhury A.A., Manohar N., Witek M.A., Woldeyes M.A., Majumdar R., Qian K.K., Kimball W.D., Xu S., Lanzaro A., Truskett T.M. and Johnston K.P. "Subclass Effects on Self-Association and Viscosity of Monoclonal Antibodies at High Concentrations." Mol. Pharmaceutics., 20, 6, 2991–3008, 2023. doi: 10.1021/acs.molpharmaceut.3c00023. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  6. Combs J., Bozdag M., Cravey L. D., Kota A., McKenna R., Angeli A., Carta F., & Supuran C. T. "New Insights into Conformationally Restricted Carbonic Anhydrase Inhibitors". Molecules, 28, 2, Article 2. 2023. doi: 10.3390/molecules28020890. Instrument: ID7B2 (HPBio MX & FlexX)

  7. Cui G., Botuyan M.V., Drané P., Hu Q., Bragantini B., Thompson J.R., Schuller D.J., Detappe A., Perfetti M.T., James L.I., Frye S.V., Chowdhury D., Mer G. "An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering." bioRxiv preprint, 2023. doi: 10.1101/2023.04.20.534960.  Instrument: A1

  8. Eilers G., Gupta K., Allen A., Montermoso S., Murali H., Sharp R., Hwang Y., Bushman F. D., & Van Duyne G. "Structure of a HIV-1 IN-Allosteric inhibitor complex at 2.93 Å resolution: Routes to inhibitor optimization". PLoS Pathogens, 19, 3, 2023. doi: 10.1371/journal.ppat.1011097. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  9. Ford R.R., Gilbert P.H., Gillilan R., Huang Q., Donnelly R., Qian K.K., Allen D.P., Wagner N.J., Liu Y. "Micelle Formation and Phase Separation of Poloxamer 188 and Preservative Molecules in Aqueous Solutions Studied by Small Angle X-ray Scattering". J Pharm Sci., 112, 3, 731-739, 2023. doi: 10.1016/j.xphs.2022.09.019. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  10. Ghosh D. "Structures and functions of human placental aromatase and steroid sulfatase, two key enzymes in estrogen biosynthesis." Steroids, 196, 109249, 2023. doi: 10.1016/j.steroids.2023.109249. Instrument: A1, F2

  11. Guerrero L., Ebrahim A., Riley B.T., Kim M., Huang Q., Finke A.D., Keedy D.A. "Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase". bioRxiv, 2023. doi: 10.1101/2023.05.02.538097 Instrument: ID7B2 (HPBio MX & FlexX)

  12. Huang Q., Szebenyi D.M.E. "Crystal structure of a type III Rubisco in complex with its product 3-phosphoglycerate". Proteins, 91, 3, 330-337, 2023. doi: 10.1002/prot.26431. Instrument: ID7B2 (HPBio MX & FlexX)

  13. Huang Q., Szebenyi  D.M.E. "The alarmone ppGpp selectively inhibits the isoform A of the human small GTPase Sar1". Proteins, 91, 4, 518-531, 2023. doi: 10.1002/prot.26445. Instrument: A1, F1, ID7A1 (HP BioSAXS & BioSAXS)

  14. Huang X., Suit E., Zhu J., Ge B., Gerdes F., Klinke C., Wang Z. "Diffusion-Mediated Nucleation and Growth of fcc and bcc Nanocrystal Superlattices with Designable Assembly of Freestanding 3D Supercrystals". J Am Chem Soc.,145, 8, 4500-4507, 2023. doi: 10.1021/jacs.2c11120. Instrument: ID7B2 (HPBio MX & FlexX), B2

  15. Illava G., Gillilan R., Ando N. "Development of in-line anoxic small-angle X-ray scattering and structural characterization of an oxygen-sensing transcriptional regulator". J. Biol. Chem., 105039, 2023. doi: 10.1016/j.jbc.2023.105039. Instrument: ID7B2 (HPBio MX & FlexX)

  16. Jakkampudi T., Lin Q., Mitra S., Vijai A., Qin W., Kang A., Chen J., Ryan E., Wang R., Gong Y., Heinrich F., Song J., Di Y-P. (P). and Tristram-Nagle S. "Lung SPLUNC1 Peptide Derivatives in the Lipid Membrane Headgroup Kill Gram-Negative Planktonic and Biofilm Bacteria". Biomacromolecules, 24, 6, 2804–2815, 2023. doi: 10.1021/acs.biomac.3c00218. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  17. Kautzsch K., Ortiz B. R., Mallayya K., Plumb J., Pokharel G., Ruff J.P.C., Islam Z., Kim E-A., Seshadri R., and Wilson S.D. "Structural evolution of the kagome superconductors AV3Sb5 (A = K, Rb, and Cs) through charge density wave order". Phys. Rev. Materials 7, 024806, 2023. doi: 10.1103/PhysRevMaterials.7.024806 Instrument:: ID4B (QM2) 

  18. Liu D., Feng S., Huang Q., Sun S., Dong G., Long F., Milazzo M., and Wang M. "Soft, Strong, Tough, and Durable Bio-Hydrogels Via Maximizing Elastic Entropy". Adv. Funct. Mater., 2023. doi: 10.1002/adfm.202300426 Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  19. McPherson K.S., Rizzo A.A., Erlandsen H., Chatterjee N., Walker G.C., Korzhnev D.M. "Evolution of Rev7 interactions in eukaryotic TLS DNA polymerase Polζ". J. Biol. Chem., 299(2):102859, 2023. doi: 10.1016/j.jbc.2022.102859. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  20. McLeod M.J., Tran N., McCluskey G.D., Gillis T.D., Bearne S.L., Holyoak T. "A metal-dependent conformational change provides a structural basis for the inhibition of CTP synthase by gemcitabine-5′-triphosphate." Wiley Online Library, 2023. doi: 10.1002/pro.4648. Instrument: ID7B2 (HPBio MX & FlexX)

  21. Meisburger S.P., Ando N. "Processing macromolecular diffuse scattering data." 2023. bioRxiv preprint. doi: 10.1101/2023.06.04.543637. Instrument: F1

  22. Meisburger S.P., Case D.A., Ando N. "Robust total X-ray scattering workflow to study correlated motion of proteins in crystals". Nat. Commun., 14, 1, 1228, 2023. doi: 10.1038/s41467-023-36734-3. Instrument: ID7B2 (HPBio MX & FlexX)

  23. Mitra S., Coopershlyak M., Li Y., Chandersekhar B., Koenig R., Chen M-T., Evans B., Heinrich F., Deslouches B., Tristram-Nagle S. "Novel Helical Trp- and Arg-Rich Antimicrobial Peptides Locate Near Membrane Surfaces and Rigidify Lipid Model Membranes." Wiley Online Library, 2023. doi: 10.1002/anbr.202300013. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  24. Page C.G., Cao J., Oblinsky D.G., MacMillan S.N., Dahagam S., Lloyd R.M., Charnock S.J., Scholes G.D. and Hyster T.K. "Regioselective Radical Alkylation of Arenes Using Evolved Photoenzymes". J. Am. Chem. Soc., 145, 21, 11866–11874, 2023. doi: 10.1021/jacs.3c03607.  

  25. Shao Z., Schnitzer N., Ruf J., Gorobtsov O.Y., Dai C., Goodge B.H., Yang T., Nair H., Stoica V.A., Freeland J.W., Ruff J.P., Chen L-Q., Schlom D.G., Shen K.M., Kourkoutis L.F., Singer A. "Real-space imaging of periodic nanotextures in thin films via phasing of diffraction data." Proc. Natl. Acad. Sci USA, 120(28):e2303312120, 2023. doi: 10.1073/pnas.2303312120. 

  26. Sharma S., Ebrahim A., & Keedy D. A. "Room-temperature serial synchrotron crystallography of the human phosphatase PTP1B". Acta Crystallographica Section F: Structural Biology Communications, 79, 1, Article 1, 2023. doi: 10.1107/S2053230X22011645. Instrument: ID7B2 (HPBio MX & FlexX)

  27. Tang Q., Gulkis M., Çağlayan M. "Structures of LIG1 uncover the mechanism of sugar discrimination against a ribonucleotide at 3’- and 5’-end of the nick DNA." Preprint:bioRxiv, doi: 10.1101/2022.08.26.505476. Instrument: ID7B2 (HPBio MX & FlexX)

  28. Tei R., Bagde S.R., Fromme J.C. & Baskin J.M. "Activity-based directed evolution of a membrane editor in mammalian cells." Nature Chemistry, 15, 1030–1039, 2023. doi:10.1038/s41557-023-01214-0. Instrument: ID7B2 (HPBio MX & FlexX)

  29. Wang J., Koduru T., Harish B., McCallum S.A., Larsen K.P., Patel K.S., Peters E.V., Gillilan R.E., Puglisi E.V., Puglisi J.D., Makhatadze G., Royer C.A. "Pressure pu shes tRNALys3 into excited conformational states." PNAS, 120, 9, 26, e2215556120, 2023. doi: 10.1073/pnas.2215556120. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  30. Watkins M.B., Wang H., Burnim A. and Ando N. "Conformational switching and flexibility in cobalamin-dependent methionine synthase studied by small-angle X-ray scattering and cryoelectron microscopy". PNAS, 120 (26), 2023. doi:10.1073/pnas.2302531120. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  31. Wittenborn E.C., Thomas W.C., Houghton K.A., Wirachman E.S., Wu Y., and Marletta M.A. "Role of the Coiled-Coil Domain in Allosteric Activity Regulation in Soluble Guanylate Cyclase." Biochemistry, 62, 10, 1568–1576, 2023. doi: 10.1021/acs.biochem.3c00052. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  32. Yang Y., Louisia S., Yu S., Jin J., Roh I., Chen C., Fo Wang C., Muller D.A., Abruña H.D., Yang P. "Operando studies reveal active Cu nanograins for CO2 electroreduction". Nature, 614, 7947, 262-269, 2023. doi: 10.1038/s41586-022-05540-0.  Instrument: ID2A (PIPOXS)

  33. Zhang M., Liu Y., Zuo X., Qian S., Pingali S.V., Gillilan R.E., Huang Q., and Zhang D. "pH-Dependent Solution Micellar Structure of Amphoteric Polypeptoid Block Copolymers with Positionally Controlled Ionizable Sites". Biomacromolecules, 2023. doi: 10.1021/acs.biomac.3c00407. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  34. Zhu Z., Goel P. N., Zheng C., Nagai Y., Lam L., Samanta A., Ji M., Zhang H., & Greene M. I. "HED, a Human-Engineered Domain, Confers a Unique Fc-Binding Activity to Produce a New Class of Humanized Antibody-like Molecules". International Journal of Molecular Sciences, 24,7, Article 7, 2023.doi: 10.3390/ijms24076477. Instrument: A1

  35. Zielinski K.A., Katz A.M., Calvey G.D., Pabit S.A., Milano S.K., Aplin C., Emeterio J.S., Cerione R.A., and Pollack L. "Chaotic advection mixer for capturing transient states of diverse biological macromolecular systems with time-resolved small-angle X-ray scattering." IUCr J., 10, 3, 363-375, 2023.  doi: 10.1107/S2052252523003482. Instrument: ID7A1 (HP BioSAXS & BioSAXS)