Publications 2023

Crystal structure of afRubisco

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

  1. Biswas S., Hecht A.L., Noble S.A., Huang Q., Gillilan R.E., Xu A.Y. "Understanding the Impacts of Molecular and Macromolecular Crowding Agents on Protein-Polymer Complex Coacervates." Biomacromolecules, 24, 11, 4771-4782, 2023. doi: 10.1021/acs.biomac.3c00545. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  2. Chen C, Tang W, Chen X, Kang Z, Ding S, Scott K, Wang S, Li Z, Ruff JPC, Hashimoto M, Lu DH, Jozwiak C, Bostwick A, Rotenberg E, da Silva Neto EH, Birgeneau RJ, Chen Y, Louie SG, Wang Y, He Y. "Anomalous excitonic phase diagram in band-gap-tuned Ta2Ni(Se,S)5 ". Nat. Commun. 14, 7512, 2023. doi: 10.1038/s41467-023-43365-1. Instrument:: ID4B (QM2)

  3. 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)

  4. 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)

  5. 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

  6. 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)

  7. 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)

  8. 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)

  9. 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." Nat. Commun., 14, 1, 6091, 2023. doi: 10.1038/s41467-023-41821-6. Instrument: A1

  10. 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)

  11. Feijóo J., Yang Y., Fonseca Guzman M.V., Vargas A., Chen C., Pollock C.J., Yang P. "Operando High-Energy-Resolution X-ray Spectroscopy of Evolving Cu Nanoparticle Electrocatalysts for CO2 Reduction." J. Am. Chem. Soc., 145, 37, 20208-20213, 2023. doi: 10.1021/jacs.3c08182. Instrument: ID2A (PIPOXS)

  12. 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)

  13. 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

  14. 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)

  15. Gustafson S.E., Ludwig W., Rodriguez-Lamas R., Yildirim C., Shanks K.S., Detlefs C., Sangid M.D. "Revealing 3D intragranular micromechanical fields at triple junctions". Acta Materialia, 260, 2023. doi: 10.1016/j.actamat.2023.119300. 

  16. 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)

  17. 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)

  18. 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

  19. 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., 299, 8, 105039, 2023. doi: 10.1016/j.jbc.2023.105039. Instrument: ID7B2 (HPBio MX & FlexX)

  20. 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)

  21. 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)

  22. Lee E., McLeod M.J., Redzic J.S., Marcolin B., Thorne R.E., Agarwal P., Eisenmesser E.Z. "Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle." Front Mol. Biosci., 2023; 10: 1244587, 2023. doi: 10.3389/fmolb.2023.1244587. Instrument: ID7B2 (HPBio MX & FlexX)

  23. Li Y., Li Q., Gillilan R.E., Abbaspourrad A. "Reversible disassembly-reassembly of C-phycocyanin in pressurization-depressurization cycles of high hydrostatic pressure". Int. J. Biol Macromol, 253, Pt. 8, 127623. doi: 10.1016/j.ijbiomac.2023.127623. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  24. 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)

  25. 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)

  26. 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)

  27. Meisburger S.P., Ando N. "Processing macromolecular diffuse scattering data." Methods Enzymol., 688, 43-86, 2023. doi: 10.1016/bs.mie.2023.06.010. Instrument: F1

  28. 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)

  29. 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)

  30. 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.  

  31. Pei X., Bhatt N., Wang H., Ando N., Meisburger S.P. "Introduction to diffuse scattering and data collection." Methods Enzymol., 688, 1-42, 2023. doi: 10.1016/bs.mie.2023.07.007. Instrument: ID7B2 (HPBio MX & FlexX)

  32. Pollock C.J., Debefve L.M. " Resonant Excitation Unlocks Chemical Selectivity of Platinum Lβ Valence-to-Core X-ray Emission Spectra." Inorg. Chem., 62, 34,13681-13691, 2023. doi: 10.1021/acs.inorgchem.3c01930. Instrument: ID2A (PIPOXS)

  33. 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." PNAS USA, 120, 28, 2023. doi: 10.1073/pnas.2303312120. Instrument: A2

  34. 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)

  35. Smieska L., Guerinot M.L., Olson Hoal K., Reid M., Vatamaniuk O. "Synchrotron science for sustainability: life cycle of metals in the environment." Metallomics. 15, 8, 2023. doi: 10.1093/mtomcs/mfad041

  36. 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)

  37. 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)

  38. Tran, N., Dasari, S., Barwell, S.A.E., McLeod M.J., Kalyaanamoorthy S., Holyoak T., Ganesan A. "The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease". Nat Commun 14, 5625. 2023. doi.org: 10.1038/s41467-023-40023-4. Instrument: ID7B2 (HPBio MX & FlexX)

  39. Vatamaniuk M.Z., Huang R., Zhao Z., Lei X.G. "SXRF for Studying the Distribution of Trace Metals in the Pancreas and Liver". Antioxidants (Basel), 1, 12, 4, 846, 2023. doi: 10.3390/antiox12040846. Instrument:F3

  40. 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 pushes tRNALys3 into excited conformational states." PNAS, 120, 9, 26, e2215556120, 2023. doi: 10.1073/pnas.2215556120. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  41. 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)

  42. 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)

  43. 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)

  44. Yang Y., Shao Y.T., Abruña H.D., Muller D.A., Yang P. "Operando Electrochemical Liquid-Cell 4D-STEM Studies of Dynamic Evolution of Cu Nanocatalysts for CO2 Reduction." Microscopy and Microanalysis, 29, 1, 1300–1301, 2023. doi: 10.1093/micmic/ozad067.665. Instrument: ID2A (PIPOXS)

  45. Xu W., Lang S., Wang K., Zeng R., Li H., Feng X., Krumov M.R., Bak S.M., Pollock C.J., Yeo J., Du Y., Abruña H.D. "Fundamental mechanistic insights into the catalytic reactions of Li─S redox by Co single-atom electrocatalysts via operando methods." Sci., Adv., 9, 33, 2023. doi: 10.1126/sciadv.adi5108. Instrument: ID2A (PIPOXS)

  46. 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)

  47. 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

  48. 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)

  49. Thomas Keller, Dylan Barbagallo, Natalya Sheremetyeva, Tushar Kanti Ghosh, Katherine S. Shanks, Geoffroy Hautier, Ian Baker. "The phase transformation behavior of Mn-Al rare-earth-free permanent magnets" Journal of Magnetism and Magnetic Materials,Volume 587,2023,171331,ISSN 0304-8853, https://doi.org/10.1016/j.jmmm.2023.171331

  50. Dalton Shade; Exploring Grain-scale Cyclic Deformation by Coupling High Energy X-ray Diffraction with Signatures; December 2023

  51. Cheng Chen, Xiang Chen, Weichen Tang, Zhenglu Li, Siqi Wang, Shuhan Ding, Chris Jozwiak, Aaron Bostwick, Eli Rotenberg, Makoto Hashimoto, Donghui Lu, Jacob PC Ruff, Steven G Louie, Robert Birgeneau, Yulin Chen, Yao Wang, Yu He; Lattice fluctuation induced pseudogap in quasi-one-dimensional Ta2NiSe5; Physical Review Research 5, 043089 (2023); https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.5.043089

  52. Shunran Li, Xian Xu, Conrad A. Kocoj, Chenyu Zhou, Yanyan Li, Du Chen, Joseph A. Bennett, Sunhao Liu, Lina Quan, Suchismita Sarker, Mingzhao Liu, Diana Y. Qiu & Peijun Guo; Large exchange-driven intrinsic circular dichroism of a chiral 2D hybrid perovskite; Nat Commun 15, 2573 (2024). https://doi.org/10.1038/s41467-024-46851-2

  53. K. Saini, A. N. Nair, A. Yadav, L. G. Enriquez, C. J. Pollock, S. D. House, S. Yang, X. Guo, S. T. Sreenivasan, Nickel-Based Single-Molecule Catalysts with Synergistic Geometric Transition and Magnetic Field-Assisted Spin Selection Outperform RuO2 for Oxygen Evolution. Adv. Energy Mater. 2023, 13, 2302170. https://doi.org/10.1002/aenm.202302170

  54. Tran, N., Dasari, S., Barwell, S.A.E. et al. The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease. Nat Commun 14, 5625 (2023). https://doi.org/10.1038/s41467-023-40023-4