Publications 2022

F2 beamline

Schematic illustration of the experimental setup for the in-situ high-energy X-ray diffraction measurements during uniaxial tensile loading at the F2 beamline, CHESS, Ithaca, USA.

  1. Allsopp R., Pavlova A., Cline T., Salyapongse A.M., Gillilan R.E., Di Y.P., Deslouches B., Klauda J.B., Gumbart J.C., Tristram-Nagle S. "Antimicrobial Peptide Mechanism Studied by Scattering-Guided Molecular Dynamics Simulation."J. Phys. Chem. B., 126, 36, 6922-6935, 2022. doi: 10.1021/acs.jpcb.2c03193. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  2. Aplin C., Milano S.K., Zielinski K.A., Pollack L., and Cerione R.A. "Evolving Experimental Techniques for Structure-Based Drug Design." J. Phys. Chem.,  B, 126, 35, 6599–6607, 2022. doi: 10.1021/acs.jpcb.2c04344. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  3. Barrit D, Tang MC, Munir R, Li R, Zhao K, Smilgies DM. "Processing of Lead Halide Perovskite Thin Films Studied with In-Situ Real-Time X-ray Scattering". ACS Appl Mater Interfaces. 2022. doi: 10.1021/acsami.2c03153. Instrument: D1

  4. Bonardi A., Bua S., Combs J., Lomelino C., Andring J., Osman S. M., Toti A., Di Cesare Mannelli L., Gratteri P., Ghelardini C., McKenna R., Nocentini A., & Supuran C. T. "The three-tails approach as a new strategy to improve selectivity of action of sulphonamide inhibitors against tumour-associated carbonic anhydrase IX and XII". Journal of Enzyme Inhibition and Medicinal Chemistry, 37, 1, 930–939, 2022. doi: 10.1080/14756366.2022.2053526. Instrument: F1

  5. Bozdag M., Cravey L., Combs J., Kota A., McKenna R., Angeli A., Selleri S., Carta F., & Supuran C. T. "Small Molecule Alkoxy Oriented Selectiveness on Human Carbonic Anhydrase II and IX Inhibition". ChemMedChem, 17, 11, 2022. doi: 10.1002/cmdc.202200148. Instrument: F1

  6. Burnim A.A., Spence M.A., Xu D., Jackson C.J. & Ando N. "Comprehensive phylogenetic analysis of the ribonucleotide reductase family reveals an ancestral clade. eLife 11, e79790, 2022. doi: 10.7554/eLife.79790 Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  7. Caglayan M., Tang Q., Gulkis M. "Structures of LIG1 uncover a lack of sugar discrimination against a ribonucleotide at the 3'-end of nick DNA", Research Square preprint, 2022. doi:10.21203/rs.3.rs-1998177/v1. Instrument: ID7B2 (HPBio MX & FlexX)

  8. Gibson J.M., Cui H., Ali M.Y., Zhao X., Debler E.W., Zhao J., Trybus K.M., Solmaz R., Wang C. "Coil-to-α-helix transition at the Nup358-BicD2 interface activates BicD2 for dynein recruitment." Structural Biology and Molecular Biophysics, 2022. doi: 10.7554/eLife.74714. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  9. Dass A., Gabourel A., Pagan D., Moridi A. " Laser based directed energy deposition system for operando synchrotron x-ray experiments". Rev. Sci. Instrum., 93, 7, 075106, 2022. doi:10.1063/5.0081186. Instrument: ID3A (FAST)

  10. Doll S.G., Meshkin H., Bryer A.J., Li F., Ko Y.H., Lokareddy R.K., Gillilan R.E., Gupta K., Perilla J.R., Cingolani G. "Recognition of the TDP-43 nuclear localization signal by importin α1/β." Cell Rep., 28, 39, 13, 111007, 2022. doi:10.1016/j.celrep.2022.111007. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  11. Philipp H.T., Tate M.W., Shanks K.S., Mele L., Peemen M., Dona P., Hartong R., van Veen G., Shao Y.T., Chen Z., Thom-Levy J., Muller D.A., Gruner S.M. "

  12. Florio T.J., Lokareddy R.K., Yeggoni D.P., Sankhala R.S., Ott C.A., Gillilan R.E., Cingolani G. "Differential recognition of canonical NF-κB dimers by Importin α3". Nat. Commun., 8, 13, 1, 1207, 2022. doi: 10.1038/s41467-022-28846-z . Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  13. Frontini F, Lebert BW, Cho KK, Song MS, Cho BK, Pollock CJ, Kim YJ. "Intermediate valence state in YbB4revealed by resonant x-ray emission spectroscopy." J. Phy.s Condens. Matter., 34, 34, 2022. doi: 10.1088/1361-648X/ac7629. Instrument: ID2A (PIPOXS)

  14. Gillilan R.E. "High-pressure SAXS, deep life, and extreme biophysics". Methods in Enzymology (Academic Press, 2022. doi:10.1016/bs.mie.2022.08.025. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  15. Huang Q, Szebenyi D.M.E. "Crystal structure of a type III Rubisco in complex with its product 3-phosphoglycerate." Proteins, 1- 8, 2022. doi.org/10.1002/prot.26431. Instrument: F1

  16. 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, 2022. doi: 10.1002/prot.26445. Instrument: A1, F1, ID7A1 (HP BioSAXS & BioSAXS)

  17. Kozlov G., Mattijssen S., Jiang J., Nyandwi S., Sprules T., Iben J. R., Coon, S. L., Gaidamakov S., Noronha A. M., Wilds C. J., Maraia R. J., & Gehring K. "Structural basis of 3’-end poly(A) RNA recognition by LARP1". Nucleic Acids Research, 50, 16, 9534–9547. 2022. doi: 10.1093/nar/gkac696. Instrument: ID7B2 (HPBio MX & FlexX)

  18. Lim R.E., Pagan D.C., Bernier J.V., Shade P.A., Rollett A.D. "Grain reorientation and stress-state evolution during cyclic loading of an α-Ti alloy below the elastic limit". International Journal of Fatigue, 156, 106614, 2022. doi:10.1016/j.ijfatigue.2021.106614 Instrument: F2

  19. Lisitskaya L., Shin Y., Agapov A., Olina A., Kropocheva E., Ryazansky S., Aravin A.A., Esyunina D., Murakami K.S.,  & Kulbachinskiy A. "Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity." Nature Communications, 13, 4624, 2022. doi: 10.1038/s41467-022-32079-5. Instrument: ID7B2 (HPBio MX & FlexX)

  20. Lokareddy R.K., Hou C-F.D., Doll S.G., Li F., Gillilan R.E., Forti F., Horner D.S., Briani F., Cingolani G. "Terminase Subunits from the Pseudomonas-Phage E217". J. Mol. Biol., 167799, 2022. doi: 10.1016/j.jmb.2022.167799. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  21. Lussier-Price M., Wahba H. M., Mascle X. H., Cappadocia L., Bourdeau V., Gagnon C., Igelmann S., Sakaguchi K., Ferbeyre G., & Omichinski J. G. "Zinc controls PML nuclear body formation through regulation of a paralog specific auto-inhibition in SUMO1". Nucleic Acids Research, 50, 4, 8331–8348, 2022. doi: 10.1093/nar/gkac620. Instrument: F1

  22. Lv B.Q., Zong A., Wu D., Rozhkov A.V., Fine B.V., Chen S.D., Hashimoto M., Lu D.H., Li M., Huang Y.B., Ruff J.P.C., Walko D.A., Chen Z.H., Hwang I., Su Y., Shen X., Wang X., Han F., Po H.C., Wang Y., Jarillo-Herrero P., Wang X., Zhou H., Sun C.J., Wen H., Shen Z.X., Wang N.L., Gedik N. "Unconventional Hysteretic Transition in a Charge Density Wave". Phys Rev Lett., 128, 3, 036401, 2022. doi: 10.1103/PhysRevLett.128.036401. 

  23. Marshall C. J., Qayyum M. Z., Walker J. E., Murakami K. S., & Santangelo T. J. "The structure and activities of the archaeal transcription termination factor Eta detail vulnerabilities of the transcription elongation complex". Proceedings of the National Academy of Sciences, 119, 32, 2022. doi: /10.1073/pnas.2207581119. Instrument: F1

  24. Maschmann Z. A., Chua T. K., Chandrasekaran S., Ibáñez H., & Crane B. R. "Redox properties and PAS domain structure of the Escherichia coli energy sensor Aer indicate a multistate sensing mechanism. Journal of Biological Chemistry", 298, 12, 102598, 2022. doi: 10.1016/j.jbc.2022.102598 Instrument: ID7B2 (HPBio MX & FlexX)

  25. Meisburger S.P., Case D.A., Ando N. "Robust total X-ray scattering workflow to study correlated motion of proteins in crystals".  bioRxiv preprint, 2022. doi:10.1101/2022.08.22.504832. Instrument: ID7B2 (HPBio MX & FlexX)

  26. Milano S.K., Huang Q., Nguyen T-T.T, Ramachandran S., Finke A., Kriksunov I., Schuller D.J., Szebenyi D.M., Arenholz E., McDermott L.E., Sukumar N., CerioneR.A., and Katt W.P. "New insights into the molecular mechanisms of glutaminase C inhibitors in cancer cells using serial room temperature crystallography" J. Biol. Chem., 298, 101535; 2022. doi:10.1016/j.jbc.2021.101535 Instrument: ID 7B2 (HPBio MX & FlexX)

  27. Milano S.K., Szebenyi M.D., Cerione A.R.A. "Serial Room Temperature Crystal Loading, Data Collection, and Data Processing of Human Glutaminase C in Complex with Allosteric Inhibitors." Bio. Protoc., 2022. doi: 10.21769/BioProtoc.4509. Instrument: ID 7B2 (HPBio MX & FlexX)

  28. Miller R.C., Cummings C., Huang Q., Ando N., Gillilan R.E. "Inline small-angle X-ray scattering-coupled chromatography under extreme hydrostatic pressure". Protein Science, 31, 2022. doi:10.1002/pro.4489 Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  29. Narayanan A., Narwal M., Majowicz S. A., Varricchio C., Toner S. A., Ballatore C., Brancale A., Murakami K. S., & Jose J. "Identification of SARS-CoV-2 inhibitors targeting Mpro and PLpro using in-cell-protease assay". Communications Biology, 5, 1, Article 1, 2022. doi: 10.1038/s42003-022-03090-9. Instrument: ID 7B2 (HPBio MX & FlexX)

  30. Neding B, Pagan DC, Hektor J, Hedström P. "Formation of Dislocations and Stacking Faults in Embedded Individual Grains during In Situ Tensile Loading of an Austenitic Stainless Steel". Materials (Basel), 14, 20, 5919, 2022. doi: 10.3390/ma14205919. Instrument: ID3A (FAST)

  31. Neding B., Tian Y., Ko L.Y.P., Hedström P.  "Correlating temperature-dependent stacking fault energy and in-situ bulk deformation behavior for a metastable austenitic stainless steel". Materials Science and Engineering: A, 832, 142403, 2022. doi:10.1016/j.msea.2021.142403 Instrument: ID3A (FAST)

  32. Nguyen P., Eshaque R., Garland B. A., Dang A., & Suits M. D. L. "Degradation of chondroitin sulfate A by a PUL-like operon in Tannerella forsythia". PLOS ONE, 17, 9, 2022. doi:10.1371/journal.pone.0272904. Instrument: ID 7B2 (HPBio MX & FlexX)

  33. Pedrini B., Finke A.D., Marsh M., Luporini P., Vallesi A., Alimenti C. "Crystal structure of the pheromone Er-13 from the ciliate Euplotes raikovi, with implications for a protein-protein association model in pheromone/receptor interactions". J. Struct. Biol., 214(1):107812, 2022. doi: 10.1016/j.jsb.2021.107812

  34. Osipov E. M., Munawar A. H., Beelen S., Fearon D., Douangamath A., Wild C., Weeks S. D., Aerschot A. V., Delft F. von, & Strelkov V. S. "Discovery of novel druggable pockets on polyomavirus VP1 through crystallographic fragment-based screening to develop capsid assembly inhibitors". RSC Chemical Biology, 3, 8, 1013–1027, 2022. doi: 10.1039/D2CB00052K. Instrument: ID F1

  35. Park K.C., Martin C.R., Leith G.A., Thaggard G.C., Wilson G.R., Yarbrough B.J., Kankanamalage B.K.P.M, Kittikhunnatham P., Mathur A., Jatoi I., Manzi M.A., Lim J., Lehman-Andino I., Hernandez-Jimenez A., Amoroso J.W., DiPrete D.P., Liu Y., Schaeperkoetter J., Misture S.T, Phillpot S.R., Hu S., Li Y., Leydier A., Proust V., Grandjean A., Smith M.D., and Shustova N.B. "Capture Instead of Release: Defect-Modulated Radionuclide Leaching Kinetics in Metal–Organic Frameworks" Journal of the American Chemical Society, 144 (35), 16139-16149, 2022. doi: 10.1021/jacs.2c06905. Instrument: ID2A (PIPOXS)

  36. Schneps C.M., Ganguly A., and Crane B.R. "Room-temperature serial synchrotron crystallography of Drosophila cryptochrome." Acta Cryst., D78, 975-985, 2022. doi:10.1107/S2059798322007008 Instrument: ID7B2 (HPBio MX & FlexX)

  37. Sharma S., Ebrahim A., Keedy D.A. "Room-temperature serial synchrotron crystallography of apo PTP1B". bioRxiv preprint, 2022. doi:10.1101/2022.07.28.501725. Instrument: ID7B2 (HPBio MX & FlexX)

  38. Stinville J.C., Hestroffer J.M., Charpagne M.A., Polonsky A.T., Echlin M.P., Torbet C.J., Valle V., Nygren K.E., Miller M.P., Klaas O., Loghin A., Beyerlein I.J., Pollock T.M. "Multi-modal Dataset of a Polycrystalline Metallic Material: 3D Microstructure and Deformation Fields". Sci. Data., 9,1,460, 2022. doi:10.1038/s41597-022-01525-w.

  39. Tang Q., Gulkis M., McKenna R. & Caglayan M. "Structures of LIG1 that engage with mutagenic mismatches inserted by polβ in base excision repair". Nature Communications, 13, 3860, 2022. doi:10.1038/s41467-022-31585-w Instrument: ID7B2 (HPBio MX & FlexX)

  40. Tei R., Bagde S.K., Fromme J.C., Baskin J.M. "Activity-based directed evolution of a membrane editor in mammalian cells". bioRxiv preprint, 2022. doi:10.1101/2022.09.26.509516. Instrument: ID7B2 (HPBio MX & FlexX)

  41. Thompson, K.D., Danielson E.P., Peterson K.N., Nocevski N.O., Boock J.T. and Berberich J.A. "The Amphoteric Surfactant N,N-Dimethyldodecylamine N-Oxide Unfolds β-Lactoglobulin above the Critical Micelle Concentration". Langmuir, 38, 4090–4101, 2022. doi:10.1021/acs.langmuir.2c00172 Instrument: ID7A1 (HP BioSAXS & BioSAXS) ​

  42. Tran N., Dasari S., Barwell S., McLeod M.J., Kalyaanamoorthy S., Holyoak T., Ganesan A. "The H163A Mutation Unravels an Oxidized Conformation of the SARS-CoV-2 Main Protease and Opens a New Avenue for Anti-Viral Therapeutic Design." Preprint: bioRxiv, 2022. doi: 10.1101/2022.12.16.520794. Instrument: ID7B2 (HPBio MX & FlexX)

  43. Trewhella J., Vachette P., Bierma J., Blanchet C., Brookes E., Chakravarthy S., Chatzimagas L., Cleveland T.E. IV., Cowieson N., Crossett B., Duff A.P., Franke D., Gabel F., Gillilan R.E., Graewert M., Grishaev A., Guss J.M., Hammel M., Hopkins J., Huang Q., Hub J.S., Hura G.L., Irving T.C., Jeffries C.M., Jeong C., Kirby N., Krueger S., Martel A., Matsui T., Li N., Pérez J., Porcar L., Prangé T., Rajkovic I., Rocco M., Rosenberg D.J., Ryan T.M., Seifert S., Sekiguchi H., Svergun D., Teixeira S., Thureau A., Weiss T.M., Whitten A.E., Wood K.  and Zuow X. "A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking". Acta Crystallographica, D 78, 2022. doi: 10.1107/S2059798322009184 Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  44. Triantafyllou C., Pagan D.C., McBride A. "Quantifying the effect of macrozones on the cold-dwell fatigue response of UD-rolled Ti-6Al-4V using high-energy X-ray diffraction". Materials Science and Engineering, A, 834, 142498, 2022. doi:10.1016/j.msea.2021.142498 Instrument: F2

  45. Venderley J., Mallayya K., Matty M., Krogstad M., Ruff J., Pleiss G., Kishore V., Mandrus D., Phelan D., Poudel L., Wilson A.G., Weinberger K., Upreti P., Norman M., Rosenkranz S., Osborn R., Kim E.A. "Harnessing interpretable and unsupervised machine learning to address big data from modern X-ray diffraction". PNAS USA. 119, 24,119, 2022. doi:10.1073/pnas.2109665119 Instrument: ID4B (QM2) 

  46. Wang J., Zhang S., Zeghouf M., Cherfils J., McCallum A.A., Richard E.Gillilan R.E., Royer C.A. "Pressure study reveals conformational landscapes and structural transitions of small GTPase". Biophysical Journal, 121, 3, 1, 181a, 2022. doi:10.1016/j.bpj.2021.11.1833 Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  47. Xiao T., NagaokaY., WangX., JiangT., LaMontagne  D., Zhang  Q.,  Cao  C., Diao  X., Qiu  J.,  Lu  Y., Wang Z.,  Cao   Y. C. "Nanocrystals with metastable high-pressure phases under ambient conditions". Science, 9, 377, 6608:870-874, 2022. doi: 10.1126/science.abq7684  Instrument: B2

  48. Xing H., Rodger A., Comer J., Picco A.S., Huck-Iriart C., Ezell E.L., and Conda-Sheridan M. "Urea-Modified Self-Assembling Peptide Amphiphiles That Form Well-Defined Nanostructures and Hydrogels for Biomedical Applications."ACS Appl. Bio Mater, 5, 10, 4599–4610, 2022. doi: 10.1021/acsabm.2c00158. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  49. Xu A.Y., Clark N.J., Pollastrini J., Espinoza M., Kim H-J., Kanapuram S., Kerwin B., Treuheit M.J., Krueger S., McAuley A. and Curtis J.E. "Effects of Monovalent Salt on Protein-Protein Interactions of
    Dilute and Concentrated Monoclonal Antibody Formulations". Antibodies, 11, 24, 2022. doi:10.3390/antib11020024 Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  50. Yu L., Pavlica E., Li R., Zhong Y., Silva C., Bratina G., Müller C., Amassian A., Stingelin N. "Conjugated Polymer Mesocrystals with Structural and Optoelectronic Coherence and Anisotropy in Three Dimensions ". Adv Mater., 34, 1. doi:10.1002/adma.202103002. 

  51. Zhang S., McCallum S.A., Gillilan R.E., Wang J., Royer C.A. "High Pressure CPMG and CEST Reveal That Cavity Position Dictates Distinct Dynamic Disorder in the PP32 Repeat Protein". J. Phys. Chem. B., 126, 50, 10597-10607, 2022. doi: 10.1021/acs.jpcb.2c05498. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  52. Zhang X. "Unveiling microstructure-property correlations in nuclear materials with high-energy synchrotron X-ray techniques". Journal of Nuclear Materials, 561, 153572, 2022. doi: 10.1016/j.jnucmat.2022.153572 Instrument: F2

  53. Zovo K., Pupart H., Wieren A.V., Gillilan R.E., Huang Q., Majumdar S., and Lukk T. "Substitution of the Methionine Axial Ligand of the T1 Copper for the Fungal-like Phenylalanine Ligand (M298F) Causes Local Structural Perturbations that Lead to Thermal Instability and Reduced Catalytic Efficiency of the Small Laccase from Streptomyces coelicolor A3(2)". ACS Omega, 7(7), 6184–6194, 2022. doi: 10.1021/acsomega.1c06668 Instrument: ID7A1 (HP BioSAXS & BioSAXS)