2023 Publications

  1. Vitali J, Nix JC, Newman HE, Colaneri MJ. Crystal structure of Methanococcus jannaschii dihydroorotase. Proteins. 2023 Jan;91(1):91-98. doi: 10.1002/prot.26412. Epub 2022 Aug 24. PMID: 35978488

  2. Kaur G, Ren R, Hammel M, Horton JR, Yang J, Cao Y, He C, Lan F, Lan X, Blobel GA, Blumenthal RM, Zhang X, Cheng X. “Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410-DNA interaction using small angle X-ray scattering.” Nucleic acids research 2023 Jan 20

  3. Chinnam NB, Syed A, Hura GL, Hammel M, Tainer JA, Tsutakawa SE. “Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution.” Methods in enzymology 2023 ;678:351-376

  4. Brosey CA, Shen R, Moiani D, Jones DE, Burnett K, Hura GL, Tainer JA. “Applying HT-SAXS to chemical ligand screening.” Methods in enzymology 2023 ;678:331-350

  5. Murray DT, Shin DS, Classen S, Brosey CA, Hura GL. “Visualizing and accessing correlated SAXS data sets with Similarity Maps and Simple Scattering web resources.” Methods in enzymology 2023 ;678:411-440

  6. Dowling QM, Volkman HE, Gray EE, Ovchinnikov S, Cambier S, Bera AK, Sankaran B, Johnson MR, Bick MJ, Kang A, Stetson DB, King NP. Computational design of constitutively active cGAS. Nat Struct Mol Biol. 2023 Jan;30(1):72-80. doi: 10.1038/s41594-022-00862-z. Epub 2023 Jan 2. PMID: 36593311

  7. O’Herin CB, Moriuchi YW, Bemis TA, Kohlbrand AJ, Burkart MD, Cohen SM Development of Human Carbonic Anhydrase II Heterobifunctional Degraders.  J Med Chem. 2023 Feb 23;66(4):2789-2803. doi: 10.1021/acs.jmedchem.2c01843. Epub 2023 Feb 3. PMID: 36735827

  8. Parkins A, Das P, Prahaladan V, Rangel VM, Xue L, Sankaran B, Bhandari V, Pantouris G. Structure. 2,5-Pyridinedicarboxylic acid is a bioactive and highly selective inhibitor of D-dopachrome tautomerase. 2023 Mar 2;31(3):355-367.e4. doi: 10.1016/j.str.2023.01.008. Epub 2023 Feb 17. PMID: 36805127

  9. Tsutsumi N, Hwang S, Waghray D, Hansen S, Jude KM, Wang N, Miao Y, Glassman CR, Caveney NA, Janda CY, Hannoush RN, Garcia KC. Structure of the Wnt-Frizzled-LRP6 initiation complex reveals the basis for coreceptor discrimination. Proc Natl Acad Sci U S A. 2023 Mar 14;120(11):e2218238120. doi: 10.1073/pnas.2218238120. Epub 2023 Mar 9. PMID: 36893265

  10. Prabhakar PK, Pereira JH, Taujale R, Shao W, Bharadwaj VS, Chapla D, Yang JY, Bomble YJ, Moremen KW, Kannan N, Hammel M, Adams PD, Scheller HV, Urbanowicz BR.Structural and biochemical insight into a modular β-1,4-galactan synthase in plants. Nat Plants. 2023 Mar;9(3):486-500. doi: 10.1038/s41477-023-01358-4. Epub 2023 Feb 27. PMID: 36849618

  11. Thakur AK, Miller SE, Liau NPD, Hwang S, Hansen S, de Sousa E Melo F, Sudhamsu J, Hannoush RN. Synthetic Multivalent Disulfide-Constrained Peptide Agonists Potentiate Wnt1/β-Catenin Signaling via LRP6 Coreceptor Clustering. ACS Chem Biol. 2023 Apr 21;18(4):772-784. doi: 10.1021/acschembio.2c00753. Epub 2023 Mar 9. PMID: 36893429

  12. Brettrager EJ, Cuya SM, Tibbs ZE, Zhang J, Falany CN, Aller SG, van Waardenburg RCAM. N-terminal domain of tyrosyl-DNA phosphodiesterase I regulates topoisomerase I-induced toxicity in cells. Sci Rep. 2023 Jan 25;13(1):1377. doi: 10.1038/s41598-023-28564-6. PMID: 36697463

  13. Martinez-D’Alto A, Yan X, Detomasi TC, Sayler RI, Thomas WC, Talbot NJ, Marletta MA.Characterization of a unique polysaccharide monooxygenase from the plant pathogen Magnaporthe oryzae. Proc Natl Acad Sci U S A. 2023 Feb 21;120(8):e2215426120. doi:10.1073/pnas.2215426120. Epub 2023 Feb 15. PMID: 36791100

  14. Zaragoza JPT, Offenbacher AR, Hu S, Gee CL, Firestein ZM, Minnetian N, Deng Z, Fan F, Iavarone AT, Klinman JP. Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase. Proc Natl Acad Sci U S A. 2023 Mar 7;120(10):e2211630120. doi: 10.1073/pnas.2211630120. Epub 2023 Mar 3. PMID: 36867685

  15. Demir M, Russelburg LP, Lin WJ, Trasviña-Arenas CH, Huang B, Yuen PK, Horvath MP, David SS. Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism. Nucleic Acids Res. 2023 Feb 22;51(3):1034-1049. doi: 10.1093/nar/gkac1246. PMID: 36631987

  16. Salinas R, Cannistraci E, Schumacher MA.Structure of the T. brucei kinetoplastid RNA editing substrate-binding complex core component, RESC5. PLoS One. 2023 Mar 2;18(3):e0282155. doi: 10.1371/journal.pone.0282155. eCollection 2023. PMID: 36862634

  17. Gerben SR, Borst AJ, Hicks DR, Moczygemba I, Feldman D, Coventry B, Yang W, Bera AK, Miranda M, Kang A, Nguyen H, Baker D. Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins. Biochemistry. 2023 Jan 17;62(2):358-368. doi: 10.1021/acs.biochem.2c00497. Epub 2023 Jan 10. PMID: 36627259

  18. Zhu P, Nguyen KT, Estelle AB, Sluchanko NN, Mehl RA, Cooley RB. Genetic encoding of 3-nitro-tyrosine reveals the impacts of 14-3-3 nitration on client binding and dephosphorylation. Protein Sci. 2023 Mar;32(3):e4574. doi: 10.1002/pro.4574. PMID: 36691781

  19. Murray DT, Shin DS, Classen S, Brosey CA, Hura GL.Visualizing and accessing correlated SAXS data sets with Similarity Maps and Simple Scattering web resources. Methods Enzymol. 2023;678:411-440. doi: 10.1016/bs.mie.2022.09.024. Epub 2022 Nov 3. PMID: 36641216

  20. Kaur G, Ren R, Hammel M, Horton JR, Yang J, Cao Y, He C, Lan F, Lan X, Blobel GA, Blumenthal RM, Zhang X, Cheng X. Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410-DNA interaction using small angle X-ray scattering. Nucleic Acids Res. 2023 Feb 28;51(4):1674-1686. doi: 10.1093/nar/gkac1274. PMID: 36660822

  21. Wang JYJ, Khmelinskaia A, Sheffler W, Miranda MC, Antanasijevic A, Borst AJ, Torres SV, Shu C, Hsia Y, Nattermann U, Ellis D, Walkey C, Ahlrichs M, Chan S, Kang A, Nguyen H, Sydeman C, Sankaran B, Wu M, Bera AK, Carter L, Fiala B, Murphy M, Baker D, Ward AB, King NP.Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc Natl Acad Sci U S A. 2023 Mar 14;120(11):e2214556120. doi: 10.1073/pnas.2214556120. Epub 2023 Mar 8. PMID: 36888664

  22. Rodarte JV, Baehr C, Hicks D, Liban TL, Weidle C, Rupert PB, Jahan R, Wall A, McGuire AT, Strong RK, Runyon S, Pravetoni M, Pancera M.Structures of drug-specific monoclonal antibodies bound to opioids and nicotine reveal a common mode of binding. Structure. 2023 Jan 5;31(1):20-32.e5. doi: 10.1016/j.str.2022.11.008. Epub 2022 Dec 12. PMID: 36513069

  23. Gahbauer S, Correy GJ, Schuller M, Ferla MP, Doruk YU, Rachman M, Wu T, Diolaiti M, Wang S, Neitz RJ, Fearon D, Radchenko DS, Moroz YS, Irwin JJ, Renslo AR, Taylor JC, Gestwicki JE, von Delft F, Ashworth A, Ahel I, Shoichet BK, Fraser JS. Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proc Natl Acad Sci U S A. 2023 Jan 10;120(2):e2212931120. doi: 10.1073/pnas.2212931120. Epub 2023 Jan 4. PMID: 36598939

  24. Tamadonfar KO, Di Venanzio G, Pinkner JS, Dodson KW, Kalas V, Zimmerman MI, Bazan Villicana J, Bowman GR, Feldman MF, Hultgren SJ.Structure-function correlates of fibrinogen binding by Acinetobacter adhesins critical in catheter-associated urinary tract infections. Proc Natl Acad Sci U S A. 2023 Jan 24;120(4):e2212694120. doi: 10.1073/pnas.2212694120. Epub 2023 Jan 18. PMID: 36652481

  25. Sharon I, McKay GA, Nguyen D, Schmeing TM. Discovery of cyanophycin dipeptide hydrolase enzymes suggests widespread utility of the natural biopolymer cyanophycin.

  26. Proc Natl Acad Sci U S A. 2023 Feb 21;120(8):e2216547120. doi: 10.1073/pnas.2216547120. Epub 2023 Feb 17. PMID: 36800389

  27. Macdonald R, Mahoney BJ, Soule J, Goring AK, Ford J, Loo JA, Cascio D, Clubb RT. The Shr receptor from Streptococcus pyogenes uses a cap and release mechanism to acquire heme-iron from human hemoglobin. Proc Natl Acad Sci U S A. 2023 Jan 31;120(5):e2211939120. doi: 10.1073/pnas.2211939120. Epub 2023 Jan 24. PMID: 36693107

  28. Tambo CS, Tripathi S, Perera BGK, Maly DJ, Bridges AJ, Kiss G, Rubin SM. Biolayer Interferometry Assay for Cyclin-Dependent Kinase-Cyclin Association Reveals Diverse Effects of Cdk2 Inhibitors on Cyclin Binding Kinetics. ACS Chem Biol. 2023 Feb 17;18(2):431-440. doi: 10.1021/acschembio.3c00015. Epub 2023 Feb 1. PMID: 36724382

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