Publications 2024

Highlights & Publications 2024

S. aureus Eap
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Mapping DNA on Carbon Nanotubes
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  1. Kibler RD, Lee S, Kennedy MA, Wicky BIM, Lai SM, Kostelic MM, Carr A, Li X, Chow CM, Nguyen TK, Carter L, Wysocki VH, Stoddard BL, Baker D. “Design of pseudosymmetric protein hetero-oligomers.” Nature communications 2024 Dec 18 ;15(1):10684 link
  2. Cartwright M, Parakra R, Oduwole A, Zhang F, Deredge DJ, Smith AT. “Identification of an Intrinsically Disordered Region (IDR) in Arginyltransferase 1 (ATE1).” Biochemistry 2024 Dec 17 ;63(24):3236-3249 link
  3. Patt E, Classen S, Hammel M, Schneidman-Duhovny D. “Predicting RNA Structure and Dynamics with Deep Learning and Solution Scattering.” Biophysical journal 2024 Dec 24 link
  4. Allert MJ, Kumar S, Wang Y, Beese LS, Hellinga HW. “Accurate Identification of Periplasmic Urea-binding Proteins by Structure- and Genome Context-assisted Functional Analysis.” Journal of molecular biology 2024 Nov 15 ;436(22):168780 link
  5. Gan J, Juang V, Wang K, Xia Z, Ackermann R, Yu M, Dorsey KH, Lin W, Wang X, Wang Y, Liang J, Zheng J, Xu X, Park JH, Schwendeman A. “Reverse engineering of Onivyde® – Irinotecan liposome injection.” International journal of pharmaceutics 2024 Nov 27 ;669:125000 link
  6. Kc S, Nguyen KH, Nicholson V, Walgren A, Trent T, Gollub E, Romero-Perez PS, Holehouse AS, Sukenik S, Boothby TC. “Disordered proteins interact with the chemical environment to tune their protective function during drying.” eLife 2024 Nov 19 ;13link
  7. Khan SA, Hicks A, Leite WC, Byrnes J, Gorai B, Mroginski MA, O’Neill H, Miller AF. “Extended conformations of bifurcating electron transfer flavoprotein constitute up to half the population, possibly mediating conformational change.” Chemical science 2024 Oct 23 ;15(45):18796-817 link
  8. Fan Y, Rigas D, Kim LJ, Chang FP, Zang N, McKee K, Kemball CC, Yu Z, Winkler P, Su WC, Jessen P, Hura GL, Chen T, Koenig SG, Nagapudi K, Leung D, Yen CW. “Physicochemical and structural insights into lyophilized mRNA-LNP from lyoprotectant and buffer screenings.” Journal of controlled release : official journal of the Controlled Release Society 2024 Sep ;373:727-737 link
  9. Sirirungruang S, Blay V, Scott YF, Pereira JH, Hammel M, Barnum CR, Adams PD, Shih PM. “Structural and biochemical basis for regiospecificity of the flavonoid glycosyltransferase UGT95A1.” The Journal of biological chemistry 2024 Sep ;300(9):107602 link
  10. Jiang H, Jude KM, Wu K, Fallas J, Ueda G, Brunette TJ, Hicks DR, Pyles H, Yang A, Carter L, Lamb M, Li X, Levine PM, Stewart L, Garcia KC, Baker D. “De novo design of buttressed loops for sculpting protein functions.” Nature chemical biology 2024 Aug ;20(8):974-980 link
  11. Hackett JC, Krueger S, Urban VS, Zárate-Pérez F. “Small angle scattering reveals the orientation of cytochrome P450 19A1 in lipoprotein nanodiscs.” Journal of inorganic biochemistry 2024 Aug ;257:112579 link
  12. Mishra N, Gido CD, Herdendorf TJ, Hammel M, Hura GL, Fu ZQ, Geisbrecht BV. “S. aureus Eap is a polyvalent inhibitor of neutrophil serine proteases.” The Journal of biological chemistry 2024 Aug 02 :107627 link
  13. Sholes A, Asongakap R, Jaconski S, Monroe J, Berndsen CE. “Potassium cations expand the conformation ensemble of Arabidopsis thaliana β-amylase2 (BAM2).” microPublication biology 2024 ;2024link
  14. Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D. “De novo design of proteins housing excitonically coupled chlorophyll special pairs.” Nature chemical biology 2024 Jul ;20(7):906-915 link
  15. McElroy C, Ihms E, Yadav DK, Holmquist M, Wadwha V, Wysocki V, Gollnick P, Foster M. “Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis.” bioRxiv : the preprint server for biology 2023 Jun 30 link
  16. Chinnam NB, Thapar R, Arvai AS, Sarker AH, Soll JM, Paul T, Syed A, Rosenberg DJ, Hammel M, Bacolla A, Katsonis P, Asthana A, Tsai MS, Ivanov I, Lichtarge O, Silverman RH, Mosammaparast N, Tsutakawa SE, Tainer JA. “ASCC1 structures and bioinformatics reveal a novel helix-clasp-helix RNA-binding motif linked to a two-histidine phosphodiesterase.” The Journal of biological chemistry 2024 Jun ;300(6):107368 link
  17. Edman NI, Phal A, Redler RL, Schlichthaerle T, Srivatsan SR, Ehnes DD, Etemadi A, An SJ, Favor A, Li Z, Praetorius F, Gordon M, Vincent T, Marchiano S, Blakely L, Lin C, Yang W, Coventry B, Hicks DR, Cao L, Bethel N, Heine P, Murray A, Gerben S, Carter L, Miranda M, Negahdari B, Lee S, Trapnell C, Zheng Y, Murry CE, Schweppe DK, Freedman BS, Stewart L, Ekiert DC, Schlessinger J, Shendure J, Bhabha G, Ruohola-Baker H, Baker D. “Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies.” Cell 2024 Jul 11 ;187(14):3726-3740.e43 link
  18. McElroy CA, Ihms EC, Kumar Yadav D, Holmquist ML, Wadhwa V, Wysocki VH, Gollnick P, Foster MP. “Solution structure, dynamics and tetrahedral assembly of Anti-TRAP, a homo-trimeric triskelion-shaped regulator of tryptophan biosynthesis in Bacillus subtilis.” Journal of structural biology: X 2024 Dec ;10:100103 link
  19. Salinas ND, Ma R, McAleese H, Ouahes T, Long CA, Miura K, Lambert LE, Tolia NH. “A Self-Assembling Pfs230D1-Ferritin Nanoparticle Vaccine Has Potent and Durable Malaria Transmission-Reducing Activity.” Vaccines 2024 May 16 ;12(5)link
  20. Tamilselvan E, Sotomayor M. “CELSR1, a core planar cell polarity protein, features a weakly adhesive and flexible cadherin ectodomain.” Structure (London, England : 1993) 2024 Apr 04 ;32(4):476-491.e5 link
  21. Brosey CA, Link TM, Shen R, Moiani D, Burnett K, Hura GL, Jones DE, Tainer JA. “Chemical screening by time-resolved X-ray scattering to discover allosteric probes.” Nature chemical biology 2024 Apr 26 link
  22. Ruocco V, Grünwald-Gruber C, Rad B, Tscheliessnig R, Hammel M, Strasser R. “Effects of N-glycans on the structure of human IgA2.” Frontiers in molecular biosciences 2024 ;11:1390659 link
  23. Huddy TF, Hsia Y, Kibler RD, Xu J, Bethel N, Nagarajan D, Redler R, Leung PJY, Weidle C, Courbet A, Yang EC, Bera AK, Coudray N, Calise SJ, Davila-Hernandez FA, Han HL, Carr KD, Li Z, McHugh R, Reggiano G, Kang A, Sankaran B, Dickinson MS, Coventry B, Brunette TJ, Liu Y, Dauparas J, Borst AJ, Ekiert D, Kollman JM, Bhabha G, Baker D. “Blueprinting extendable nanomaterials with standardized protein blocks.” Nature 2024 Mar ;627(8005):898-904 link
  24. Hu Q, Botuyan MV, Mer G. “Identification of a conserved α-helical domain at the N terminus of human DNA methyltransferase 1.” The Journal of biological chemistry 2024 Mar ;300(3):105775 link
  25. Balakrishnan S, Adolph M, Tsai MS, Akizuki T, Gallagher K, Cortez D, Chazin WJ. “Structure of RADX and mechanism for regulation of RAD51 nucleofilaments.” Proceedings of the National Academy of Sciences of the United States of America 2024 Mar 19 ;121(12):e2316491121 link
  26. Dykeman-Bermingham PA, Bogen MP, Chittari SS, Grizzard SF, Knight AS. “Tailoring Hierarchical Structure and Rare Earth Affinity of Compositionally Identical Polymers via Sequence Control.” Journal of the American Chemical Society 2024 Mar 27 ;146(12):8607-8617 link
  27. Kim LJ, Shin D, Leite WC, O’Neill H, Ruebel O, Tritt A, Hura GL. “Simple Scattering: Lipid nanoparticle structural data repository.” Frontiers in molecular biosciences 2024 ;11:1321364 link
  28. Zhao W, Lin JS, Nielsen JE, Sørensen K, Wadurkar AS, Ji J, Barron AE, Nangia S, Libera MR. “Supramolecular Peptoid Structure Strengthens Complexation with Polyacrylic Acid Microgels.” Biomacromolecules 2024 Feb 12 ;25(2):1274-1281 link
  29. Bennett AL, Edwards R, Kosheleva I, Saunders C, Bililign Y, Williams A, Bubphamala P, Manosouri K, Anasti K, Saunders KO, Alam SM, Haynes BF, Acharya P, Henderson R. “Microsecond dynamics control the HIV-1 Envelope conformation.” Science advances 2024 Feb 02 ;10(5):eadj0396 link
  30. Nelson AD, Wang L, Laffey KG, Becher LRE, Parks CA, Hoffmann MM, Galeano BK, Mangalam A, Teixeiro E, White TA, Schrum AG, Cannon JF, Gil D. “Rigid crosslinking of the CD3 complex leads to superior T cell stimulation.” Frontiers in immunology 2024 ;15:1434463 link
  31. Sholes A, Asongakap R, Jaconski S, Monroe J, Berndsen CE. “Potassium cations expand the conformation ensemble of Arabidopsis thaliana β-amylase2 (BAM2).” microPublication biology 2024 ;2024link
  32. Luo Y, Hao H, Wang Z, Ong CY, Dutcher R, Xu Y, Liu J, Pedersen LC, Xu D. “Heparan sulfate promotes TRAIL-induced tumor cell apoptosis.” eLife 2024 Jan 24 ;12link
  33. Lin DY, Kueffer LE, Juneja P, Wales TE, Engen JR, Andreotti AH. “Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states.” eLife 2024 Jan 08 ;12link
  34. Yadav P, Gupta M, Wazahat R, Islam Z, Tsutakawa SE, Kamthan M, Kumar P. “Structural basis for the role of C-terminus acidic tail of Saccharomyces cerevisiae ubiquitin-conjugating enzyme (Rad6) in E3 ligase (Bre1) mediated recognition of histones.” International journal of biological macromolecules 2024 Jan ;254(Pt 2):127717 link
  35. Woltz R, Schweibenz B, Tsutakawa SE, Zhao C, Ma L, Shurina B, Hura GL, John R, Vorobiev S, Swapna G, Solotchi M, Tainer JA, Krug RM, Patel SS, Montelione GT. “The NS1 protein of influenza B virus binds 5′-triphosphorylated dsRNA to suppress RIG-I activation and the host antiviral response.” bioRxiv : the preprint server for biology 2024 Jan 24 link
  36. Murray DT, Ge X, Schut GJ, Rosenberg DJ, Hammel M, Bierma JC, Hille R, Adams MWW, Hura GL. “Correlating Conformational Equilibria with Catalysis in the Electron Bifurcating EtfABCX of Thermotoga maritima.” Biochemistry 2024 Jan 02 ;63(1):128-140 link
  37. Roger M, Leone P, Blackburn NJ, Horrell S, Chicano TM, Biaso F, Giudici-Orticoni MT, Abriata LA, Hura GL, Hough MA, Sciara G, Ilbert M. “Beyond the coupled distortion model: structural analysis of the single domain cupredoxin AcoP, a green mononuclear copper centre with original features.” Dalton transactions (Cambridge, England : 2003) 2024 Jan 23 ;53(4):1794-1808 link
  38. Rosenberg DJ, Cunningham FJ, Hubbard JD, Goh NS, Wang JW, Nishitani S, Hayman EB, Hura GL, Landry MP, Pinals RL. “Mapping the Morphology of DNA on Carbon Nanotubes in Solution Using X-ray Scattering Interferometry.” Journal of the American Chemical Society 2024 Jan 10 ;146(1):386-398 link

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