Highlights & Publications 2022

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  1. Bermeo S, Favor A, Chang YT, Norris A, Boyken SE, Hsia Y, Haddox HK, Xu C, Brunette TJ, Wysocki VH, Bhabha G, Ekiert DC, Baker D. “De novo design of obligate ABC-type heterotrimeric proteins.” Nature structural & molecular biology 2022 Dec ;29(12):1266-1276 link
  2. Trewhella J, Vachette P, Bierma J, Blanchet C, Brookes E, Chakravarthy S, Chatzimagas L, Cleveland TE, Cowieson N, Crossett B, Duff AP, Franke D, Gabel F, Gillilan RE, Graewert M, Grishaev A, Guss JM, Hammel M, Hopkins J, Huang Q, Hub JS, Hura GL, Irving TC, Jeffries CM, Jeong C, Kirby N, Krueger S, Martel A, Matsui T, Li N, Pérez J, Porcar L, Prangé T, Rajkovic I, Rocco M, Rosenberg DJ, Ryan TM, Seifert S, Sekiguchi H, Svergun D, Teixeira S, Thureau A, Weiss TM, Whitten AE, Wood K, Zuo X. “A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking.” Acta crystallographica. Section D, Structural biology 2022 Nov 01 ;78(Pt 11):1315-1336 link
  3. Lyons NS, Bogner AN, Tanner JJ, Sobrado P. “Kinetic and Structural Characterization of a Flavin-Dependent Putrescine N-Hydroxylase from Acinetobacter baumannii.” Biochemistry 2022 Nov 15 ;61(22):2607-2620 link
  4. Mauriello GE, Moncure GE, Nowzari RA, Miller CJ, Wright NT. “The N-terminus of obscurin is flexible in solution.” Proteins 2022 Oct 28 link
  5. Van V, Ejimogu NE, Bui TS, Smith AT. “The Structure of Saccharomyces cerevisiae Arginyltransferase 1 (ATE1).” Journal of molecular biology 2022 Sep 08 ;434(21):167816 link
  6. Lin JS, Bekale LA, Molchanova N, Nielsen JE, Wright M, Bacacao B, Diamond G, Jenssen H, Santa Maria PL, Barron AE. “Anti-persister and Anti-biofilm Activity of Self-Assembled Antimicrobial Peptoid Ellipsoidal Micelles.” ACS infectious diseases 2022 Sep 09 ;8(9):1823-1830 link
  7. Kim M, Kim HS, D’Souza A, Gallagher K, Jeong E, Topolska-Wós A, Ogorodnik Le Meur K, Tsai CL, Tsai MS, Kee M, Tainer JA, Yeo JE, Chazin WJ, Schärer OD. “Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair.” Proceedings of the National Academy of Sciences of the United States of America 2022 Aug 23 ;119(34):e2207408119 link
  8. Pham VV, Gao M, Meagher JL, Smith JL, D’Souza VM. “A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA.” Communications biology 2022 Aug 15 ;5(1):819 link
  9. Rosenberg DJ, Hura GL, Hammel M. “Size exclusion chromatography coupled small angle X-ray scattering with tandem multiangle light scattering at the SIBYLS beamline.” Methods in enzymology 2022 ;677:191-219 link
  10. Liu AK, Pereira JH, Kehl AJ, Rosenberg DJ, Orr DJ, Chu SKS, Banda DM, Hammel M, Adams PD, Siegel JB, Shih PM. “Structural plasticity enables evolution and innovation of RuBisCO assemblies.” Science advances 2022 Aug 26 ;8(34):eadc9440 link
  11. Cantara WA, Pathirage C, Hatterschide J, Olson ED, Musier-Forsyth K. “Phosphomimetic S207D Lysyl-tRNA Synthetase Binds HIV-1 5’UTR in an Open Conformation and Increases RNA Dynamics.” Viruses 2022 Jul 16 ;14(7)link
  12. Ehm T, Philipp J, Barkey M, Ober M, Brinkop AT, Simml D, von Westphalen M, Nickel B, Beck R, Rädler JO. “3D-printed SAXS chamber for controlled in situ dialysis and optical characterization.” Journal of synchrotron radiation 2022 Jul 01 ;29(Pt 4):1014-1019 link
  13. McGinnis RJ, Brambley CA, Stamey B, Green WC, Gragg KN, Cafferty ER, Terwilliger TC, Hammel M, Hollis TJ, Miller JM, Gainey MD, Wallen JR. “A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence.” Nature communications 2022 Jul 14 ;13(1):4105 link
  14. Mahoney BJ, Takayesu A, Zhou A, Cascio D, Clubb RT. “The structure of the Clostridium thermocellum RsgI9 ectodomain provides insight into the mechanism of biomass sensing.” Proteins 2022 07 ;90(7):1457-1467 link
  15. Childers KC, Peters SC, Lollar P, Spencer HT, Doering CB, Spiegel PC. “SAXS analysis of the intrinsic tenase complex bound to a lipid nanodisc highlights intermolecular contacts between factors VIIIa/IXa.” Blood advances 2022 Jun 14 ;6(11):3240-3254 link
  16. Lin F, Yu SB, Liu YY, Liu CZ, Lu S, Cao J, Qi QY, Zhou W, Li X, Liu Y, Tian J, Li ZT. “Porous Polymers as Universal Reversal Agents for Heparin Anticoagulants through an Inclusion-Sequestration Mechanism.” Advanced materials (Deerfield Beach, Fla.) 2022 Jun ;34(23):e2200549 link
  17. Liau NPD, Johnson MC, Izadi S, Gerosa L, Hammel M, Bruning JM, Wendorff TJ, Phung W, Hymowitz SG, Sudhamsu J. “Structural basis for SHOC2 modulation of RAS signalling.” Nature 2022 Jun 29 link
  18. Sarode A, Fan Y, Byrnes AE, Hammel M, Hura GL, Fu Y, Kou P, Hu C, Hinz FI, Roberts J, Koenig SG, Nagapudi K, Hoogenraad CC, Chen T, Leung D, Yen CW. “Predictive high-throughput screening of PEGylated lipids in oligonucleotide-loaded lipid nanoparticles for neuronal gene silencing.” Nanoscale advances 2022 May 03 ;4(9):2107-2123 link
  19. Norton-Baker B, Mehrabi P, Kwok AO, Roskamp KW, Rocha MA, Sprague-Piercy MA, von Stetten D, Miller RJD, Martin RW. “Deamidation of the human eye lens protein γS-crystallin accelerates oxidative aging.” Structure (London, England : 1993) 2022 05 05 ;30(5):763-776.e4 link
  20. Ravenburg CM, Riney MB, Monroe JD, Berndsen CE. “The BAM7 gene in Zea mays encodes a protein with similar structural and catalytic properties to Arabidopsis BAM2.” Acta crystallographica. Section D, Structural biology 2022 May 01 ;78(Pt 5):560-570 link
  21. Sestok AE, Brown JB, Obi JO, O’Sullivan SM, Garcin ED, Deredge DJ, Smith AT. “A fusion of the Bacteroides fragilis ferrous iron import proteins reveals a role for FeoA in stabilizing GTP-bound FeoB.” The Journal of biological chemistry 2022 04 ;298(4):101808 link
  22. Sweeney DT, Krueger S, Sen K, Hackett JC. “Structures and Dynamics of Anionic Lipoprotein Nanodiscs.” The journal of physical chemistry. B 2022 04 21 ;126(15):2850-2862 link
  23. Courbet A, Hansen J, Hsia Y, Bethel N, Park YJ, Xu C, Moyer A, Boyken SE, Ueda G, Nattermann U, Nagarajan D, Silva DA, Sheffler W, Quispe J, Nord A, King N, Bradley P, Veesler D, Kollman J, Baker D. “Computational design of mechanically coupled axle-rotor protein assemblies.” Science (New York, N.Y.) 2022 04 22 ;376(6591):383-390 link
  24. Hawkins WD, Leary KA, Andhare D, Popelka H, Klionsky DJ, Ragusa MJ. “Dimerization-dependent membrane tethering by Atg23 is essential for yeast autophagy.” Cell reports 2022 04 19 ;39(3):110702 link
  25. Chandrasekharan NP, Ravenburg CM, Roy IR, Monroe JD, Berndsen CE. “Solution structure and assembly of β-amylase 2 from Arabidopsis thaliana.” Acta crystallographica. Section D, Structural biology 2020 Apr 01 ;76(Pt 4):357-365 link
  26. Chinnam NB, Syed A, Burnett KH, Hura GL, Tainer JA, Tsutakawa SE. “Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights.” Methods in molecular biology (Clifton, N.J.) 2022 ;2444:43-68 link
  27. Rosenberg DJ, Syed A, Tainer JA, Hura GL. “Monitoring Nuclease Activity by X-Ray Scattering Interferometry Using Gold Nanoparticle-Conjugated DNA.” Methods in molecular biology (Clifton, N.J.) 2022 ;2444:183-205 link
  28. Yachnin BJ, Azouz LR, White RE, Minetti CASA, Remeta DP, Tan VM, Drake JM, Khare SD. “Massively parallel, computationally guided design of a proenzyme.” Proceedings of the National Academy of Sciences of the United States of America 2022 Apr 12 ;119(15):e2116097119 link
  29. Siang S, Underbakke ES, Roche J. “Intricate coupling between the transactivation and basic-leucine zipper domains governs phosphorylation of transcription factor ATF4 by casein kinase 2.” The Journal of biological chemistry 2022 03 ;298(3):101633 link
  30. Nielsen JE, Alford MA, Yung DBY, Molchanova N, Fortkort JA, Lin JS, Diamond G, Hancock REW, Jenssen H, Pletzer D, Lund R, Barron AE. “Self-Assembly of Antimicrobial Peptoids Impacts Their Biological Effects on ESKAPE Bacterial Pathogens.” ACS infectious diseases 2022 03 11 ;8(3):533-545 link
  31. Clanor PB, Buchholz C, Hayes JE, Friedman MA, White AM, Enke RA, Berndsen CE. “Structural and functional analysis of the human Cone-rod homeobox transcription factor.” Proteins 2022 Mar 07 link
  32. Lim SA, Zhou J, Martinko AJ, Wang YH, Filippova EV, Steri V, Wang D, Remesh SG, Liu J, Hann B, Kossiakoff AA, Evans MJ, Leung KK, Wells JA. “Targeting a proteolytic neoepitope on CUB domain containing protein 1 (CDCP1) for RAS-driven cancers.” The Journal of clinical investigation 2022 02 15 ;132(4)link
  33. Canny MD, Latham MP. “LRET-derived HADDOCK structural models describe the conformational heterogeneity required for DNA cleavage by the Mre11-Rad50 DNA damage repair complex.” eLife 2022 Jan 27 ;11link
  34. Krakow J, Hammel M, Zhu Y, Hillier BJ, Paolella B, Desmarais A, Wall R, Chen TT, Pei R, Karunatilake C, DuBridge R, Vinogradova M. “Structural arrangement of the VH and VL domains in the COBRA™ T-cell engaging single-chain diabody.” Antibody therapeutics 2022 Jan ;5(1):1-10 link
  35. Schriber E A, Paley D, Bolotovsky R, Rosenberg D J, Sierra R G, Aquila A, Mendez D, Sauter N K, Brewster A S, Hohman J N, et al. “Chemical crystallography by serial femtosecond X-ray diffraction.” Nature 19 January 2022. 601, 360-365 (2022).

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