Publications

Acknowledgements

Are you about to publish a paper made possible by the SIBYLS beamline? If so we would greatly appreciate it if you would acknowledge the beamline, support staff, and our funding sources. This is critical in order for us to maintain SIBYLS beamline as a world class facility for SAXS and MX experiments.
This work was conducted at the Advanced Light Source (ALS), a national user facility operated by Lawrence Berkeley National Laboratory on behalf of the Department of Energy, Office of Basic Energy Sciences, through the Integrated Diffraction Analysis Technologies (IDAT) program, supported by DOE Office of Biological and Environmental Research. Additional support comes from the National Institute of Health project ALS-ENABLE (P30 GM124169) and a High-End Instrumentation Grant S10OD018483.
Additional acknowledgments to add if the manuscript is resulting from the SBDR P01 project.
Efforts to apply SAXS and crystallography to characterize eukaryotic pathways relevant to human cancers are supported in part by National Cancer Institute grant Structural Biology of DNA Repair (SBDR) CA92584.
If you received substantive help from beamline staff please also consider either adding them as a co-author or mentioning them in the acknowledgments.

2021

  1. Stachowski TR, Snell ME, Snell EH. “A SAXS-based approach to rationally evaluate radical scavengers – toward eliminating radiation damage in solution and crystallographic studies.” Journal of synchrotron radiation 2021 Sep 01 ;28(Pt 5):1309-1320 link
  2. Lees-Miller JP, Cobban A, Katsonis P, Bacolla A, Tsutakawa SE, Hammel M, Meek K, Anderson DW, Lichtarge O, Tainer JA, Lees-Miller SP. “Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease.” Progress in biophysics and molecular biology 2021 Aug ;163:87-108 link
  3. Ueda G, Antanasijevic A, Fallas JA, Sheffler W, Copps J, Ellis D, Hutchinson GB, Moyer A, Yasmeen A, Tsybovsky Y, Park YJ, Bick MJ, Sankaran B, Gillespie RA, Brouwer PJ, Zwart PH, Veesler D, Kanekiyo M, Graham BS, Sanders RW, Moore JP, Klasse PJ, Ward AB, King NP, Baker D. “Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens.” eLife 2020 08 04 ;9link
  4. Hambarde S, Tsai CL, Pandita RK, Bacolla A, Maitra A, Charaka V, Hunt CR, Kumar R, Limbo O, Le Meur R, Chazin WJ, Tsutakawa SE, Russell P, Schlacher K, Pandita TK, Tainer JA. “EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart.” Molecular cell 2021 07 15 ;81(14):2989-3006.e9 link
  5. Leite WC, Weiss KL, Phillips G, Zhang Q, Qian S, Tsutakawa SE, Coates L, O’Neill H. “Conformational Dynamics in the Interaction of SARS-CoV-2 Papain-like Protease with Human Interferon-Stimulated Gene 15 Protein.” The journal of physical chemistry letters 2021 Jun 17 ;12(23):5608-5615 link
  6. Paar M, Fengler VH, Rosenberg DJ, Krebs A, Stauber RE, Oettl K, Hammel M. “Albumin in patients with liver disease shows an altered conformation.” Communications biology 2021 06 14 ;4(1):731 link
  7. Wilamowski M, Hammel M, Leite W, Zhang Q, Kim Y, Weiss KL, Jedrzejczak R, Rosenberg DJ, Fan Y, Wower J, Bierma JC, Sarker AH, Tsutakawa SE, Pingali SV, O’Neill HM, Joachimiak A, Hura GL. “Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication.” Biophysical journal 2021 Jun 29 link
  8. Hammel M, Tainer JA. “X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology.” Protein science : a publication of the Protein Society 2021 May 30 link
  9. Yu Z, Ku AF, Anglin JL, Sharma R, Ucisik MN, Faver JC, Li F, Nyshadham P, Simmons N, Sharma KL, Nagarajan S, Riehle K, Kaur G, Sankaran B, Storl-Desmond M, Palmer SS, Young DW, Kim C, Matzuk MM. “Discovery and characterization of bromodomain 2-specific inhibitors of BRDT.” Proceedings of the National Academy of Sciences of the United States of America 2021 Mar 02 ;118(9)link
  10. McConnell SA, McAllister RA, Amer BR, Mahoney BJ, Sue CK, Chang C, Ton-That H, Clubb RT. “Sortase-assembled pili in Corynebacterium diphtheriae are built using a latch mechanism.” Proceedings of the National Academy of Sciences of the United States of America 2021 Mar 23 ;118(12)link
  11. Wang X, Pereira JH, Tsutakawa S, Fang X, Adams PD, Mukhopadhyay A, Lee TS. “Efficient production of oxidized terpenoids via engineering fusion proteins of terpene synthase and cytochrome P450.” Metabolic engineering 2021 03 ;64:41-51 link
  12. Walker RG, Kattamuri C, Goebel EJ, Zhang F, Hammel M, Tainer JA, Linhardt RJ, Thompson TB. “Heparin-mediated dimerization of follistatin.” Experimental biology and medicine (Maywood, N.J.) 2021 Feb ;246(4):467-482 link
  13. Lapenta F, Aupič J, Vezzoli M, Strmšek Ž, Da Vela S, Svergun DI, Carazo JM, Melero R, Jerala R. “Self-assembly and regulation of protein cages from pre-organised coiled-coil modules.” Nature communications 2021 02 11 ;12(1):939 link
  14. Thapar R, Wang JL, Hammel M, Ye R, Liang K, Sun C, Hnizda A, Liang S, Maw SS, Lee L, Villarreal H, Forrester I, Fang S, Tsai MS, Blundell TL, Davis AJ, Lin C, Lees-Miller SP, Strick TR, Tainer JA. “Mechanism of efficient double-strand break repair by a long non-coding RNA.” Nucleic acids research 2021 01 25 ;49(2):1199-1200 link
  15. Yu D, Kaur G, Blumenthal RM, Zhang X, Cheng X. “Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima.” The Journal of biological chemistry 2021 Jan 08 :100270 link
  16. Ben-Sasson AJ, Watson JL, Sheffler W, Johnson MC, Bittleston A, Somasundaram L, Decarreau J, Jiao F, Chen J, Mela I, Drabek AA, Jarrett SM, Blacklow SC, Kaminski CF, Hura GL, De Yoreo JJ, Kollman JM, Ruohola-Baker H, Derivery E, Baker D. “Design of biologically active binary protein 2D materials.” Nature 2021 01 ;589(7842):468-473 link
  17. Gunn KH, Gutgsell AR, Xu Y, Johnson CV, Liu J, Neher SB. “Comparison of angiopoietin-like protein 3 and 4 reveals structural and mechanistic similarities.” Jan 2021, The Journal of biological chemistry ;296:100312 link
  18. Hsia Y, Mout R, Sheffler W, Edman NI, Vulovic I, Park YJ, Redler RL, Bick MJ, Bera AK, Courbet A, Kang A, Brunette TJ, Nattermann U, Tsai E, Saleem A, Chow CM, Ekiert D, Bhabha G, Veesler D, Baker D. “Design of multi-scale protein complexes by hierarchical building block fusion.” Nature communications 2021 04 16 ;12(1):2294 link
  19. Hodge CD, Rosenberg DJ, Grob P, Wilamowski M, Joachimiak A, Hura GL, Hammel M. “Rigid monoclonal antibodies improve detection of SARS-CoV-2 nucleocapsid protein.” mAbs ;13(1):1905978 link
  20. Hammel M, Rashid I, Sverzhinsky A, Pourfarjam Y, Tsai MS, Ellenberger T, Pascal JM, Kim IK, Tainer JA, Tomkinson AE. “An atypical BRCT-BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex.” Nucleic acids research 2021 01 11 ;49(1):306-321 link