Highlights & Publications 2021

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  1. 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 Jan 11 ;49(1):306-321 link
  2. 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 Jan 25 ;49(2):1199-1200 link
  3. 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 Jan ;589(7842):468-473 link
  4. 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 Feb 11 ;12(1):939 link
  5. 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):e2021102118 link
  6. 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):e2019649118 link
  7. 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 Mar ;64:41-51 link
  8. 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 Apr 16 ;12(1):2294 link
  9. 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 Jun 14 ;4(1):731 link
  10. 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
  11. 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 Jul 15 ;81(14):2989-3006.e9 link
  12. Gupta K, Wen Y, Ninan NS, Raimer AC, Sharp R, Spring AM, Sarachan KL, Johnson MC, Van Duyne GD, Matera AG. “Assembly of higher-order SMN oligomers is essential for metazoan viability and requires an exposed structural motif present in the YG zipper dimer.” Nucleic acids research 2021 Jul 21 ;49(13):7644-7664 link
  13. 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 Aug 03 ;120(15):3152-3165 link
  14. Wilson DM, Deacon AM, Duncton MAJ, Pellicena P, Georgiadis MM, Yeh AP, Arvai AS, Moiani D, Tainer JA, Das D. “Fragment- and structure-based drug discovery for developing therapeutic agents targeting the DNA Damage Response.” Progress in biophysics and molecular biology 2021 Aug ;163:130-142 link
  15. 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
  16. Borowska MT, Drees C, Yarawsky AE, Viswanathan M, Ryan SM, Bunker JJ, Herr AB, Bendelac A, Adams EJ. “The molecular characterization of antibody binding to a superantigen-like protein from a commensal microbe.” Proceedings of the National Academy of Sciences of the United States of America 2021 Sep 28 ;118(39):e2023898118 link
  17. 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 Sep ;30(9):1735-1756 link
  18. Garrigues RJ, Powell-Pierce AD, Hammel M, Skare JT, Garcia BL. “A Structural Basis for Inhibition of the Complement Initiator Protease C1r by Lyme Disease Spirochetes.” Journal of immunology (Baltimore, Md. : 1950) 2021 Dec 01 ;207(11):2856-2867 link
  19. Yang B, Yu SB, Zhang PQ, Wang ZK, Qi QY, Wang XQ, Xu XH, Yang HB, Wu ZQ, Liu Y, Ma D, Li ZT. “Self-Assembly of a Bilayer 2D Supramolecular Organic Framework in Water.” Angewandte Chemie (International ed. in English) 2021 Dec 06 ;60(50):26268-26275 link
  20. Alexander LT, Lepore R, Kryshtafovych A, Adamopoulos A, Alahuhta M, Arvin AM, Bomble YJ, Böttcher B, Breyton C, Chiarini V, Chinnam NB, Chiu W, Fidelis K, Grinter R, Gupta GD, Hartmann MD, Hayes CS, Heidebrecht T, Ilari A, Joachimiak A, Kim Y, Linares R, Lovering AL, Lunin VV, Lupas AN, Makbul C, Michalska K, Moult J, Mukherjee PK, Nutt WS, Oliver SL, Perrakis A, Stols L, Tainer JA, Topf M, Tsutakawa SE, Valdivia-Delgado M, Schwede T. “Target highlights in CASP14: Analysis of models by structure providers.” Proteins 2021 Dec ;89(12):1647-1672 link
  21. Moiani D, Link TM, Brosey CA, Katsonis P, Lichtarge O, Kim Y, Joachimiak A, Ma Z, Kim IK, Ahmed Z, Jones DE, Tsutakawa SE, Tainer JA. “An efficient chemical screening method for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2.” Methods in enzymology 2021 ;661:407-431 link
  22. Schriber EA, Rosenberg DJ, Kelly RP, Ghodsi A, Hohman JN. “Investigation of Nucleation and Growth at a Liquid-Liquid Interface by Solvent Exchange and Synchrotron Small-Angle X-Ray Scattering.” Frontiers in chemistry 2021 ;9:593637 link
  23. 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 ;296:100270 link
  24. 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.” The Journal of biological chemistry 2021 ;296:100312 link
  25. 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 2021 ;13(1):1905978 link

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