Highlights & Publications 2020

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  1. Reyes-Aldrete E, Dill EA, Bussetta C, Szymanski MR, Diemer G, Maindola P, White MA, Bujalowski WM, Choi KH, Morais MC. “Biochemical and Biophysical Characterization of the dsDNA Packaging Motor from the Lactococcus lactis Bacteriophage Asccphi28.” Viruses 2020 12 23 ;13(1)link
  2. Uhlemann EE, Yu CH, Patry J, Dolgova N, Lutsenko S, Muyldermans S, Dmitriev OY. “Nanobodies against the metal binding domains of ATP7B as tools to study copper transport in the cell.” Metallomics : integrated biometal science 2020 12 23 ;12(12):1941-1950 link
  3. 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.) 2020 Nov 16 :1535370220966296 link
  4. 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 2020 11 04 ;48(19):10953-10972 link
  5. Stachowski TR, Snell ME, Snell EH. “SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique.” PloS one 2020 ;15(11):e0239702 link
  6. 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 2020 Oct 06 link
  7. Zeng Y, Ren R, Kaur G, Hardikar S, Ying Z, Babcock L, Gupta E, Zhang X, Chen T, Cheng X. “The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation.” Genes & development 2020 Oct 01 link
  8. Xu C, Lu P, Gamal El-Din TM, Pei XY, Johnson MC, Uyeda A, Bick MJ, Xu Q, Jiang D, Bai H, Reggiano G, Hsia Y, Brunette TJ, Dou J, Ma D, Lynch EM, Boyken SE, Huang PS, Stewart L, DiMaio F, Kollman JM, Luisi BF, Matsuura T, Catterall WA, Baker D. “Computational design of transmembrane pores.” Nature 2020 09 ;585(7823):129-134 link
  9. Wyatt JW, Korasick DA, Qureshi IA, Campbell AC, Gates KS, Tanner JJ. “Inhibition, crystal structures, and in-solution oligomeric structure of aldehyde dehydrogenase 9A1.” Archives of biochemistry and biophysics 2020 Sep 30 ;691:108477 link
  10. Banda DM, Pereira JH, Liu AK, Orr DJ, Hammel M, He C, Parry MAJ, Carmo-Silva E, Adams PD, Banfield JF, Shih PM. “Novel bacterial clade reveals origin of form I Rubisco.” Nature plants 2020 Sep ;6(9):1158-1166 link
  11. Pinals RL, Yang D, Rosenberg DJ, Chaudhary T, Crothers AR, Iavarone AT, Hammel M, Landry M. “Quantitative Protein Corona Composition and Dynamics on Carbon Nanotubes in Biological Environments.” Angewandte Chemie (International ed. in English) 2020 Sep 15 link
  12. Hammel M, Rosenberg DJ, Bierma J, Hura GL, Lees-Miller SP, Tainer JA. “Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM.” Progress in biophysics and molecular biology 2020 Sep 20 link
  13. Dominguez-Martin MA, Hammel M, Gupta S, Lechno-Yossef S, Sutter M, Rosenberg DJ, Chen Y, Petzold CJ, Ralston CY, Polívka T, Kerfeld CA. “Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP.” Scientific reports 2020 Sep 23 ;10(1):15564 link
  14. 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
  15. Eckelmann BJ, Bacolla A, Wang H, Ye Z, Guerrero EN, Jiang W, El-Zein R, Hegde ML, Tomkinson AE, Tainer JA, Mitra S. “XRCC1 promotes replication restart, nascent fork degradation and mutagenic DNA repair in BRCA2-deficient cells.” NAR Cancer 2020 Sep ;2(3):zcaa013 link
  16. Brambley C, Bolay A, Salvo H, Jansch A, Yared T, Miller J, Wallen J, Weiland M. “Structural Characterization of Sphingomonas sp.KT-1 PahZ1-Catalyzed Biodegradaton of Thermally Synthesized Poly(aspartic acid)”. ACS Sustainable chem. Eng. 2020,8, 29, 10701-10713
  17. Sloutsky R, Dziedzic N, Dunn MJ, Bates RM, Torres-Ocampo AP, Boopathy S, Page B, Weeks JG, Chao LH, Stratton MM. “Heterogeneity in human hippocampal CaMKII transcripts reveals allosteric hub-dependent regulation.” Science signaling 2020 07 21 ;13(641)link
  18. Bhargava HK, Tabata K, Byck JM, Hamasaki M, Farrell DP, Anishchenko I, DiMaio F, Im YJ, Yoshimori T, Hurley JH. “Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.” Proc. Natl. Acad. Sci. U.S.A. 2020 Jul 21 ;117(29):17003-17010 link
  19. Jiao L, Shubbar M, Yang X, Zhang Q, Chen S, Wu Q, Chen Z, Rizo J, Liu X. “A partially disordered region connects gene repression and activation functions of EZH2.” Proc. Natl. Acad. Sci. U.S.A. 2020 Jul 06 link
  20. Huang L, Wright M, Yang S, Blachowicz L, Makowski L, Roux B. “Glycine substitution in SH3-SH2 connector of Hck tyrosine kinase causes population shift from assembled to disassembled state.” Biochim Biophys Acta Gen Subj 2020 Jul ;1864(7):129604 link
  21. Schellenberg MJ, Appel CD, Riccio AA, Butler LR, Krahn JM, Liebermann JA, Cortés-Ledesma F, Williams RS. “Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2.” Nucleic acids research 2020 06 19 ;48(11):6310-6325 link
  22. Kumar J, Kaur G, Ren R, Lu Y, Lin K, Li J, Huang Y, Patel A, Barton MC, Macfarlan T, Zhang X, Cheng X. “KRAB domain of ZFP568 disrupts TRIM28-mediated abnormal interactions in cancer cells.” NAR cancer 2020 Jun ;2(2):zcaa007 link
  23. Marcum RD, Reyes AA, He Y. “Structural Insights into the Evolutionarily Conserved BAF Chromatin Remodeling Complex.” Biology (Basel) 2020 Jun 30 ;9(7)link
  24. Crickard JB, Moevus CJ, Kwon Y, Sung P, Greene EC. “Rad54 Drives ATP Hydrolysis-Dependent DNA Sequence Alignment during Homologous Recombination.” Cell 2020 Jun 11 ;181(6):1380-1394.e18 link
  25. Yan NL, Santos-Martins D, Rennella E, Sanchez BB, Chen JS, Kay LE, Wilson IA, Morgan GJ, Forli S, Kelly JW. “Structural basis for the stabilization of amyloidogenic immunoglobulin light chains by hydantoins.” Bioorg. Med. Chem. Lett. 2020 Aug 15 ;30(16):127356 link
  26. Remesh SG, Verma SC, Chen JH, Ekman AA, Larabell CA, Adhya S, Hammel M. “Nucleoid remodeling during environmental adaptation is regulated by HU-dependent DNA bundling.” Nat Commun 2020 Jun 09 ;11(1):2905 link
  27. Schellenberg MJ, Appel CD, Riccio AA, Butler LR, Krahn JM, Liebermann JA, Cortés-Ledesma F, Williams RS. “Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2.” Nucleic Acids Res. 2020 Jun 19 ;48(11):6310-6325 link
  28. DuPrez K, He F, Chen Z, Hilario E, Fan L. “Structural basis of the XPB-Bax1 complex as a dynamic helicase-nuclease machinery for DNA repair.” Nucleic Acids Res. 2020 Jun 19 ;48(11):6326-6339 link
  29. Tsutakawa SE, Sarker AH, Ng C, Arvai AS, Shin DS, Shih B, Jiang S, Thwin AC, Tsai MS, Willcox A, Her MZ, Trego KS, Raetz AG, Rosenberg D, Bacolla A, Hammel M, Griffith JD, Cooper PK, Tainer JA. “Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations.” Proc. Natl. Acad. Sci. U.S.A. 2020 Jun 23 ;117(25):14127-14138 link
  30. Oh DY, Matsumoto Y, Kitajiri SI, Kim NKD, Kim MY, Kim AR, Lee M, Lee C, Tomkinson AE, Katsuno T, Kim SY, Shin HW, Han JH, Lee S, Park WY, Choi BY. “POLD1 variants leading to reduced polymerase activity can cause hearing loss without syndromic features.” Hum. Mutat. 2020 May ;41(5):913-920 link
  31. Seacrist CD, Kuenze G, Hoffmann RM, Moeller BE, Burke JE, Meiler J, Blind RD. “Integrated Structural Modeling of Full-Length LRH-1 Reveals Inter-domain Interactions Contribute to Receptor Structure and Function.” Structure 2020 May 19 link
  32. Laciak AR, Korasick DA, Gates KS, Tanner JJ. “Structural analysis of pathogenic mutations targeting Glu427 of ALDH7A1, the hot spot residue of pyridoxine-dependent epilepsy.” J. Inherit. Metab. Dis. 2020 May ;43(3):635-644 link
  33. Gorelik A, Illes K, Nagar B. “Crystal Structure of the Mannose-6-Phosphate Uncovering Enzyme.” Structure (London, England : 1993) 2020 04 07 ;28(4):426-436.e3 link
  34. 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
  35. Zandarashvili L, Langelier MF, Velagapudi UK, Hancock MA, Steffen JD, Billur R, Hannan ZM, Wicks AJ, Krastev DB, Pettitt SJ, Lord CJ, Talele TT, Pascal JM, Black BE. “Structural basis for allosteric PARP-1 retention on DNA breaks.” Science 2020 04 03 ;368(6486)link
  36. Brunette TJ, Bick MJ, Hansen JM, Chow CM, Kollman JM, Baker D. “Modular repeat protein sculpting using rigid helical junctions.” Proc. Natl. Acad. Sci. U.S.A. 2020 Apr 03 link
  37. Chen Z, Kibler RD, Hunt A, Busch F, Pearl J, Jia M, VanAernum ZL, Wicky BIM, Dods G, Liao H, Wilken MS, Ciarlo C, Green S, El-Samad H, Stamatoyannopoulos J, Wysocki VH, Jewett MC, Boyken SE, Baker D. “De novo design of protein logic gates.” Science 2020 04 03 ;368(6486):78-84 link
  38. 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
  39. Wei KY, Moschidi D, Bick MJ, Nerli S, McShan AC, Carter LP, Huang PS, Fletcher DA, Sgourakis NG, Boyken SE, Baker D. “Computational design of closely related proteins that adopt two well-defined but structurally divergent folds.” Proc. Natl. Acad. Sci. U.S.A. 2020 03 31 ;117(13):7208-7215 link
  40. Stachowski TR, Snell ME, Snell EH. “Structural insights into conformational switching in latency-associated peptide between transforming growth factor β-1 bound and unbound states.” IUCrJ 2020 Mar 01 ;7(Pt 2):238-252 link
  41. Topolska-Woś AM, Sugitani N, Cordoba JJ, Le Meur KV, Le Meur RA, Kim HS, Yeo JE, Rosenberg D, Hammel M, Schärer OD, Chazin WJ. “A key interaction with RPA orients XPA in NER complexes.” Nucleic Acids Res. 2020 02 28 ;48(4):2173-2188 link
  42. Smith IW, d’Aquino AE, Coyle CW, Fedanov A, Parker ET, Denning G, Spencer HT, Lollar P, Doering CB, Spiegel PC. “The 3.2 Å structure of a bioengineered variant of blood coagulation factor VIII indicates two conformations of the C2 domain.” Journal of thrombosis and haemostasis : JTH 2020 01 ;18(1):57-69 link
  43. Russelburg LP, O’Shea Murray VL, Demir M, Knutsen KR, Sehgal SL, Cao S, David SS, Horvath MP. “Structural Basis for Finding OG Lesions and Avoiding Undamaged G by the DNA Glycosylase MutY.” ACS chemical biology 2020 01 17 ;15(1):93-102 link
  44. Berry KN, Brett TJ. “Structural and Biophysical Analysis of the CLCA1 VWA Domain Suggests Mode of TMEM16A Engagement.” Cell Rep 2020 Jan 28 ;30(4):1141-1151.e3 link
  45. Gao ZZ, Wang ZK, Wei L, Yin G, Tian J, Liu CZ, Wang H, Zhang DW, Zhang YB, Li X, Liu Y, Li ZT. “Water-Soluble 3D Covalent Organic Framework that Displays an Enhanced Enrichment Effect of Photosensitizers and Catalysts for the Reduction of Protons to H2.” ACS Appl Mater Interfaces 2020 Jan 08 ;12(1):1404-1411 link
  46. Herrmann J, Li PN, Jabbarpour F, Chan ACK, Rajkovic I, Matsui T, Shapiro L, Smit J, Weiss TM, Murphy MEP, Wakatsuki S. “A bacterial surface layer protein exploits multistep crystallization for rapid self-assembly.” Proc. Natl. Acad. Sci. U.S.A. 2020 01 07 ;117(1):388-394 link
  47. Tsai CL, Tripp P, Sivabalasarma S, Zhang C, Rodriguez-Franco M, Wipfler RL, Chaudhury P, Banerjee A, Beeby M, Whitaker RJ, Tainer JA, Albers SV. “The structure of the periplasmic FlaG-FlaF complex and its essential role for archaellar swimming motility.” Nat Microbiol 2020 01 ;5(1):216-225 link
  48. Weinhardt V, Chen JH, Ekman AA, Guo J, Remesh SG, Hammel M, McDermott G, Chao W, Oh S, Le Gros MA, Larabell CA. “Switchable resolution in soft x-ray tomography of single cells.” PLoS ONE 2020 ;15(1):e0227601 link

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