Highlights & Publications 2019

De novo design of tunable, pH-driven conformational changes.
Boyken SE, Benhaim MA, Busch F, Jia M, Bick MJ, Choi H, Klima JC, Chen Z, Walkey C, Mileant A, Sahasrabuddhe A, Wei KY, Hodge EA, Byron S, Quijano-Rubio A, Sankaran B, King NP, Lippincott-Schwartz J, Wysocki VH, Lee KK, Baker D. Science 2019 05 17 ;364(6441):658-664
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Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.
Brosey CA, Tainer JA., Curr. Opin. Struct. Biol. 2019 Jun 13
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Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences.
Hura GL, Hodge CD, Rosenberg D, Guzenko D, Duarte JM, Monastyrskyy B, Grudinin S, Kryshtafovych A, Tainer JA, Fidelis K, Tsutakawa SE., Proteins 2019 12 ;87(12):1298-1314
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  1. Hura GL, Hodge CD, Rosenberg D, Guzenko D, Duarte JM, Monastyrskyy B, Grudinin S, Kryshtafovych A, Tainer JA, Fidelis K, Tsutakawa SE. “Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences.” Proteins 2019 12 ;87(12):1298-1314 link
  2. Reimer JM, Eivaskhani M, Harb I, Guarné A, Weigt M, Schmeing TM. “Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility.” Science 2019 11 08 ;366(6466)link
  3. Foster B, Rosenberg D, Salvo H, Stephens KL, Bintz BJ, Hammel M, Ellenberger T, Gainey MD, Wallen J. “Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome.” Biochemistry 2019 Oct 29 link
  4. Xuan S, Jiang X, Spencer RK, Li NK, Prendergast D, Balsara NP, Zuckermann RN. “Atomic-level engineering and imaging of polypeptoid crystal lattices.” Proc. Natl. Acad. Sci. U.S.A. 2019 Oct 21 link
  5. Urusova DV, Kinsella RL, Salinas ND, Haurat MF, Feldman MF, Tolia NH. “The structure of Acinetobacter-secreted protease CpaA complexed with its chaperone CpaB reveals a novel mode of a T2SS chaperone-substrate interaction.” J. Biol. Chem. 2019 Sep 06 ;294(36):13344-13354 link
  6. Sathyanarayanan N, Cannone G, Gakhar L, Katagihallimath N, Sowdhamini R, Ramaswamy S, Vinothkumar KR. “Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway.” Nat Commun 2019 Sep 11 ;10(1):4127 link
  7. Horst BG, Yokom AL, Rosenberg DJ, Morris KL, Hammel M, Hurley JH, Marletta MA. “Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy.” Elife 2019 Sep 30 ;8link
  8. Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. “A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites.” Nat Commun 2019 Aug 09 ;10(1):3629 link
  9. Knott GJ, Cress BF, Liu JJ, Thornton BW, Lew RJ, Al-Shayeb B, Rosenberg DJ, Hammel M, Adler BA, Lobba MJ, Xu M, Arkin AP, Fellmann C, Doudna JA. “Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a.” Elife 2019 Aug 09 ;8link
  10. Zhou Y, Millott R, Kim HJ, Peng S, Edwards RA, Skene-Arnold T, Hammel M, Lees-Miller SP, Tainer JA, Holmes CFB, Glover JNM. “Flexible Tethering of ASPP Proteins Facilitates PP-1c Catalysis.” Structure 2019 Aug 06 link
  11. Lu TW, Wu J, Aoto PC, Weng JH, Ahuja LG, Sun N, Cheng CY, Zhang P, Taylor SS. “Two PKA RIα holoenzyme states define ATP as an isoform-specific orthosteric inhibitor that competes with the allosteric activator, cAMP.” Proc. Natl. Acad. Sci. U.S.A. 2019 Aug 13 ;116(33):16347-16356 link
  12. Miller TW, Amason JD, Garcin ED, Lamy L, Dranchak PK, Macarthur R, Braisted J, Rubin JS, Burgess TL, Farrell CL, Roberts DD, Inglese J. “Quantitative high-throughput screening assays for the discovery and development of SIRPα-CD47 interaction inhibitors.” PLoS ONE 2019 ;14(7):e0218897 link
  13. Langan RA, Boyken SE, Ng AH, Samson JA, Dods G, Westbrook AM, Nguyen TH, Lajoie MJ, Chen Z, Berger S, Mulligan VK, Dueber JE, Novak WRP, El-Samad H, Baker D. “De novo design of bioactive protein switches.” Nature 2019 Aug ;572(7768):205-210 link
  14. Pyles H, Zhang S, De Yoreo JJ, Baker D. “Controlling protein assembly on inorganic crystals through designed protein interfaces.” Nature 2019 07 ;571(7764):251-256 link
  15. Stachowski T, Grant TD, Snell EH. “Structural consequences of transforming growth factor beta-1 activation from near-therapeutic X-ray doses.” J Synchrotron Radiat 2019 Jul 01 ;26(Pt 4):967-979 link
  16. Brosey CA, Tainer JA. “Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.” Curr. Opin. Struct. Biol. 2019 Jun 13 link
  17. Ge J, Remesh SG, Hammel M, Pan S, Mahan AD, Wang S, Wang X. “Functional Relevance of Interleukin-1 Receptor Inter-domain Flexibility for Cytokine Binding and Signaling.” Structure 2019 Aug 06 ;27(8):1296-1307.e5 link
  18. Boyken SE, Benhaim MA, Busch F, Jia M, Bick MJ, Choi H, Klima JC, Chen Z, Walkey C, Mileant A, Sahasrabuddhe A, Wei KY, Hodge EA, Byron S, Quijano-Rubio A, Sankaran B, King NP, Lippincott-Schwartz J, Wysocki VH, Lee KK, Baker D. “De novo design of tunable, pH-driven conformational changes.” Science 2019 05 17 ;364(6441):658-664 link
  19. D’Arcy BM, Blount J, Prakash A. “Biochemical and structural characterization of two variants of uncertain significance in the PMS2 gene.” Hum. Mutat. 2019 Apr ;40(4):458-471 link
  20. Zhu J, Muia J, Gupta G, Westfield LA, Vanhoorelbeke K, Tolia NH, Sadler JE. “Exploring the “minimal” structure of a functional ADAMTS13 by mutagenesis and small-angle X-ray scattering.” Blood 2019 Apr 25 ;133(17):1909-1918 link
  21. Y Meng, L Xu-Bo, G Zhong-Zheng, W Yi-Peng, H Jun-Li, W Hui, Z Dan-Wei, L Yi, L Zhan-Ting “A pore-expanded supramolecular organic framework and its enrichment of photosensitizers and catalysts for visible-light-induced hydrogen production.“Org. Chem. Front. 2019 Apr 16; 6(10):1698-1704
  22. Amiri H, Noller HF. “Structural evidence for product stabilization by the ribosomal mRNA helicase.” RNA 2019 03 ;25(3):364-375 link
  23. Yan, M., X.-B. Liu, Z.-Z. Gao, Y.-P. Wu, J.-L. Hou, H. Wang, D.-W. Zhang, Y. Liu, and Z.-T. Li. “A pore-expanded supramolecular organic framework and its enrichment of photosensitizers and catalysts for visible-light-induced hydrogen production.” Org. Chem. Front. March 2019 ;6:1698–1704. doi:10.1039/C9QO00382G.
  24. Shahul Hameed UF, Liao C, Radhakrishnan AK, Huser F, Aljedani SS, Zhao X, Momin AA, Melo FA, Guo X, Brooks C, Li Y, Cui X, Gao X, Ladbury JE, Jaremko Ł, Jaremko M, Li J, Arold ST. “H-NS uses an autoinhibitory conformational switch for environment-controlled gene silencing.” Nucleic Acids Res. 2019 03 18 ;47(5):2666-2680 link
  25. Klass SH, Smith MJ, Fiala TA, Lee JP, Omole AO, Han BG, Downing KH, Kumar S, Francis MB. “Self-Assembling Micelles Based on an Intrinsically Disordered Protein Domain.” J. Am. Chem. Soc. 2019 Mar 13 ;141(10):4291-4299 link
  26. Chanthamontri CK, Jordan DS, Wang W, Wu C, Lin Y, Brett TJ, Gross ML, Leung DW. “The Ebola Viral Protein 35 N-Terminus Is a Parallel Tetramer.” Biochemistry 2019 Feb 12 ;58(6):657-664 link
  27. Bryant JM, Blind RD. “Signaling through non-membrane nuclear phosphoinositide binding proteins in human health and disease.” J. Lipid Res. 2019 Feb ;60(2):299-311 link
  28. Liu LK, Tanner JJ. “Crystal Structure of Aldehyde Dehydrogenase 16 Reveals Trans-Hierarchical Structural Similarity and a New Dimer.” J. Mol. Biol. 2019 Feb 01 ;431(3):524-541 link
  29. Qualley DF, Cooper SE, Ross JL, Olson ED, Cantara WA, Musier-Forsyth K. “Solution Conformation of Bovine Leukemia Virus Gag Suggests an Elongated Structure.” J. Mol. Biol. 2019 Mar 15 ;431(6):1203-1216 link
  30. Korasick DA, Končitíková R, Kopečná M, Hájková E, Vigouroux A, Moréra S, Becker DF, Šebela M, Tanner JJ, Kopečný D. “Structural and Biochemical Characterization of Aldehyde Dehydrogenase 12, the Last Enzyme of Proline Catabolism in Plants.” J Mol Biol. 2019 Feb 1;431(3):576-592. link
  31. Chen Z, Boyken SE, Jia M, Busch F, Flores-Solis D, Bick MJ, Lu P, VanAernum ZL, Sahasrabuddhe A, Langan RA, Bermeo S, Brunette TJ, Mulligan VK, Carter LP, DiMaio F, Sgourakis NG, Wysocki VH, Baker D. “Programmable design of orthogonal protein heterodimers.” Nature 2019 01 ;565(7737):106-111 link
  32. West AM, Rosenberg SC, Ur SN, Lehmer MK, Ye Q, Hagemann G, Caballero I, Usón I, MacQueen AJ, Herzog F, Corbett KD. “A conserved filamentous assembly underlies the structure of the meiotic chromosome axis.“Elife. 2019 Jan 18;8. pii: e40372. doi: 10.7554/eLife.40372. link

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