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. 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:e40372 link
  2. 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 Jan ;565(7737):106-111 link
  3. Liu LK, Tanner JJ. “Crystal Structure of Aldehyde Dehydrogenase 16 Reveals Trans-Hierarchical Structural Similarity and a New Dimer.” Journal of molecular biology 2019 Feb 01 ;431(3):524-541 link
  4. 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.” Journal of molecular biology 2019 Feb 01 ;431(3):576-592 link
  5. 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
  6. Bryant JM, Blind RD. “Signaling through non-membrane nuclear phosphoinositide binding proteins in human health and disease.” Journal of lipid research 2019 Feb ;60(2):299-311 link
  7. 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.” Journal of the American Chemical Society 2019 Mar 13 ;141(10):4291-4299 link
  8. Qualley DF, Cooper SE, Ross JL, Olson ED, Cantara WA, Musier-Forsyth K. “Solution Conformation of Bovine Leukemia Virus Gag Suggests an Elongated Structure.” Journal of molecular biology 2019 Mar 15 ;431(6):1203-1216 link
  9. 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 research 2019 Mar 18 ;47(5):2666-2680 link
  10. Amiri H, Noller HF. “Structural evidence for product stabilization by the ribosomal mRNA helicase.” RNA (New York, N.Y.) 2019 Mar ;25(3):364-375 link
  11. 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
  12. D’Arcy BM, Blount J, Prakash A. “Biochemical and structural characterization of two variants of uncertain significance in the PMS2 gene.” Human mutation 2019 Apr ;40(4):458-471 link
  13. 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 (New York, N.Y.) 2019 May 17 ;364(6441):658-664 link
  14. Stachowski T, Grant TD, Snell EH. “Structural consequences of transforming growth factor beta-1 activation from near-therapeutic X-ray doses.” Journal of synchrotron radiation 2019 Jul 01 ;26(Pt 4):967-979 link
  15. Pyles H, Zhang S, De Yoreo JJ, Baker D. “Controlling protein assembly on inorganic crystals through designed protein interfaces.” Nature 2019 Jul ;571(7764):251-256 link
  16. 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 (London, England : 1993) 2019 Aug 06 ;27(8):1296-1307.e5 link
  17. 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.” Nature communications 2019 Aug 09 ;10(1):3629 link
  18. 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 ;8:e49110 link
  19. 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.” Proceedings of the National Academy of Sciences of the United States of America 2019 Aug 13 ;116(33):16347-16356 link
  20. 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
  21. 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.” The Journal of biological chemistry 2019 Sep 06 ;294(36):13344-13354 link
  22. 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.” Nature communications 2019 Sep 11 ;10(1):4127 link
  23. 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 ;8:e50634 link
  24. 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 (London, England : 1993) 2019 Oct 01 ;27(10):1485-1496.e4 link
  25. Brosey CA, Tainer JA. “Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.” Current opinion in structural biology 2019 Oct ;58:197-213 link
  26. Xuan S, Jiang X, Spencer RK, Li NK, Prendergast D, Balsara NP, Zuckermann RN. “Atomic-level engineering and imaging of polypeptoid crystal lattices.” Proceedings of the National Academy of Sciences of the United States of America 2019 Nov 05 ;116(45):22491-22499 link
  27. Reimer JM, Eivaskhani M, Harb I, Guarné A, Weigt M, Schmeing TM. “Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility.” Science (New York, N.Y.) 2019 Nov 08 ;366(6466):eaaw4388 link
  28. Foster BM, Rosenberg D, Salvo H, Stephens KL, Bintz BJ, Hammel M, Ellenberger T, Gainey MD, Wallen JR. “Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome.” Biochemistry 2019 Nov 12 ;58(45):4466-4479 link
  29. 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 Dec ;87(12):1298-1314 link
  30. 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
  31. Yan M, Liu XB, Gao ZZ, Wu YP, Hou JL, Wang H, Zhang DW, Liu Y, Li ZT. “A pore-expanded supramolecular organic framework and its enrichment of photosensitizers and catalysts for visible-light-induced hydrogen production.” Organic Chemistry Frontiers 2019 ;6(10):1698-1704

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