Publications 2023

Highlights & Publications 2023

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Rubisco
SAXS curves for Limnocylindria sp. unbound (Apo) and bound to transition state analog (CABP) against AlphaFold model.
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3-dimenstional protein crystals
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  1. Mahoney BJ, Goring AK, Wang Y, Dasika P, Zhou A, Grossbard E, Cascio D, Loo JA, Clubb RT. “Development and atomic structure of a new fluorescence-based sensor to probe heme transfer in bacterial pathogens.” Journal of inorganic biochemistry 2023 Dec ;249:112368 link
  2. Bethel NP, Borst AJ, Parmeggiani F, Bick MJ, Brunette TJ, Nguyen H, Kang A, Bera AK, Carter L, Miranda MC, Kibler RD, Lamb M, Li X, Sankaran B, Baker D. “Precisely patterned nanofibres made from extendable protein multiplexes.” Nature chemistry 2023 Dec ;15(12):1664-1671 link
  3. Cordoba JJ, Mullins EA, Salay LE, Eichman BF, Chazin WJ. “Flexibility and Distributive Synthesis Regulate RNA Priming and Handoff in Human DNA Polymerase α-Primase.” Journal of molecular biology 2023 Dec 15 ;435(24):168330 link
  4. Martinez-Yamout MA, Nasir I, Shnitkind S, Ellis JP, Berlow RB, Kroon G, Deniz AA, Dyson HJ, Wright PE. “Glutamine-rich regions of the disordered CREB transactivation domain mediate dynamic intra- and intermolecular interactions.” Proceedings of the National Academy of Sciences of the United States of America 2023 Nov 21 ;120(47):e2313835120 link
  5. Motycka B, Csarman F, Rupp M, Schnabel K, Nagy G, Karnpakdee K, Scheiblbrandner S, Tscheliessnig R, Oostenbrink C, Hammel M, Ludwig R. “Amino Acid Residues Controlling Domain Interaction and Interdomain Electron Transfer in Cellobiose Dehydrogenase.” Chembiochem : a European journal of chemical biology 2023 Nov 16 ;24(22):e202300431 link
  6. Liu AK, Kaeser B, Chen L, West-Roberts J, Taylor-Kearney LJ, Lavy A, Günzing D, Li WJ, Hammel M, Nogales E, Banfield JF, Shih PM. “Deep-branching evolutionary intermediates reveal structural origins of form I rubisco.” Current biology : CB 2023 Nov 11 link
  7. Doyle LA, Takushi B, Kibler RD, Milles LF, Orozco CT, Jones JD, Jackson SE, Stoddard BL, Bradley P. “De novo design of knotted tandem repeat proteins.” Nature communications 2023 Oct 24 ;14(1):6746 link
  8. Swift ML, Zhou R, Syed A, Moreau LA, Tomasik B, Tainer JA, Konstantinopoulos PA, D’Andrea AD, He YJ, Chowdhury D. “Dynamics of the DYNLL1-MRE11 complex regulate DNA end resection and recruitment of Shieldin to DSBs.” Nature structural & molecular biology 2023 Oct ;30(10):1456-1467 link
  9. Li Z, Wang S, Nattermann U, Bera AK, Borst AJ, Yaman MY, Bick MJ, Yang EC, Sheffler W, Lee B, Seifert S, Hura GL, Nguyen H, Kang A, Dalal R, Lubner JM, Hsia Y, Haddox H, Courbet A, Dowling Q, Miranda M, Favor A, Etemadi A, Edman NI, Yang W, Weidle C, Sankaran B, Negahdari B, Ross MB, Ginger DS, Baker D. “Accurate computational design of three-dimensional protein crystals.” Nature materials 2023 Oct 16 link
  10. Sweeney DT, Zárate-Pérez F, Stokowa-Sołtys K, Hackett JC. “Induced Fit Describes Ligand Binding to Membrane-Associated Cytochrome P450 3A4.” Molecular pharmacology 2023 Oct ;104(4):154-163 link
  11. Cordoba JJ, Mullins EA, Salay LE, Eichman BF, Chazin WJ. “Flexibility and Distributive Synthesis Regulate RNA Priming and Handoff in Human DNA Polymerase α-Primase.” Journal of molecular biology 2023 Oct 24 ;435(24):168330 link
  12. Warden MS, DeRose EF, Tamayo JV, Mueller GA, Gavis ER, Hall TMT. “The translational repressor Glorund uses interchangeable RNA recognition domains to recognize Drosophila nanos.” Nucleic acids research 2023 Sep 08 ;51(16):8836-8849 link
  13. Cui G, Botuyan MV, Drané P, Hu Q, Bragantini B, Thompson JR, Schuller DJ, Detappe A, Perfetti MT, James LI, Frye SV, Chowdhury D, Mer G. “An autoinhibited state of 53BP1 revealed by small molecule antagonists and protein engineering.” Nature communications 2023 Sep 29 ;14(1):6091 link
  14. Hur Y, Huynh J, Leong E, Dosanjh R, Charvat AF, Vu MH, Alam Z, Lee YT, Cabreros CC, Carroll EC, Hura GL, Wang N. “The differing effects of a dual acting regulator on SIRT1.” Frontiers in molecular biosciences 2023 ;10:1260489 link
  15. McKay CE, Cheng J, Tanner JJ. “Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold.” Scientific reports 2023 Aug 18 ;13(1):13496 link
  16. Xu Q, Ma F, Yang D, Li Q, Yan L, Ou J, Zhang L, Liu Y, Zhan Q, Li R, Wei Q, Hu H, Wang Y, Li X, Zhang S, Yang J, Chai S, Du Y, Wang L, Zhang E, Zhang G. “Rice-produced classical swine fever virus glycoprotein E2 with herringbone-dimer design to enhance immune responses.” Plant biotechnology journal 2023 Aug 12 link
  17. O’Brien Laramy MN, Costa AP, Cebrero YM, Joseph J, Sarode A, Zang N, Kim LJ, Hofmann K, Wang S, Goyon A, Koenig SG, Hammel M, Hura GL. “Process Robustness in Lipid Nanoparticle Production: A Comparison of Microfluidic and Turbulent Jet Mixing.” Molecular pharmaceutics 2023 Aug 07 ;20(8):4285-4296 link
  18. Salinas ND, Ma R, Dickey TH, McAleese H, Ouahes T, Long CA, Miura K, Lambert LE, Tolia NH. “A potent and durable malaria transmission-blocking vaccine designed from a single-component 60-copy Pfs230D1 nanoparticle.” NPJ vaccines 2023 Aug 18 ;8(1):124 link
  19. Longo MA, Roy S, Chen Y, Tomaszowski KH, Arvai AS, Pepper JT, Boisvert RA, Kunnimalaiyaan S, Keshvani C, Schild D, Bacolla A, Williams GJ, Tainer JA, Schlacher K. “RAD51C-XRCC3 structure and cancer patient mutations define DNA replication roles.” Nature communications 2023 Jul 24 ;14(1):4445 link
  20. Pang Y, Huang M, Fan Y, Yeh HW, Xiong Y, Ng HL, Ai HW. “Development, Characterization, and Structural Analysis of a Genetically Encoded Red Fluorescent Peroxynitrite Biosensor.” ACS chemical biology 2023 Jun 16 ;18(6):1388-1397 link
  21. Hammel M, Fan Y, Sarode A, Byrnes AE, Zang N, Kou P, Nagapudi K, Leung D, Hoogenraad CC, Chen T, Yen CW, Hura GL. “Correlating the Structure and Gene Silencing Activity of Oligonucleotide-Loaded Lipid Nanoparticles Using Small-Angle X-ray Scattering.” ACS nano 2023 Jun 27 ;17(12):11454-11465 link
  22. Motycka B, Csarman F, Tscheliessnig R, Hammel M, Ludwig R. “Resolving domain positions of cellobiose dehydrogenase by small angle X-ray scattering.” The FEBS journal 2023 Jun 08 link
  23. Gedara SH, Wood E, Gustafson A, Liang C, Hung SH, Savage J, Phan P, Luthra A, de Crécy-Lagard V, Dedon P, Swairjo MA, Iwata-Reuyl D. “7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system.” Nucleic acids research 2023 May 08 ;51(8):3836-3854 link
  24. Wu K, Bai H, Chang YT, Redler R, McNally KE, Sheffler W, Brunette TJ, Hicks DR, Morgan TE, Stevens TJ, Broerman A, Goreshnik I, DeWitt M, Chow CM, Shen Y, Stewart L, Derivery E, Silva DA, Bhabha G, Ekiert DC, Baker D. “De novo design of modular peptide-binding proteins by superhelical matching.” Nature 2023 Apr ;616(7957):581-589 link
  25. Mauriello GE, Moncure GE, Nowzari RA, Miller CJ, Wright NT. “The N-terminus of obscurin is flexible in solution.” Proteins 2023 Apr ;91(4):485-496 link
  26. Lutz ID, Wang S, Norn C, Courbet A, Borst AJ, Zhao YT, Dosey A, Cao L, Xu J, Leaf EM, Treichel C, Litvicov P, Li Z, Goodson AD, Rivera-Sánchez P, Bratovianu AM, Baek M, King NP, Ruohola-Baker H, Baker D. “Top-down design of protein architectures with reinforcement learning.” Science (New York, N.Y.) 2023 Apr 21 ;380(6642):266-273 link
  27. Díaz Casas A, Cordoba JJ, Ferrer BJ, Balakrishnan S, Wurm JE, Pastrana-Ríos B, Chazin WJ. “Binding by calmodulin is coupled to transient unfolding of the third FF domain of Prp40A.” Protein science : a publication of the Protein Society 2023 Apr ;32(4):e4606 link
  28. Pratsinis A, Fan Y, Portmann M, Hammel M, Kou P, Sarode A, Ringler P, Kovacik L, Lauer ME, Lamerz J, Hura GL, Yen CW, Keller M. “Impact of non-ionizable lipids and phase mixing methods on structural properties of lipid nanoparticle formulations.” International journal of pharmaceutics 2023 Apr 25 ;637:122874 link
  29. Prabhakar PK, Pereira JH, Taujale R, Shao W, Bharadwaj VS, Chapla D, Yang JY, Bomble YJ, Moremen KW, Kannan N, Hammel M, Adams PD, Scheller HV, Urbanowicz BR. “Structural and biochemical insight into a modular β-1,4-galactan synthase in plants.” Nature plants 2023 Mar ;9(3):486-500 link
  30. Kaur G, Ren R, Hammel M, Horton JR, Yang J, Cao Y, He C, Lan F, Lan X, Blobel GA, Blumenthal RM, Zhang X, Cheng X. “Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410-DNA interaction using small angle X-ray scattering.” Nucleic acids research 2023 Feb 28 ;51(4):1674-1686 link
  31. Martinez-D’Alto A, Yan X, Detomasi TC, Sayler RI, Thomas WC, Talbot NJ, Marletta MA. “Characterization of a unique polysaccharide monooxygenase from the plant pathogen Magnaporthe oryzae.” Proceedings of the National Academy of Sciences of the United States of America 2023 Feb 21 ;120(8):e2215426120 link
  32. Gerben SR, Borst AJ, Hicks DR, Moczygemba I, Feldman D, Coventry B, Yang W, Bera AK, Miranda M, Kang A, Nguyen H, Baker D. “Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins.” Biochemistry 2023 Jan 17 ;62(2):358-368 link
  33. Kappes EC, Kattamuri C, Czepnik M, Yarawsky AE, Brûlé E, Wang Y, Ongaro L, Herr AB, Walton KL, Bernard DJ, Thompson TB. “Follistatin Forms a Stable Complex With Inhibin A That Does Not Interfere With Activin A Antagonism.” Endocrinology 2023 Jan 09 ;164(3)link
  34. Paraan M, Nasef M, Chou-Zheng L, Khweis SA, Schoeffler AJ, Hatoum-Aslan A, Stagg SM, Dunkle JA. “The structure of a Type III-A CRISPR-Cas effector complex reveals conserved and idiosyncratic contacts to target RNA and crRNA among Type III-A systems.” PloS one 2023 ;18(6):e0287461 link
  35. Macdonald R, Mahoney BJ, Soule J, Goring AK, Ford J, Loo JA, Cascio D, Clubb RT. “The Shr receptor from Streptococcus pyogenes uses a cap and release mechanism to acquire heme-iron from human hemoglobin.” Proceedings of the National Academy of Sciences of the United States of America 2023 Jan 31 ;120(5):e2211939120 link
  36. Gerben SR, Borst AJ, Hicks DR, Moczygemba I, Feldman D, Coventry B, Yang W, Bera AK, Miranda M, Kang A, Nguyen H, Baker D. “Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins.” Biochemistry 2023 Jan 17 ;62(2):358-368 link
  37. Tsai WJ, Lai YH, Shi YA, Hammel M, Duff AP, Whitten AE, Wilde KL, Wu CM, Knott R, Jeng US, Kang CY, Hsu CY, Wu JL, Tsai PJ, Chiang-Ni C, Wu JJ, Lin YS, Liu CC, Senda T, Wang S. “Structural basis underlying the synergism of NADase and SLO during group A Streptococcus infection.” Communications biology 2023 Jan 31 ;6(1):124 link
  38. Kaur G, Ren R, Hammel M, Horton JR, Yang J, Cao Y, He C, Lan F, Lan X, Blobel GA, Blumenthal RM, Zhang X, Cheng X. “Allosteric autoregulation of DNA binding via a DNA-mimicking protein domain: a biophysical study of ZNF410-DNA interaction using small angle X-ray scattering.” Nucleic acids research 2023 Jan 20 link
  39. Chinnam NB, Syed A, Hura GL, Hammel M, Tainer JA, Tsutakawa SE. “Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution.” Methods in enzymology 2023 ;678:351-376 link
  40. Brosey CA, Shen R, Moiani D, Jones DE, Burnett K, Hura GL, Tainer JA. “Applying HT-SAXS to chemical ligand screening.” Methods in enzymology 2023 ;678:331-350 link
  41. Murray DT, Shin DS, Classen S, Brosey CA, Hura GL. “Visualizing and accessing correlated SAXS data sets with Similarity Maps and Simple Scattering web resources.” Methods in enzymology 2023 ;678:411-440 link

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