Oligooxopiperazines as helix mimetics

Oligooxopiperazines

The Arora lab is interested in protein design. They have demonstrated that oligooxopiperazines (shown on the left) are a new class of nonpeptidic helix mimetics derived from amino acids and featuring chiral backbones. Oligooxopiperazine dimers adopt stable conformations that reproduce the arrangement of i, i+4, and i+7 residues on an α-helix (shown in green on the right). This work has been published in Org. Lett. 12:1588 (2010).

 

 

Representative Student Publications

(* indicates student in Molecular Biophysics Program)

  1. Czyzewski BC* and Wang DN. Identification and characterization of a bacterial hydrosulfide ion channel. Nature. 483:494-497 (2012)

  2. Decker KB, James TD*, Stibitz S, Hinton DM. The Bordetella pertussis model of exquisite gene control by the global transcription factor BvgA. Microbiology. In press. (2012)

  3. Gorny MK, Pan R, Williams C, Wang XH, Volsky B, O'Neal T, Spurrier B*, Sampson JM, Li L, Seaman MS, Kong XP, Zolla-Pazner S. Functional and immunochemical cross-reactivity of V2-specific monoclonal antibodies from HIV-1-infected individuals. Virology 427:198-207. (2012)

  4. Kirigin FF*, Lindstedt K, Sellars M, Ciofani M, Low SL, Jones L, Bell F, Pauli F, Bonneau R, Myers RM, Littman DR, Chong MM. Dynamic microRNA gene transcription and processing during T cell development. J Immunol. 188:3257-67. (2012)

  5. Bartelle BB*, Berríos-Otero CA, Rodriguez JJ, Friedland AE, Aristizábal O, Turnbull DH. Novel genetic approach for in vivo vascular imaging in mice. Circ Res. 110:938-47. (2012)

  6. Baltz AG, Munschauer M, Schwanhäusser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K*, Milek M, Wyler E, Bonneau R, Selbach M, Dieterich C, Landthaler M. The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts.  Mol Cell. 46:674-90. (2012)

  7. Lin, PC*; Xu RM. Structure and assembly of the SF3a splicing factor complex of U2 snRNP. EMBO J. 31:1579-1590. (2012)

  8. Gonsalves, FC; Klein, K*; Carson, BB; Katz, S; Ekas, LA; Evans, S; Nagourney, R; Cardozo, T; Brown, AMC; Dasgupta, R. Feature Article: From the Cover: An RNAi-based chemical genetic screen identifies three small-molecule inhibitors of the Wnt/wingless signaling pathway. PNAS 108:5954-63, (2011)

  9. Nans A*, Mohandas N, Stokes DL. Native ultrastructure of the red cell cytoskeleton by cryo-electron tomography. Biophys J. 101:2341-50 (2011)

  10. Mancusso R*, Karpowich NK, Czyzewski BC* and Wang DN. Simple screening method for improving membrane protein thermostability. Methods. 55:324-329. (2011)

  11. Spurrier B*, Sampson JM, Totrov M, Li H, O'Neal T, Williams C, Robinson J, Gorny MK, Zolla-Pazner S, Kong XP. Structural analysis of human and macaque mAbs 2909 and 2.5B: implications for the configuration of the quaternary neutralizing epitope of HIV-1 gp120. Structure. 19: 691-9. (2011)

  12. Zhou Z, Feng H, Zhou BR, Ghirlando R, Hu K, Zwolak A*, Miller Jenkins LM, Xiao H, Tjandra N, Wu C, Bai Y. Structural basis for recognition of centromere histone variant CenH3 by the chaperone Scm3. Nature. 472:234-7. (2011)

  13. Zwolak A*, Uruno T, Piszczek G, Hammer JA 3rd, Tjandra N. Molecular basis for barbed end uncapping by CARMIL homology domain 3 of mouse CARMIL-1. J Biol Chem. 285:29014-26. (2010)

  14. Zwolak A*, Fujiwara I, Hammer JA 3rd, Tjandra N. Structural basis for capping protein sequestration by myotrophin (V-1). J Biol Chem. 285:25767-81. (2010)

  15. Zhong S, Malecek K*, Perez-Garcia A, Krogsgaard M. Retroviral transduction of T-cell receptors in mouse T-cells. J Vis Exp. pii: 2307. (2010)

  16. Nans, A.*, Einheber, S., Salzer J.L. & Stokes, D.L. Electron tomography of paranodal septate-like junctions and the associated axonal and glial cytoskeletons in the central nervous system. J Neuro Res 89:310-319 (2010).

  17. Waight, A.B.*, Love, J. & Wang, D.N. Structure and mechanism of a pentameric formate channel. Nat Struct Mol Biol 17, 31-7 (2010).

  18. James, T.D.*, Cashel, M. & Hinton, D. A. A mutation within the b subunit of E. coli RNA polymerase impairs transcription from bacteriophage T4 middle promoters. J Bacteriol 192, 5580-87 (2010).

  19. Bergamin, E.*, Hallock, P.T., Burden, S.J. & Hubbard, S.R. The cytoplasmic adaptor Dok7 activates the receptor tyrosin kinase MuSK via dimerization. Mol Cell 38, 100-9 (2010).

  20. Depetris, R. S.*, Wu, J. & Hubbard, S. R. Structural and functional studies of the Ras-associating and pleckstrin-homology domains of Grb10 and Grb14. Nat Struct Mol Biol 16, 833-9 (2009).

  21. Spellman, D. S.*, Deinhardt, K., Darie, C. C., Chao, M. V. & Neubert, T. A. Stable isotopic labeling by amino acids in cultured primary neurons: application to brain-derived neurotrophic factor-dependent phosphotyrosine-associated signaling. Mol Cell Proteomics 7, 1067-76 (2008). Cover.

  22. Deans, A. E.*, Wadghiri, Y. Z., Berrios-Otero, C. A. & Turnbull, D. H. Mn enhancement and respiratory gating for in utero MRI of the embryonic mouse central nervous system. Magn Reson Med 59, 1320-8 (2008).

  23. Pomfret, A. J.*, Rice, W. J. & Stokes, D. L. Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases. J Struct Biol 157, 106-16 (2007).

  24. Bergamin, E.*, Wu, J., Hubbard, S. R. Structural basis for phosphotyrosine recognition by suppressor of cytokine signaling-3. Structure 14, 1285-92 (2006).

  25. Huang, Y., Lemieux, M. J*., Song, J., Auer, M. & Wang, D. N. Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science 301, 616-20 (2003).