Kobe:Publications

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2008

1. Androulakis S, Schmidberger J, Bate MA, DeGori R, Beitz A, Keong C, Cameron B, McGowan S, Porter CJ, Harrison A, Hunter J, Martin JL, Kobe B, Dobson RC, Parker MW, Whisstock JC, Gray J, Treloar A, Groenewegen D, Dickson N, and Buckle AM. Federated repositories of X-ray diffraction images. Acta Crystallogr D Biol Crystallogr. 2008 Jul;D64(Pt 7):810-4. DOI:10.1107/S0907444908015540 |
2. Saunders NF, Brinkworth RI, Huber T, Kemp BE, and Kobe B. Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites. BMC Bioinformatics. 2008 May 26;9:245. DOI:10.1186/1471-2105-9-245 |
3. Saunders NF and Kobe B. The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W286-90. DOI:10.1093/nar/gkn279 |
4. Frith MC, Saunders NF, Kobe B, and Bailey TL. Discovering sequence motifs with arbitrary insertions and deletions. PLoS Comput Biol. 2008 May 9;4(4):e1000071. DOI:10.1371/journal.pcbi.1000071 |
5. Lonic A, Barry EF, Quach C, Kobe B, Saunders N, and Guthridge MA. Fibroblast growth factor receptor 2 phosphorylation on serine 779 couples to 14-3-3 and regulates cell survival and proliferation. Mol Cell Biol. 2008 May;28(10):3372-85. DOI:10.1128/MCB.01837-07 |
6. Mueller DS, Kampmann T, Yennamalli R, Young PR, Kobe B, and Mark AE. Histidine protonation and the activation of viral fusion proteins. Biochem Soc Trans. 2008 Feb;36(Pt 1):43-5. DOI:10.1042/BST0360043 |

2007

7. Cowieson NP, Miles AJ, Robin G, Forwood JK, Kobe B, Martin JL, and Wallace BA. Evaluating protein:protein complex formation using synchrotron radiation circular dichroism spectroscopy. Proteins. 2008 Mar;70(4):1142-6. DOI:10.1002/prot.21631 |
8. Thakur AS, Robin G, Guncar G, Saunders NF, Newman J, Martin JL, and Kobe B. Improved success of sparse matrix protein crystallization screening with heterogeneous nucleating agents. PLoS One. 2007 Oct 31;2(10):e1091. DOI:10.1371/journal.pone.0001091 |
9. Forwood JK, Thakur AS, Guncar G, Marfori M, Mouradov D, Meng W, Robinson J, Huber T, Kellie S, Martin JL, Hume DA, and Kobe B. Structural basis for recruitment of tandem hotdog domains in acyl-CoA thioesterase 7 and its role in inflammation. Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10382-7. DOI:10.1073/pnas.0700974104 |
10. Schmidt SA, Williams SJ, Wang CI, Sornaraj P, James B, Kobe B, Dodds PN, Ellis JG, and Anderson PA. Purification of the M flax-rust resistance protein expressed in Pichia pastoris. Plant J. 2007 Jun;50(6):1107-17. DOI:10.1111/j.1365-313X.2007.03104.x |
11. Guncar G, Wang CI, Forwood JK, Teh T, Catanzariti AM, Ellis JG, Dodds PN, and Kobe B. The use of Co2+ for crystallization and structure determination, using a conventional monochromatic X-ray source, of flax rust avirulence protein. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Mar 1;63(Pt 3):209-13. DOI:10.1107/S1744309107004599 |
12. Wang CI, Guncar G, Forwood JK, Teh T, Catanzariti AM, Lawrence GJ, Loughlin FE, Mackay JP, Schirra HJ, Anderson PA, Ellis JG, Dodds PN, and Kobe B. Crystal structures of flax rust avirulence proteins AvrL567-A and -D reveal details of the structural basis for flax disease resistance specificity. Plant Cell. 2007 Sep;19(9):2898-912. DOI:10.1105/tpc.107.053611 |

2006

13. Bogoyevitch MA and Kobe B. Uses for JNK: the many and varied substrates of the c-Jun N-terminal kinases. Microbiol Mol Biol Rev. 2006 Dec;70(4):1061-95. DOI:10.1128/MMBR.00025-06 |
14. Puri M, Robin G, Cowieson N, Forwood JK, Listwan P, Hu SH, Guncar G, Huber T, Kellie S, Hume DA, Kobe B, and Martin JL. Focusing in on structural genomics: the University of Queensland structural biology pipeline. Biomol Eng. 2006 Dec;23(6):281-9. DOI:10.1016/j.bioeng.2006.09.002 |
15. Kampmann T, Mueller DS, Mark AE, Young PR, and Kobe B. The Role of histidine residues in low-pH-mediated viral membrane fusion. Structure. 2006 Oct;14(10):1481-7. DOI:10.1016/j.str.2006.07.011 |
16. Kurz M, Cowieson NP, Robin G, Hume DA, Martin JL, Kobe B, and Listwan P. Incorporating a TEV cleavage site reduces the solubility of nine recombinant mouse proteins. Protein Expr Purif. 2006 Nov;50(1):68-73. DOI:10.1016/j.pep.2006.05.006 |
17. Dodds PN, Lawrence GJ, Catanzariti AM, Teh T, Wang CI, Ayliffe MA, Kobe B, and Ellis JG. Direct protein interaction underlies gene-for-gene specificity and coevolution of the flax resistance genes and flax rust avirulence genes. Proc Natl Acad Sci U S A. 2006 Jun 6;103(23):8888-93. DOI:10.1073/pnas.0602577103 |
18. Serek R, Forwood JK, Hume DA, Martin JL, and Kobe B. Crystallization of the C-terminal domain of the mouse brain cytosolic long-chain acyl-CoA thioesterase. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Feb 1;62(Pt 2):133-5. DOI:10.1107/S1744309106000030 |
19. Cowieson NP, Wensley B, Listwan P, Hume DA, Kobe B, and Martin JL. An automatable screen for the rapid identification of proteins amenable to refolding. Proteomics. 2006 Mar;6(6):1750-7. DOI:10.1002/pmic.200500056 |
20. Brinkworth RI, Munn AL, and Kobe B. Protein kinases associated with the yeast phosphoproteome. BMC Bioinformatics. 2006 Jan 31;7:47. DOI:10.1186/1471-2105-7-47 |
21. Mouradov D, Craven A, Forwood JK, Flanagan JU, García-Castellanos R, Gomis-Rüth FX, Hume DA, Martin JL, Kobe B, and Huber T. Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking. Protein Eng Des Sel. 2006 Jan;19(1):9-16. DOI:10.1093/protein/gzi070 |

2005

22. Listwan P, Cowieson N, Kurz M, Hume DA, Martin JL, and Kobe B. Modification of recombinatorial cloning for small affinity tag fusion protein construct generation. Anal Biochem. 2005 Nov 15;346(2):327-9. DOI:10.1016/j.ab.2005.06.016 |
23. Kobe B, Kampmann T, Forwood JK, Listwan P, and Brinkworth RI. Substrate specificity of protein kinases and computational prediction of substrates. Biochim Biophys Acta. 2005 Dec 30;1754(1-2):200-9. DOI:10.1016/j.bbapap.2005.07.036 |
24. Cowieson NP, Listwan P, Kurz M, Aagaard A, Ravasi T, Wells C, Huber T, Hume DA, Kobe B, and Martin JL. Pilot studies on the parallel production of soluble mouse proteins in a bacterial expression system. J Struct Funct Genomics. 2005;6(1):13-20. DOI:10.1007/s10969-005-0462-7 |
25. Ren G, Wang J, Brinkworth R, Winsor B, Kobe B, and Munn AL. Verprolin cytokinesis function mediated by the Hof one trap domain. Traffic. 2005 Jul;6(7):575-93. DOI:10.1111/j.1600-0854.2005.00300.x |
26. Fontes MR, Teh T, Riell RD, Park SB, Standaert RF, and Kobe B. Crystallization and preliminary X-ray diffraction analysis of importin-alpha complexed with NLS peptidomimetics. Biochim Biophys Acta. 2005 Jun 15;1750(1):9-13. DOI:10.1016/j.bbapap.2005.03.014 |
27. Aagaard A, Listwan P, Cowieson N, Huber T, Ravasi T, Wells CA, Flanagan JU, Kellie S, Hume DA, Kobe B, and Martin JL. An inflammatory role for the mammalian carboxypeptidase inhibitor latexin: relationship to cystatins and the tumor suppressor TIG1. Structure. 2005 Feb;13(2):309-17. DOI:10.1016/j.str.2004.12.013 |

2004

28. Huber T and Kobe B. Comment on 'protein isoelectric point as a predictor for increased crystallization screening efficiency'. Bioinformatics. 2004 Sep 22;20(14):2169-70; author reply 2171-4. DOI:10.1093/bioinformatics/bth452 |
29. Lay CS, Wilson KA, Kobe B, Kemp BE, Drummer HE, and Poumbourios P. Expression and biochemical analysis of the entire HIV-2 gp41 ectodomain: determinants of stability map to N- and C-terminal sequences outside the 6-helix bundle core. FEBS Lett. 2004 Jun 4;567(2-3):183-8. DOI:10.1016/j.febslet.2004.04.054 |

2003

30. Fontes MR, Teh T, Toth G, John A, Pavo I, Jans DA, and Kobe B. Role of flanking sequences and phosphorylation in the recognition of the simian-virus-40 large T-antigen nuclear localization sequences by importin-alpha. Biochem J. 2003 Oct 15;375(Pt 2):339-49. DOI:10.1042/BJ20030510 |
31. Smyth DR, Mrozkiewicz MK, McGrath WJ, Listwan P, and Kobe B. Crystal structures of fusion proteins with large-affinity tags. Protein Sci. 2003 Jul;12(7):1313-22. DOI:10.1110/ps.0243403 |
32. Fontes MR, Teh T, Jans D, Brinkworth RI, and Kobe B. Structural basis for the specificity of bipartite nuclear localization sequence binding by importin-alpha. J Biol Chem. 2003 Jul 25;278(30):27981-7. DOI:10.1074/jbc.M303275200 |
33. Wooh JW, Kidd RD, Martin JL, and Kobe B. Comparison of three commercial sparse-matrix crystallization screens. Acta Crystallogr D Biol Crystallogr. 2003 Apr;59(Pt 4):769-72. DOI:10.1107/s0907444903002919 |
34. Brinkworth RI, Breinl RA, and Kobe B. Structural basis and prediction of substrate specificity in protein serine/threonine kinases. Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):74-9. DOI:10.1073/pnas.0134224100 |

2002

35. Horne J, Jennings IG, Teh T, Gooley PR, and Kobe B. Structural characterization of the N-terminal autoregulatory sequence of phenylalanine hydroxylase. Protein Sci. 2002 Aug;11(8):2041-7. DOI:10.1110/ps.4560102 |
36. Kajava AV and Kobe B. Assessment of the ability to model proteins with leucine-rich repeats in light of the latest structural information. Protein Sci. 2002 May;11(5):1082-90. DOI:10.1110/ps.4010102 |
37. Brinkworth RI, Horne J, and Kobe B. A computational analysis of substrate binding strength by phosphorylase kinase and protein kinase A. J Mol Recognit. 2002 Mar-Apr;15(2):104-11. DOI:10.1002/jmr.563 |

2001

38. Kobe B and Kajava AV. The leucine-rich repeat as a protein recognition motif. Curr Opin Struct Biol. 2001 Dec;11(6):725-32. DOI:10.1016/s0959-440x(01)00266-4 |
39. Catimel B, Teh T, Fontes MR, Jennings IG, Jans DA, Howlett GJ, Nice EC, and Kobe B. Biophysical characterization of interactions involving importin-alpha during nuclear import. J Biol Chem. 2001 Sep 7;276(36):34189-98. DOI:10.1074/jbc.M103531200 |
40. Kobe B. Crystallization and crystal structure determination of ribonuclease A-ribonuclease inhibitor protein complex. Methods Mol Biol. 2001;160:201-11. DOI:10.1385/1-59259-233-3:201 |
41. Blanchard H, Fontes MR, Hammet A, Pike BL, Teh T, Gleichmann T, Gooley PR, Kobe B, and Heierhorst J. Crystallization and preliminary X-ray diffraction studies of FHA domains of Dun1 and Rad53 protein kinases. Acta Crystallogr D Biol Crystallogr. 2001 Mar;57(Pt 3):459-61. DOI:10.1107/s0907444901002116 |
42. Jennings IG, Teh T, and Kobe B. Essential role of the N-terminal autoregulatory sequence in the regulation of phenylalanine hydroxylase. FEBS Lett. 2001 Jan 19;488(3):196-200. DOI:10.1016/s0014-5793(00)02426-1 |

2000

43. Jennings IG, Cotton RG, and Kobe B. Functional analysis, using in vitro mutagenesis, of amino acids located in the phenylalanine hydroxylase active site. Arch Biochem Biophys. 2000 Dec 15;384(2):238-44. DOI:10.1006/abbi.2000.2111 |
44. Kobe B and Kajava AV. When protein folding is simplified to protein coiling: the continuum of solenoid protein structures. Trends Biochem Sci. 2000 Oct;25(10):509-15. DOI:10.1016/s0968-0004(00)01667-4 |
45. Jennings IG, Cotton RG, and Kobe B. Structural interpretation of mutations in phenylalanine hydroxylase protein aids in identifying genotype-phenotype correlations in phenylketonuria. Eur J Hum Genet. 2000 Sep;8(9):683-96. DOI:10.1038/sj.ejhg.5200518 |
46. Maerz AL, Center RJ, Kemp BE, Kobe B, and Poumbourios P. Functional implications of the human T-lymphotropic virus type 1 transmembrane glycoprotein helical hairpin structure. J Virol. 2000 Jul;74(14):6614-21. DOI:10.1128/jvi.74.14.6614-6621.2000 |
47. Montgomery J, Ilg T, Thompson JK, Kobe B, and Handman E. Identification and predicted structure of a leucine-rich repeat motif shared by Leishmania major proteophosphoglycan and Parasite Surface Antigen 2. Mol Biochem Parasitol. 2000 Apr 15;107(2):289-95. DOI:10.1016/s0166-6851(00)00186-9 |
48. Hammet A, Pike BL, Mitchelhill KI, Teh T, Kobe B, House CM, Kemp BE, and Heierhorst J. FHA domain boundaries of the dun1p and rad53p cell cycle checkpoint kinases. FEBS Lett. 2000 Apr 14;471(2-3):141-6. DOI:10.1016/s0014-5793(00)01392-2 |
49. Fontes MR, Teh T, and Kobe B. Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-alpha. J Mol Biol. 2000 Apr 14;297(5):1183-94. DOI:10.1006/jmbi.2000.3642 |

1999

50. Poumbourios P, Center RJ, Wilson KA, Kemp BE, and Kobe B. Evolutionary conservation of the membrane fusion machine. IUBMB Life. 1999 Aug;48(2):151-6. DOI:10.1080/713803503 |
51. Kobe B and Kemp BE. Active site-directed protein regulation. Nature. 1999 Nov 25;402(6760):373-6. DOI:10.1038/46478 |
52. Kobe B, Gleichmann T, Horne J, Jennings IG, Scotney PD, and Teh T. Turn up the HEAT. Structure. 1999 May;7(5):R91-7. DOI:10.1016/s0969-2126(99)80060-4 |
53. Kobe B, Jennings IG, House CM, Michell BJ, Goodwill KE, Santarsiero BD, Stevens RC, Cotton RG, and Kemp BE. Structural basis of autoregulation of phenylalanine hydroxylase. Nat Struct Biol. 1999 May;6(5):442-8. DOI:10.1038/8247 |
54. Kobe B. Autoinhibition by an internal nuclear localization signal revealed by the crystal structure of mammalian importin alpha. Nat Struct Biol. 1999 Apr;6(4):388-97. DOI:10.1038/7625 |
55. Kobe B, Center RJ, Kemp BE, and Poumbourios P. Crystal structure of human T cell leukemia virus type 1 gp21 ectodomain crystallized as a maltose-binding protein chimera reveals structural evolution of retroviral transmembrane proteins. Proc Natl Acad Sci U S A. 1999 Apr 13;96(8):4319-24. DOI:10.1073/pnas.96.8.4319 |
56. Teh T, Tiganis T, and Kobe B. Crystallization of importin alpha, the nuclear-import receptor. Acta Crystallogr D Biol Crystallogr. 1999 Feb;55(Pt 2):561-3. DOI:10.1107/s0907444998012943 |

1998

57. Kobe B. Open up review system. Nature. 1998 Dec 10;396(6711):509. DOI:10.1038/24969 |
58. Smith BS, Kobe B, Kurumbail R, Buchanan SK, Venkatramani L, Van Der Helm D, and Deisenhofer J. Crystallization and preliminary X-ray analysis of ferric enterobactin receptor FepA, an integral membrane protein from Escherichia coli. Acta Crystallogr D Biol Crystallogr. 1998 Jul 1;54(Pt 4):697-9. DOI:10.1107/s0907444997020222 |
59. Center RJ, Kobe B, Wilson KA, Teh T, Howlett GJ, Kemp BE, and Poumbourios P. Crystallization of a trimeric human T cell leukemia virus type 1 gp21 ectodomain fragment as a chimera with maltose-binding protein. Protein Sci. 1998 Jul;7(7):1612-9. DOI:10.1002/pro.5560070715 |

1997

60. Kobe B, Jennings IG, House CM, Feil SC, Michell BJ, Tiganis T, Parker MW, Cotton RG, and Kemp BE. Regulation and crystallization of phosphorylated and dephosphorylated forms of truncated dimeric phenylalanine hydroxylase. Protein Sci. 1997 Jun;6(6):1352-7. DOI:10.1002/pro.5560060626 |
61. Xu P, Mitchelhill KI, Kobe B, Kemp BE, and Zot HG. The myosin-I-binding protein Acan125 binds the SH3 domain and belongs to the superfamily of leucine-rich repeat proteins. Proc Natl Acad Sci U S A. 1997 Apr 15;94(8):3685-90. DOI:10.1073/pnas.94.8.3685 |
62. Kobe B, Heierhorst J, and Kemp BE. Intrasteric regulation of protein kinases. Adv Second Messenger Phosphoprotein Res. 1997;31:29-40. DOI:10.1016/s1040-7952(97)80006-7 |

1996

63. Kobe B and Deisenhofer J. Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A. J Mol Biol. 1996 Dec 20;264(5):1028-43. DOI:10.1006/jmbi.1996.0694 |
64. Kobe B, Heierhorst J, Feil SC, Parker MW, Benian GM, Weiss KR, and Kemp BE. Giant protein kinases: domain interactions and structural basis of autoregulation. EMBO J. 1996 Dec 16;15(24):6810-21.
65. Kobe B. Leucines on a roll. Nat Struct Biol. 1996 Dec;3(12):977-80. DOI:10.1038/nsb1296-977 |
66. Heierhorst J, Kobe B, Feil SC, Parker MW, Benian GM, Weiss KR, and Kemp BE. Ca2+/S100 regulation of giant protein kinases. Nature. 1996 Apr 18;380(6575):636-9. DOI:10.1038/380636a0 |
67. Kemp BE, Barden JA, Kobe B, House C, and Parker MW. Intrasteric regulation of calmodulin-dependent protein kinases. Adv Pharmacol. 1996;36:221-49. DOI:10.1016/s1054-3589(08)60584-0 |

1995

68. Kobe B and Deisenhofer J. Proteins with leucine-rich repeats. Curr Opin Struct Biol. 1995 Jun;5(3):409-16. DOI:10.1016/0959-440x(95)80105-7 |
69. Kobe B and Deisenhofer J. A structural basis of the interactions between leucine-rich repeats and protein ligands. Nature. 1995 Mar 9;374(6518):183-6. DOI:10.1038/374183a0 |

1994

70. Kobe B and Deisenhofer J. The leucine-rich repeat: a versatile binding motif. Trends Biochem Sci. 1994 Oct;19(10):415-21. DOI:10.1016/0968-0004(94)90090-6 |
71. Kobe B, Ma Z, and Deisenhofer J. Complex between bovine ribonuclease A and porcine ribonuclease inhibitor crystallizes in a similar unit cell as free ribonuclease inhibitor. J Mol Biol. 1994 Aug 12;241(2):288-91. DOI:10.1006/jmbi.1994.1502 |

1993

72. Kobe B and Deisenhofer J. Crystal structure of porcine ribonuclease inhibitor, a protein with leucine-rich repeats. Nature. 1993 Dec 23-30;366(6457):751-6. DOI:10.1038/366751a0 |
73. Rizo J, Blanco FJ, Kobe B, Bruch MD, and Gierasch LM. Conformational behavior of Escherichia coli OmpA signal peptides in membrane mimetic environments. Biochemistry. 1993 May 11;32(18):4881-94. DOI:10.1021/bi00069a025 |
74. Kobe B and Deisenhofer J. Crystallization and preliminary X-ray analysis of porcine ribonuclease inhibitor, a protein with leucine-rich repeats. J Mol Biol. 1993 May 5;231(1):137-40. DOI:10.1006/jmbi.1993.1263 |

1991

75. Faming Z, Kobe B, Stewart CB, Rutter WJ, and Goldsmith EJ. Structural evolution of an enzyme specificity. The structure of rat carboxypeptidase A2 at 1.9-A resolution. J Biol Chem. 1991 Dec 25;266(36):24606-12.