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; 64(Pt 7) 810-4. doi:10.1107/S0907444908015540 pmid:18566516. PubMed HubMed [BK74]
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 pmid:18501020. PubMed HubMed [BK73]
3. 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 pmid:18437229. PubMed HubMed [BK72]
4. 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 pmid:18332103. PubMed HubMed [BK71]
5. 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 pmid:18208382. PubMed HubMed [BK70]

2007

6. 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 pmid:17894344. PubMed HubMed [BK69]
7. 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 pmid:17971854. PubMed HubMed [BK68]
8. 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 pmid:17563367. PubMed HubMed [BK67]
9. 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 pmid:17461785. PubMed HubMed [BK66]
10. 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 pmid:17329816. PubMed HubMed [BK65]
11. 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 pmid:17873095. PubMed HubMed [BK64]

2006

12. 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 pmid:17158707. PubMed HubMed [BK63]
13. 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 pmid:17097918. PubMed HubMed [BK62]
14. 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 pmid:17027497. PubMed HubMed [BK61]
15. 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 pmid:16798010. PubMed HubMed [BK60]
16. 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 pmid:16731621. PubMed HubMed [BK59]
17. 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 pmid:16511283. PubMed HubMed [BK58]
18. 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 pmid:16475229. PubMed HubMed [BK57]
19. 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 pmid:16445868. PubMed HubMed [BK56]
20. 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 pmid:16249216. PubMed HubMed [BK55]

2005

21. 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 pmid:16216214. PubMed HubMed [BK54]
22. 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 pmid:16172032. PubMed HubMed [BK53]
23. 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 pmid:15965734. PubMed HubMed [BK52]
24. 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 pmid:15941409. PubMed HubMed [BK51]
25. 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 pmid:15878698. PubMed HubMed [BK50]
26. 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 pmid:15698574. PubMed HubMed [BK49]

2004

27. 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 pmid:15317693. PubMed HubMed [BK48]
28. 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 pmid:15178320. PubMed HubMed [BK47]

2003

29. 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 pmid:12852786. PubMed HubMed [BK46]
30. 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. pmid:12824478. PubMed HubMed [BK45]
31. 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 pmid:12695505. PubMed HubMed [BK44]
32. 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. pmid:12657807. PubMed HubMed [BK43]
33. 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 pmid:12502784. PubMed HubMed [BK42]

2002

34. 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. pmid:12142458. PubMed HubMed [BK41]
35. 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. pmid:11967365. PubMed HubMed [BK40]
36. 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 pmid:11954055. PubMed HubMed [BK39]

2001

37. Kobe B and Kajava AV. The leucine-rich repeat as a protein recognition motif. Curr Opin Struct Biol 2001 Dec; 11(6) 725-32. pmid:11751054. PubMed HubMed [BK38]
38. 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 pmid:11448961. PubMed HubMed [BK37]
39. 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 pmid:11265283. PubMed HubMed [BK36]
40. 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. pmid:11223532. PubMed HubMed [BK35]
41. 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. pmid:11163771. PubMed HubMed [BK34]

2000

42. 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 pmid:11368310. PubMed HubMed [BK33]
43. 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. pmid:11050437. PubMed HubMed [BK32]
44. 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 pmid:10980574. PubMed HubMed [BK31]
45. 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. pmid:10864675. PubMed HubMed [BK30]
46. 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. pmid:10779605. PubMed HubMed [BK29]
47. 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. pmid:10767410. PubMed HubMed [BK28]
48. 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 pmid:10764582. PubMed HubMed [BK27]

1999

49. 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. pmid:10794590. PubMed HubMed [BK26]
50. Kobe B and Kemp BE. Active site-directed protein regulation. Nature 1999 Nov 25; 402(6760) 373-6. doi:10.1038/46478 pmid:10586874. PubMed HubMed [BK25]
51. Kobe B, Gleichmann T, Horne J, Jennings IG, Scotney PD, and Teh T. Turn up the HEAT. Structure 1999 May; 7(5) R91-7. pmid:10378263. PubMed HubMed [BK24]
52. 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 pmid:10331871. PubMed HubMed [BK23]
53. 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 pmid:10201409. PubMed HubMed [BK22]
54. 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. pmid:10200260. PubMed HubMed [BK21]
55. 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. pmid:10089379. PubMed HubMed [BK20]

1998

56. Kobe B. Open up review system. Nature 1998 Dec 10; 396(6711) 509. doi:10.1038/24969 pmid:9859978. PubMed HubMed [BK19]
57. 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. pmid:9761879. PubMed HubMed [BK18]
58. 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. pmid:9684894. PubMed HubMed [BK17]

1997

59. 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. pmid:9194198. PubMed HubMed [BK16]
60. 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. pmid:9108038. PubMed HubMed [BK15]
61. Kobe B, Heierhorst J, and Kemp BE. Intrasteric regulation of protein kinases. Adv Second Messenger Phosphoprotein Res 1997; 31 29-40. pmid:9344239. PubMed HubMed [BK14]

1996

62. 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 pmid:9000628. PubMed HubMed [BK13]
63. 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. pmid:9003756. PubMed HubMed [BK12]
64. Kobe B. Leucines on a roll. Nat Struct Biol 1996 Dec; 3(12) 977-80. pmid:8946845. PubMed HubMed [BK11]
65. 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 pmid:8602266. PubMed HubMed [BK10]
66. Kemp BE, Barden JA, Kobe B, House C, and Parker MW. Intrasteric regulation of calmodulin-dependent protein kinases. Adv Pharmacol 1996; 36 221-49. pmid:8783562. PubMed HubMed [BK09]

1995

67. Kobe B and Deisenhofer J. Proteins with leucine-rich repeats. Curr Opin Struct Biol 1995 Jun; 5(3) 409-16. pmid:7583641. PubMed HubMed [BK08]
68. 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 pmid:7877692. PubMed HubMed [BK07]

1994

69. Kobe B and Deisenhofer J. The leucine-rich repeat: a versatile binding motif. Trends Biochem Sci 1994 Oct; 19(10) 415-21. pmid:7817399. PubMed HubMed [BK06]
70. 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 pmid:8057371. PubMed HubMed [BK05]

1993

71. 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 pmid:8264799. PubMed HubMed [BK04]
72. 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. pmid:8387821. PubMed HubMed [BK03]
73. 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 pmid:8496959. PubMed HubMed [BK02]

1992

1991

74. 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. pmid:1761558. PubMed HubMed [BK01]