Prediction of localization and interactions of apoptotic proteins

Journal of Biomedical Science

Volumn 16, Issue 1, 2009, Pages

  Vaecha, Miroslav ^a   Zimmermann, Michal ^a   Amrichová, Jana ^a   Ulman, Vladimír ^a   Matula, Pavel ^a   Kozubek, Michal ^a  

^a MASARYK UNIVERSITY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

APOPTOSIS INDUCING FACTOR; APOPTOSIS INDUCING FACTOR HOMOLOGOUS MITOCHONDRION ASSOCIATED INDUCER OF DEATH; ENDONUCLEASE G; MITOCHONDRIAL PROTEIN; UNCLASSIFIED DRUG; CASPASE; ENDONUCLEASE;

ARTICLE; BIOINFORMATICS; CELLULAR DISTRIBUTION; COMPUTER MODEL; COMPUTER PROGRAM; CONTROLLED STUDY; CYTOPLASM; FLUORESCENCE MICROSCOPY; HUMAN; HUMAN CELL; IMAGE ANALYSIS; LIPID MEMBRANE; MOLECULAR DOCKING; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SIMULATION; APOPTOSIS; BIOLOGICAL MODEL; BIOLOGY; CHEMICAL STRUCTURE; COMPUTER SIMULATION; METABOLISM; METHODOLOGY; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; PROTEOMICS; TUMOR CELL LINE;

APOPTOSIS; CASPASES; CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ENDONUCLEASES; HUMANS; MICROSCOPY, FLUORESCENCE; MODELS, BIOLOGICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; SOFTWARE;

EID: 68349134859     PISSN: 10217770     EISSN: 14230127     Source Type: Journal    
DOI: 10.1186/1423-0127-16-59     Document Type: Article

References (60)

1. Mass spectrometric identification of proteins released from mitochondria undergoing permeability transition. SD Patterson CS Spahr E Daugas SA Susin T Irinopoulou C Koehler G Kroemer, Cell Death Differ 2000 7 137 144 10.1038/sj.cdd.4400640 10713728
2. Bcl-2 inhibits the mitochondrial release of an apoptogenic protease. SA Susin N Zamzami M Castedo T Hirsch P Marchetti A Macho E Daugas M Geuskens G Kroemer, J Exp Med 1996 184 1331 1341 8879205 10.1084/jem.184.4.1331 (Pubitemid 26354689)
3. Mitochondrial control of nuclear apoptosis. N Zamzami SA Susin P Marchetti T Hirsch I Gmez-Monterrey M Castedo G Kroemer, J Exp Med 1996 183 1533 1544 8666911 10.1084/jem.183.4.1533 (Pubitemid 26134296)
4. Endonuclease G is an apoptotic DNase when released from mitochondria. LY Li X Luo X Wang, Nature 2001 412 95 99 10.1038/35083620 11452314 (Pubitemid 32851517)
5. AMID, an apoptosis-inducing factor-homologous mitochondrion-associated protein, induces caspase-independent apoptosis. M Wu LG Xu X Li Z Zhai HB Shu, J Biol Chem 2002 277 25617 25623 10.1074/jbc.M202285200 11980907 (Pubitemid 34951879)
6. Action of recombinant human apoptotic endonuclease G on naked DNA and chromatin substrates: cooperation with exonuclease and DNase I. P Widlak LY Li X Wang WT Garrard, J Biol Chem 2001 276 48404 48409 11606588
7. Galectin-1 induces nuclear translocation of endonuclease G in caspase- and cytochrome c-independent T cell death. HP Hahn M Pang J He JD Hernandez RY Yang LY Li X Wang FT Liu LG Baum, Cell Death Differ 2004 11 1277 1286 15297883 10.1038/sj.cdd.4401485 (Pubitemid 39591773)
8. Calpain mediates excitotoxic DNA fragmentation via mitochondrial pathways in adult brains: evidence from calpastatin mutant mice. J Takano M Tomioka S Tsubuki M Higuchi N Iwata S Itohara M Maki TC Saido, J Biol Chem 2005 280 16175 16184 10.1074/jbc.M414552200 15691848 (Pubitemid 40616744)
9. Regulation of the human apoptotic DNase/RNase endonuclease G: involvement of Hsp70 and ATP. M Kalinowska W Garncarz M Pietrowska WT Garrard P Widlak, Apoptosis 2005 10 821 830 10.1007/s10495-005-0410-9 16133872 (Pubitemid 41187080)
10. Molecular characterization of mitochondrial apoptosis-inducing factor. SA Susin HK Lorenzo N Zamzami I Marzo BE Snow GM Brothers J Mangion E Jacotot P Costantini M Loeffler N Larochette DR Goodlett R Aebersold DP Siderovski JM Penninger G Kroemer, Nature 1999 397 441 446 10.1038/17135 9989411
11. Mitochondrial release of pro-apoptotic proteins: electrostatic interactions can hold cytochrome c but not Smac/DIABLO to mitochondrial membranes. RT Uren G Dewson C Bonzon T Lithgow DD Newmeyer RM Kluck, J Biol Chem 2005 280 2266 2274 10.1074/jbc.M411106200 15537572
12. Export of mitochondrial AIF in response to proapoptotic stimuli depends on processing at the intermembrane space. H Otera S Ohsakaya ZI Nagaura N Ishihara K Mihara, EMBO J 2005 24 1375 1386 15775970 10.1038/sj.emboj.7600614 (Pubitemid 40593058)
13. The harlequin mouse mutation downregulates apoptosis-inducing factor. JA Klein CM Longo-Guess MP Rossmann KL Seburn RE Hurd WN Frankel RT Bronson SL Ackerman, Nature 2002 419 367 374 10.1038/nature01034 12353028
14. Apoptosis-inducing factor is a target for ubiquitination through interaction with XIAP. JC Wilkinson AS Wilkinson S Galbán RA Csomos CS Duckett, Mol Cell Biol 2008 28 237 247 17967870 10.1128/MCB.01065-07
15. Mitochondrio-nuclear translocation of AIF in apoptosis and necrosis. E Daugas SA Susin N Zamzami KF Ferri T Irinopoulou N Larochette MC Prévost B Leber D Andrews J Penninger G Kroemer, FASEB J 2000 14 729 739 10744629
16. Translocation of apoptosis-inducing factor in cerebellar granule cells exposed to neurotoxic agents inducing oxidative stress. E Fonfría E Daré M Benelli C Sũol S Ceccatelli, Eur J Neurosci 2002 16 2013 2016 10.1046/j.1460-9568.2002.02269.x 12453066 (Pubitemid 37059589)
17. Mechanisms of AIF-mediated apoptotic DNA degradation in Caenorhabditis elegans. X Wang C Yang J Chai Y Shi D Xue, Science 2002 298 1587 1592 10.1126/science.1076194 12446902 (Pubitemid 35387191)
18. Physical interaction of apoptosis-inducing factor with DNA and RNA. N Vahsen C Candé P Dupaigne F Giordanetto RT Kroemer E Herker S Scholz N Modjtahedi F Madeo E Le Cam G Kroemer, Oncogene 2006 25 1763 1774 10.1038/sj.onc.1209206 16278674
19. AIF and cyclophilin A cooperate in apoptosis-associated chromatinolysis. C Candé N Vahsen I Kouranti E Schmitt E Daugas C Spahr J Luban RT Kroemer F Giordanetto C Garrido JM Penninger G Kroemer, Oncogene 2004 23 1514 1521 10.1038/sj.onc.1207279 14716299 (Pubitemid 38406513)
20. Heat-shock protein 70 antagonizes apoptosis-inducing factor. L Ravagnan S Gurbuxani SA Susin C Maisse E Daugas N Zamzami T Mak M Jäättelä JM Penninger C Garrido G Kroemer, Nat Cell Biol 2001 3 839 843 10.1038/ncb0901-839 11533664 (Pubitemid 32842690)
21. Cyclophilin A participates in the nuclear translocation of apoptosis-inducing factor in neurons after cerebral hypoxia-ischemia. C Zhu X Wang J Deinum Z Huang J Gao N Modjtahedi MR Neagu M Nilsson PS Eriksson H Hagberg J Luban G Kroemer K Blomgren, J Exp Med 2007 204 1741 1748 17635954 10.1084/jem.20070193 (Pubitemid 47236312)
22. Heat shock protein 70 inhibits the nuclear import of apoptosis-inducing factor to avoid DNA fragmentation in TF-1 cells during erythropoiesis. JC Lui SK Kong, FEBS Lett 2007 581 109 117 10.1016/j.febslet.2006.11.082 17182042 (Pubitemid 44960289)
23. Characterization of apoptotic pathway associated with caspase-independent excision of DNA loop domains. VT Solovyan, Exp Cell Res 2007 313 1347 1360 10.1016/j.yexcr.2007.01.025 17362930 (Pubitemid 46507446)
24. A novel p53-inducible apoptogenic gene, PRG3, encodes a homologue of the apoptosis-inducing factor (AIF). Y Ohiro I Garkavtsev S Kobayashi KR Sreekumar R Nantz BT Higashikubo SL Duffy R Higashikubo A Usheva D Gius N Kley N Horikoshi, FEBS Lett 2002 524 163 171 10.1016/S0014-5793(02)03049-1 12135761 (Pubitemid 34804854)
25. Bioinformatic and image analyses of the cellular localization of the apoptotic proteins endonuclease G, AIF, and AMID during apoptosis in human cells. M Vaecha J Amrichová M Zimmermann V Ulman E Lukáová M Kozubek, Apoptosis 2007 12 1155 1171 10.1007/s10495-007-0061-0 17347867 (Pubitemid 46890390)
26. AMID: new insights on its intracellular localization and expression at apoptosis. R Bilyy Y Kit U Hellman R Stoika, Apoptosis 2008 13 729 732 10.1007/s10495-008-0198-5 18368494
27. A knowledge base for predicting protein localization sites in eukaryotic cells. K Nakai M Kanehisa, Genomics 1992 14 897 911 10.1016/S0888-7543(05)80111- 9 1478671 (Pubitemid 23053027)
28. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. K Nakai P Horton, Trends Biochem Sci 1999 24 34 36 10.1016/S0968-0004(98)01336-X 10087920 (Pubitemid 29074461)
29. WoLF PSORT: protein localization predictor. P Horton KJ Park T Obayashi N Fujita H Harada CJ Adams-Collier K Nakai, Nucleic Acids Res 2007 35 W585 W587 17517783 10.1093/nar/gkm259
30. MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. A Höglund P Dönnes T Blum HW Adolph O Kohlbacher, Bioinformatics 2006 22 1158 1165 10.1093/bioinformatics/btl002 16428265 (Pubitemid 43779005)
31. Prediction of protein subcellular localization. CS Yu YC Chen CH Lu JK Hwang, Proteins 2006 64 643 651 10.1002/prot.21018 16752418 (Pubitemid 44100730)
32. High-resolution cytometry of FISH dots in interphase cell nuclei. M Kozubek S Kozubek E Lukáová A Mareková E Bártová M Skalníková A Jergová Cytometry 1999 36 279 293 10404143 10.1002/(SICI)1097-0320(19990801)36:4<279::AID- CYTO2>3.0.CO;2-G
33. Combined confocal and wide-field high-resolution cytometry of fluorescent in situ hybridization-stained cells. M Kozubek S Kozubek E Luká ová E Bártová M Skalníková Pe Matula Pa Matula P Jirsová A Cafourková I Koutná Cytometry 2001 45 1 12 11598941 10.1002/1097-0320(20010901)45:1<1::AID-CYTO1138>3.0.CO;2-M
34. Automated acquisition and processing of multidimensional image data in confocal in vivo microscopy. M Kozubek Pe Matula Pa Matula S Kozubek, Microsc Res Tech 2004 64 164 175 10.1002/jemt.20068 15352088 (Pubitemid 39129657)
35. Extensions of DAMAS and benefits and limitations of deconvolution in beamforming. R Dougherty, AIAA 2005 2961 http://pdf.aiaa.org/preview/ CDReadyMAERO05-1140/PV2005-2961.pdf
36. Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. RM Bennett-Lovsey AD Herbert MJ Sternberg LA Kelley, Proteins 2008 70 611 625 10.1002/prot.21688 17876813 (Pubitemid 351161924)
37. Enhanced genome annotation using structural profiles in the program 3D-PSSM. LA Kelley RM MacCallum MJ Sternberg, J Mol Biol 2000 299 499 520 10.1006/jmbi.2000.3741 10860755
38. M4T: a comparative protein structure modeling server. N Fernandez-Fuentes CJ Madrid-Aliste BK Rai JE Fajardo A Fiser, Nucleic Acids Res 2007 35 W363 W368 17517764 10.1093/nar/gkm341
39. UCSF Chimera a visualization system for exploratory research and analysis. EF Pettersen TD Goddard CC Huang GS Couch DM Greenblatt EC Meng TE Ferrin, J Comput Chem 2004 25 1605 1612 10.1002/jcc.20084 15264254
40. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. IW Davis A Leaver-Fay VB Chen JN Block GJ Kapral X Wang LW Murray WB Arendall J Snoeyink JS Richardson DC Richardson, Nucleic Acids Res 2007 35 W375 W383 17452350 10.1093/nar/gkm216
41. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. H Chen HX Zhou, Proteins 2005 61 21 35 10.1002/prot.20514 16080151 (Pubitemid 41262914)
42. DISPLAR: an accurate method for predicting DNA-binding sites on protein surfaces. H Tjong HX Zhou, Nucleic Acids Res 2007 35 1465 1477 17284455 10.1093/nar/gkm008 (Pubitemid 46592869)
43. PatchDock and SymmDock: servers for rigid and symmetric docking. D Schneidman-Duhovny Y Inbar R Nussinov HJ Wolfson, Nucleic Acids Res 2005 33 W363 W367 15980490 10.1093/nar/gki481 (Pubitemid 44529944)
44. FireDock: fast interaction refinement in molecular docking. N Andrusier R Nussinov HJ Wolfson, Proteins 2007 69 139 159 10.1002/prot.21495 17598144 (Pubitemid 47339146)
45. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. TA Tatusova TL Madden, FEMS Microbiol Lett 1999 174 247 250 10.1111/j.1574-6968.1999.tb13575.x 10339815
46. On the predictive recognition of signal peptide sequences. DJ McGeoch, Virus Res 1985 3 271 286 10.1016/0168-1702(85)90051-6 3000102 (Pubitemid 16225063)
47. A new method for predicting signal sequence cleavage sites. G von Heijne, Nucleic Acids Res 1986 14 4683 4690 3714490 10.1093/nar/14.11.4683
48. Protein import into the nucleus: an integrated view. GR Hicks NV Raikhel, Annu Rev Cell Dev Biol 1995 11 155 188 10.1146/annurev.cb.11.110195.001103 8689555
49. Genetic and biochemical studies of protein N-myristoylation. DR Johnson RS Bhatnagar LJ Knoll JI Gordon, Annu Rev Biochem 1994 63 869 914 10.1146/annurev.bi.63.070194.004253 7979256
50. A role for N-myristoylation in protein targeting: NADH-cytochrome b5 reductase requires myristic acid for association with outer mitochondrial but not ER membranes. N Borgese D Aggujaro P Carrera G Pietrini M Bassetti, J Cell Biol 1996 135 1501 1513 8978818 10.1083/jcb.135.6.1501 (Pubitemid 26427647)
51. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. A Krogh B Larsson G von Heijne EL Sonnhammer, J Mol Biol 2001 305 567 580 10.1006/jmbi.2000.4315 11152613 (Pubitemid 33032862)
52. N-Terminal myristoylation predictions by ensembles of neural networks. G Bologna C Yvon S Duvaud AL Veuthey, Proteomics 2004 4 1626 1632 10.1002/pmic.200300783 15174132 (Pubitemid 38738321)
53. N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. S Maurer-Stroh B Eisenhaber F Eisenhaber, J Mol Biol 2002 317 523 540 10.1006/jmbi.2002.5425 11955007 (Pubitemid 34722167)
54. Heat shock protein 70 binding inhibits the nuclear import of apoptosis-inducing factor. S Gurbuxani E Schmitt C Cande A Parcellier A Hammann E Daugas I Kouranti C Spahr A Pance G Kroemer C Garrido, Oncogene 2003 22 6669 6678 10.1038/sj.onc.1206794 14555980 (Pubitemid 37372207)
55. Mitochondrial effectors in caspase-independent cell death. HK Lorenzo SA Susin, FEBS Lett 2004 557 14 20 10.1016/S0014-5793(03)01464-9 14741334 (Pubitemid 38115862)
56. Caspase-independent death of Leber's hereditary optic neuropathy cybrids is driven by energetic failure and mediated by AIF and Endonuclease G. C Zanna A Ghelli AM Porcelli A Martinuzzi V Carelli M Rugolo, Apoptosis 2005 10 997 1007 10.1007/s10495-005-0742-5 16151635 (Pubitemid 41285578)
57. Hsp70 dynamics in vivo: effect of heat shock and protein aggregation. XC Zeng S Bhasin X Wu JG Lee S Maffi CJ Nichols KJ Lee JP Taylor LE Greene E Eisenberg, J Cell Sci 2004 117 4991 5000 10.1242/jcs.01373 15367583 (Pubitemid 39517515)
58. Mitochondrial release of apoptosis-inducing factor occurs downstream of cytochrome c release in response to several proapoptotic stimuli. D Arnoult P Parone JC Martinou B Antonsson J Estaquier JC Ameisen, J Cell Biol 2002 159 923 929 12486111 10.1083/jcb.200207071 (Pubitemid 36055747)
59. Critical role of calpain I in mitochondrial release of apoptosis-inducing factor in ischemic neuronal injury. G Cao J Xing X Xiao AK Liou Y Gao XM Yin RS Clark SH Graham J Chen, J Neurosci 2007 27 9278 9293 10.1523/JNEUROSCI.2826-07. 2007 17728442 (Pubitemid 47358221)
60. Discovery, regulation, and action of the major apoptotic nucleases DFF40/CAD and endonuclease G. P Widlak WT Garrard, J Cell Biochem 2005 94 1078 1087 10.1002/jcb.20409 15723341 (Pubitemid 41420231)