bhf-ucl nykjaer-2004-1 Sortilin is essential for proNGF-induced neuronal cell death. in vitro In vitro spr surface plasmon resonance Optical biosensor BIAcore(r) BIAcore(r) Optical biosensor spr predetermined predetermined participant predetermined Nykjaer A., Lee R., Teng K.K., Jansen P., Madsen P., Nielsen M.S., Jacobsen C., Kliemannel M., Schwarz E., Willnow T.E., Hempstead B.L., Petersen C.M. Cardiac - Interactions involving cardiac related proteins Human wild type Sortilin used in this paper confirmed in ref. 5 (Munk PC et al. 1999. PMID: 9927419) and by the author. TrK, P75NTR and neurotensin were human proteins (confirmed by the author). Vascular smooth muscle cells (SM-11) were from rat (confirmed by the author) an@biokemi.au.dk Nature (0028-0836) 2004 imex curation Fig 3D was not annotated because the interacting partners cannot be unambiguosly identified. The authors radioactively labelled the cells expressing both receptors, but they don't do a western blot to identify the prey. They have the control samples on the right of the figure that indicates the identity of the bands that show up in the autoradiography, but since this is a lysate sample we feel it is not enough to identify the proteins. Only protein-protein interactions nykjaer-2004-2 Sortilin is essential for proNGF-induced neuronal cell death. human-293 Homo sapiens transformed primary embryonal kidney cells Human 293 Transformed human primary embryonal kidney cells. The Cell type named 293 is synonymous with HEK-293. crosslink cross-linking study crosslink autoradiography autoradiography Nykjaer A., Lee R., Teng K.K., Jansen P., Madsen P., Nielsen M.S., Jacobsen C., Kliemannel M., Schwarz E., Willnow T.E., Hempstead B.L., Petersen C.M. Cardiac - Interactions involving cardiac related proteins Transfected 293 cells were incubated with radioiodinated pro NGF or mature NGF followed by crosslinking with with 1-ethyl-3-[3-dimethylaminopropyl] carbodiimide and DSS (Disuccinimidyl suberate). Cells were washed and lysed. The lysates were submitted to immunoprecipitation with the corresponding antibody. All precipitated proteins were analysed by SDS-PAGE and were detected by autoradiography. Human wild type Sortilin used in this paper confirmed in ref. 5 (Munk PC et al. 1999. PMID: 9927419) and by the author. TrK, P75NTR and neurotensin were human proteins (confirmed by the author). Vascular smooth muscle cells (SM-11) were from rat (confirmed by the author) an@biokemi.au.dk Nature (0028-0836) 2004 imex curation Fig 3D was not annotated because the interacting partners cannot be unambiguosly identified. The authors radioactively labelled the cells expressing both receptors, but they don't do a western blot to identify the prey. They have the control samples on the right of the figure that indicates the identity of the bands that show up in the autoradiography, but since this is a lysate sample we feel it is not enough to identify the proteins. Only protein-protein interactions nykjaer-2004-3 Sortilin is essential for proNGF-induced neuronal cell death. rat-sm-11 cells Rat- vascular smooth muscle cells rat_sm-11 cells Rat- vascular smooth muscle cells crosslink cross-linking study crosslink autoradiography autoradiography Nykjaer A., Lee R., Teng K.K., Jansen P., Madsen P., Nielsen M.S., Jacobsen C., Kliemannel M., Schwarz E., Willnow T.E., Hempstead B.L., Petersen C.M. Cardiac - Interactions involving cardiac related proteins Transfected SM-11 cells were incubated with radioiodinated proNGF followed by crosslinking with 1-ethyl-3-[3-dimethylaminopropyl] carbodiimide and DSS (Disuccinimidyl suberate). Cells were washed and lysed. The lysates were submitted to immunoprecipitation with anti p75NTR. All precipitated proteins were analysed by SDS-PAGE and were detected by autoradiography. Human wild type Sortilin used in this paper confirmed in ref. 5 (Munk PC et al. 1999. PMID: 9927419) and by the author. TrK, P75NTR and neurotensin were human proteins (confirmed by the author). Vascular smooth muscle cells (SM-11) were from rat (confirmed by the author) an@biokemi.au.dk Nature (0028-0836) 2004 imex curation Fig 3D was not annotated because the interacting partners cannot be unambiguosly identified. The authors radioactively labelled the cells expressing both receptors, but they don't do a western blot to identify the prey. They have the control samples on the right of the figure that indicates the identity of the bands that show up in the autoradiography, but since this is a lysate sample we feel it is not enough to identify the proteins. Only protein-protein interactions nykjaer-2004-4 Sortilin is essential for proNGF-induced neuronal cell death. in vitro In vitro spr surface plasmon resonance Optical biosensor BIAcore(r) BIAcore(r) Optical biosensor spr predetermined predetermined participant predetermined Nykjaer A., Lee R., Teng K.K., Jansen P., Madsen P., Nielsen M.S., Jacobsen C., Kliemannel M., Schwarz E., Willnow T.E., Hempstead B.L., Petersen C.M. Cardiac - Interactions involving cardiac related proteins The authors state that NGF binds sortilin with only a modest affinity and the biological relevance of this interaction is at best questionable. Human wild type Sortilin used in this paper confirmed in ref. 5 (Munk PC et al. 1999. PMID: 9927419) and by the author. TrK, P75NTR and neurotensin were human proteins (confirmed by the author). Vascular smooth muscle cells (SM-11) were from rat (confirmed by the author) an@biokemi.au.dk Nature (0028-0836) 2004 Only protein-protein interactions imex curation Fig 3D was not annotated because the interacting partners cannot be unambiguosly identified. The authors radioactively labelled the cells expressing both receptors, but they don't do a western blot to identify the prey. They have the control samples on the right of the figure that indicates the identity of the bands that show up in the autoradiography, but since this is a lysate sample we feel it is not enough to identify the proteins. sort_human Sortilin SORT1 Neurotensin receptor 3 Glycoprotein 95 100 kDa NT receptor protein protein human Homo sapiens Human MERPWGAADGLSRWPHGLGLLLLLQLLPPSTLSQDRLDAPPPPAAPLPRWSGPIGVSWGLRAAAAGGAFPRGGRWRRSAPGEDEECGRVRDFVAKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVPLVIMTFGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRIFRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVCLAKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASVMADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIFTSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRWTHLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDAISVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCWQTYTFTRDPIYFTGLASEPGARSMNISIWGFTESFLTSQWVSYTIDFKDILERNCEEKDYTIWLAHSTDPEDYEDGCILGYKEQFLRLRKSSVCQNGRDYVVTKQPSICLCSLEDFLCDFGYYRPENDSKCVEQPELKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLKKKCTSNFLSPEKQNSKSNSVPIILAIVGLMLVTVVAGVLIVKKYVCGGRFLVHRYSVLQQHAEANGVDGVDALDTASHTNKSGYHDDSDEDLLE p01138-pro_0000019599 NGF NGFB protein protein human Homo sapiens Human EPHSESNVPAGHTIPQAHWTKLQHSLDTALRRARSAPAAAIAARVAGQTRNITVDPRLFKKRRLRSPRVLFSTQPPREAADTQDLDFEVGGAAPFNRTHRSKR 19 121 ngf_human Beta-nerve growth factor NGF NGFB protein protein human Homo sapiens Human MSMLFYTLITAFLIGIQAEPHSESNVPAGHTIPQAHWTKLQHSLDTALRRARSAPAAAIAARVAGQTRNITVDPRLFKKRRLRSPRVLFSTQPPREAADTQDLDFEVGGAAPFNRTHRSKRSSSHPIFHRGEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDPNPVDSGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSRKAVRRA tnr16_human Tumor necrosis factor receptor superfamily member 16 NGFR TNFRSF16 Low-affinity nerve growth factor receptor Gp80-LNGFR p75 ICD Low affinity neurotrophin receptor p75NTR protein protein human Homo sapiens Human MGAGATGRAMDGPRLLLLLLLGVSLGGAKEACPTGLYTHSGECCKACNLGEGVAQPCGANQTVCEPCLDSVTFSDVVSATEPCKPCTECVGLQSMSAPCVEADDAVCRCAYGYYQDETTGRCEACRVCEAGSGLVFSCQDKQNTVCEECPDGTYSDEANHVDPCLPCTVCEDTERQLRECTRWADAECEEIPGRWITRSTPPEGSDSTAPSTQEPEAPPEQDLIASTVAGVVTTVMGSSQPVVTRGTTDNLIPVYCSILAAVVVGLVAYIAFKRWNSCKQNKQGANSRPVNQTPPPEGEKLHSDSGISVDSQSLHDQQPHTQTASGQALKGDGGLYSSLPPAKREEVEKLLNGSAGDTWRHLAGELGYQPEHIDSFTHEACPVRALLASWATQDSATLDALLAALRRIQRADLVESLCSESTATSPV p01138-pro_0000019600 Beta-nerve growth factor NGF NGFB protein protein human Homo sapiens Human SSSHPIFHRGEFSVCDSVSVWVGDKTTATDIKGKEVMVLGEVNINNSVFKQYFFETKCRDPNPVDSGCRGIDSKHWNSYCTTTHTFVKALTMDGKQAAWRFIRIDTACVCVLSRKAVRRA 122 241 ntrk1_human High affinity nerve growth factor receptor NTRK1 TRK Neurotrophic tyrosine kinase receptor type 1 TRK1-transforming tyrosine kinase protein p140-TrkA MTC TRKA Tropomyosin-related kinase A Tyrosine kinase receptor Tyrosine kinase receptor A gp140trk protein protein human Homo sapiens Human MLRGGRRGQLGWHSWAAGPGSLLAWLILASAGAAPCPDACCPHGSSGLRCTRDGALDSLHHLPGAENLTELYIENQQHLQHLELRDLRGLGELRNLTIVKSGLRFVAPDAFHFTPRLSRLNLSFNALESLSWKTVQGLSLQELVLSGNPLHCSCALRWLQRWEEEGLGGVPEQKLQCHGQGPLAHMPNASCGVPTLKVQVPNASVDVGDDVLLRCQVEGRGLEQAGWILTELEQSATVMKSGGLPSLGLTLANVTSDLNRKNVTCWAENDVGRAEVSVQVNVSFPASVQLHTAVEMHHWCIPFSVDGQPAPSLRWLFNGSVLNETSFIFTEFLEPAANETVRHGCLRLNQPTHVNNGNYTLLAANPFGQASASIMAAFMDNPFEFNPEDPIPVSFSPVDTNSTSGDPVEKKDETPFGVSVAVGLAVFACLFLSTLLLVLNKCGRRNKFGINRPAVLAPEDGLAMSLHFMTLGGSSLSPTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG neut_human Neurotensin/neuromedin N NTS protein protein human Homo sapiens Human MMAGMKIQLVCMLLLAFSSWSLCSDSEEEMKALEADFLTNMHTSKISKAHVPSWKMTLLNVCSLVNNLNSPAEETGEVHEEELVARRKLPTALDGFSLEAMLTIYQLHKICHSRAFQHWELIQEDILDTGNDKNGKEEVIKRKIPYILKRQLYENKPRRPYILKRDSYYY tnr16_rat Tumor necrosis factor receptor superfamily member 16 Ngfr Tnfrsf16 Low-affinity nerve growth factor receptor Gp80-LNGFR p75 ICD Low affinity neurotrophin receptor p75NTR protein protein rat Rattus norvegicus (Rat) Rat MRRAGAACSAMDRLRLLLLLILGVSSGGAKETCSTGLYTHSGECCKACNLGEGVAQPCGANQTVCEPCLDNVTFSDVVSATEPCKPCTECLGLQSMSAPCVEADDAVCRCAYGYYQDEETGHCEACSVCEVGSGLVFSCQDKQNTVCEECPEGTYSDEANHVDPCLPCTVCEDTERQLRECTPWADAECEEIPGRWIPRSTPPEGSDSTAPSTQEPEVPPEQDLVPSTVADMVTTVMGSSQPVVTRGTTDNLIPVYCSILAAVVVGLVAYIAFKRWNSCKQNKQGANSRPVNQTPPPEGEKLHSDSGISVDSQSLHDQQTHTQTASGQALKGDGNLYSSLPLTKREEVEKLLNGDTWRHLAGELGYQPEHIDSFTHEACPVRALLASWGAQDSATLDALLAALRRIQRADIVESLCSESTATSPV sort1-ngf-1 1500446 n/a 1500450 unspecified role unspecified role bait bait luminal domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false crigr-cho_k1 Cricetulus griseus ovary K1 cho_k1 Chinese Hamster Ovary K1 n/a 1500451 unspecified role unspecified role prey prey region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1500446 Fig 1A sort1-ngf-1 1500446 n/a 1500452 unspecified role unspecified role prey prey pro ngf sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 1500450 unspecified role unspecified role bait bait luminal domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false crigr-cho_k1 Cricetulus griseus ovary K1 cho_k1 Chinese Hamster Ovary K1 direct interaction direct interaction false false false 1500446 Fig 1A, C sort1-ngf-1 1500446 n/a 1500453 unspecified role unspecified role bait bait spofr Spodoptera frugiperda (Fall armyworm) Fall armyworm n/a 1500454 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1500446 Fig 1A sort1-ngf-1 1500446 n/a 1500452 unspecified role unspecified role prey prey pro ngf sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 1500453 unspecified role unspecified role bait bait spofr Spodoptera frugiperda (Fall armyworm) Fall armyworm direct interaction direct interaction false false false 1500446 Fig 1A sort1-ngf-1 1500446 n/a 1500455 unspecified role unspecified role bait bait mouse-myeloma Mus musculus myeloma cell line myeloma lymphoblast plasma cell line. n/a 1500454 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1500446 Fig 1A sort1-ngf-1 1500446 n/a 1500455 unspecified role unspecified role bait bait mouse-myeloma Mus musculus myeloma cell line myeloma lymphoblast plasma cell line. n/a 1500452 unspecified role unspecified role prey prey pro ngf sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1500446 Fig 1A sort1-ngf-1 1500446 n/a 1500451 competitor competitor competitor unspecified role unspecified role region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) n/a 1500452 unspecified role unspecified role prey prey pro ngf sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 1500450 unspecified role unspecified role bait bait luminal domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false crigr-cho_k1 Cricetulus griseus ovary K1 cho_k1 Chinese Hamster Ovary K1 direct interaction direct interaction false false false Fig 1c sort1-ngf-1 1500446 n/a 1500456 competitor competitor competitor unspecified role unspecified role n/a 1500452 unspecified role unspecified role prey prey pro ngf sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) n/a 1500450 unspecified role unspecified role bait bait luminal domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false crigr-cho_k1 Cricetulus griseus ovary K1 cho_k1 Chinese Hamster Ovary K1 direct interaction direct interaction false false false Fig 1C sort1-ngf-3 1500447 n/a 1500453 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1500452 unspecified role unspecified role ancillary ancillary prongf sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region 125i radiolabel 125i radiolabel I125 125I 125I I125 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1500450 unspecified role unspecified role bait bait physical association physical association false false false Fig 3A ngfr-ngf-2 1500447 n/a 1500453 unspecified role unspecified role bait bait n/a 1500450 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1500452 unspecified role unspecified role ancillary ancillary prongf sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region 125i radiolabel 125i radiolabel I125 125I 125I I125 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig 3A, 3B ngfr-ngf-1 1500447 n/a 1500454 unspecified role unspecified role prey prey region 125i radiolabel 125i radiolabel I125 125I 125I I125 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) n/a 1500453 unspecified role unspecified role bait bait physical association physical association false false false Fig 3C Addition of unlabelled mature NGF almost abolishes the radio labelled signal. Sortilin (Q99523) Neurotensin (P30990) Unlabelled NGF (P01138-PRO_0000019600) ntrk1-ngf-2 1500447 n/a 1500454 unspecified role unspecified role prey prey region 125i radiolabel 125i radiolabel I125 125I 125I I125 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) n/a 1500455 unspecified role unspecified role bait bait physical association physical association false false false Fig 3C Sortilin (Q99523) ngfr-ngf-1 1500448 n/a 1500452 unspecified role unspecified role prey prey prongf sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region 125i radiolabel 125i radiolabel I125 125I 125I I125 undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) n/a 1500457 unspecified role unspecified role bait bait physical association physical association false false false Fig. 4B Unlabelled Pro NGF (P01138, 19-241aa) Neurotensin (P30990) sort1-ngf-1 1500449 n/a 1500454 unspecified role unspecified role prey prey ecoli Escherichia coli (strain K12) n/a 1500450 unspecified role unspecified role bait bait luminal domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false crigr-cho_k1 Cricetulus griseus ovary K1 cho_k1 Chinese Hamster Ovary K1 direct interaction direct interaction false false false 1500449 Fig 1A The authors state that NGF binds (sortilin) with modest affinity but the biological relevance of this is at best questionable.