mbinfo MBInfo http://www.mechanobio.info/ http://www.mechanobio.info/ ballestrem-2006-1 Molecular mapping of tyrosine-phosphorylated proteins in focal adhesions using fluorescence resonance energy transfer. mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells fret fluorescent resonance energy transfer FRET RET FRET analysis FRET RET FRET analysis fret tag fluorescence tag visualisation by fluorescence tag fluorescence Ballestrem C., Erez N., Kirchner J., Kam Z., Bershadsky A., Geiger B. Alternative method for quantitating the FRET measurements were carried out (Fig 2A), where dequenching of the donor fluorophore following photobleaching of the acceptor was performed. Experiments involving FAK (Fig 3A, 3B, 3C, 4F, 7, 8) could not be curated since the source of FAK could not be identified or traced. benny.geiger@weizmann.ac.il J. Cell. Sci. (0021-9533) 2006 Only protein-protein interactions imex curation ballestrem-2006-2 Molecular mapping of tyrosine-phosphorylated proteins in focal adhesions using fluorescence resonance energy transfer. mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Ballestrem C., Erez N., Kirchner J., Kam Z., Bershadsky A., Geiger B. Alternative method for quantitating the FRET measurements were carried out (Fig 2A), where dequenching of the donor fluorophore following photobleaching of the acceptor was performed. Experiments involving FAK (Fig 3A, 3B, 3C, 4F, 7, 8) could not be curated since the source of FAK could not be identified or traced. benny.geiger@weizmann.ac.il J. Cell. Sci. (0021-9533) 2006 Only protein-protein interactions imex curation ballestrem-2006-3 Molecular mapping of tyrosine-phosphorylated proteins in focal adhesions using fluorescence resonance energy transfer. 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. anti bait coip anti bait coimmunoprecipitation anti bait coip anti tag western anti tag western blot anti tag western Ballestrem C., Erez N., Kirchner J., Kam Z., Bershadsky A., Geiger B. Alternative method for quantitating the FRET measurements were carried out (Fig 2A), where dequenching of the donor fluorophore following photobleaching of the acceptor was performed. Experiments involving FAK (Fig 3A, 3B, 3C, 4F, 7, 8) could not be curated since the source of FAK could not be identified or traced. benny.geiger@weizmann.ac.il J. Cell. Sci. (0021-9533) 2006 Only protein-protein interactions imex curation ballestrem-2006-4 Molecular mapping of tyrosine-phosphorylated proteins in focal adhesions using fluorescence resonance energy transfer. mouse-nih_3t3 Mus musculus Swiss NIH 3t3 embryo fibroblast cells nih_3t3 Mouse Swiss NIH embryo contact inhibited fibroblast cells fluorescence imaging fluorescence microscopy fluorescence imaging immunostaining immunostaining Ballestrem C., Erez N., Kirchner J., Kam Z., Bershadsky A., Geiger B. Alternative method for quantitating the FRET measurements were carried out (Fig 2A), where dequenching of the donor fluorophore following photobleaching of the acceptor was performed. Experiments involving FAK (Fig 3A, 3B, 3C, 4F, 7, 8) could not be curated since the source of FAK could not be identified or traced. benny.geiger@weizmann.ac.il J. Cell. Sci. (0021-9533) 2006 Only protein-protein interactions imex curation paxi_human Paxillin PXN protein protein human Homo sapiens Human MDDLDALLADLESTTSHISKRPVFLSEETPYSYPTGNHTYQEIAVPPPVPPPPSSEALNGTILDPLDQWQPSSSRFIHQQPQSSSPVYGSSAKTSSVSNPQDSVGSPCSRVGEEEHVYSFPNKQKSAEPSPTVMSTSLGSNLSELDRLLLELNAVQHNPPGFPADEANSSPPLPGALSPLYGVPETNSPLGGKAGPLTKEKPKRNGGRGLEDVRPSVESLLDELESSVPSPVPAITVNQGEMSSPQRVTSTQQQTRISASSATRELDELMASLSDFKIQGLEQRADGERCWAAGWPRDGGRSSPGGQDEGGFMAQGKTGSSSPPGGPPKPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYHNLFSPRCYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDYFDMFAPKCGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCQNCFLKLFC src_mouse Neuronal proto-oncogene tyrosine-protein kinase Src Src pp60c-src Proto-oncogene c-Src protein protein mouse Mus musculus Mouse MGSNKSKPKDASQRRRSLEPSENVHGAGGAFPASQTPSKPASADGHRGPSAAFVPPAAEPKLFGGFNSSDTVTSPQRAGPLAGGVTTFVALYDYESRTETDLSFKKGERLQIVNNTEGDWWLAHSLSTGQTGYIPSNYVAPSDSIQAEEWYFGKITRRESERLLLNAENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFNSLQQLVAYYSKHADGLCHRLTTVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMNKGSLLDFLKGETGKYLRLPQLVDMSAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGENL bcar1_rat Breast cancer anti-estrogen resistance protein 1 CRK-associated substrate p130cas Bcar1 Cas Crkas protein protein rat Rattus norvegicus (Rat) Rat MKYLVSVGAGPARRAGGLEDVSWGPRVSRRPQSYRAARHVNESLPRSAFRVPAAHGASVTPSAALGSGLPETQPEAVCRGTEKPRFAEGCKPAASRDKNVLAKALYDNVAESPDELSFRKGDIMTVLERDTQGLDGWWLCSLHGRQGIVPGNRLKILVGMYDKKPAAPGPGPPATPPQPQPSLPQGVHTPVPPASQYSPMLPTAYQPQPDNVYLVPTPSKTQQGLYQAPGPNPQFQSPPAKQTSTFSKQTPHHSFPSPATDLYQVPPGPGSPAQDIYQVPPSAGTGHDIYQVPPSLDTRSWEGTKPPAKVVVPTRVGQGYVYEASQAEQDEYDTPRHLLAPGSQDIYDVPPVRGLLPNQYGQEVYDTPPMAVKGPNGRDPLLDVYDVPPSVEKGLPPSNHHSVYDVPPSVSKDVPDGPLLREETYDVPPAFAKPKPFDPTRHPLILAAPPPDSPPAEDVYDVPPPAPDLYDVPPGLRRPGPGTLYDVPRERVLPPEVADGSVIDDGVYAVPPPAEREAPTDGKRLSASSTGSTRSSQSASSLEVVVPGREPLELEVAVETLARLQQGVSTTVAHLLDLVGSASGPGGWRSTSEPQEPPVQDLKAAVAAVHGAVHELLEFARSAVSSATHTSDRTLHAKLSRQLQKMEDVYQTLVVHGQVLDSGRGGPGFTLDDLDRLVACSRAVPEDAKQLASFLHGNASLLFRRTKAPGPGPEGSSSLHLNPTDKASSIQSRPLPSPPKFTSQDSPDGQYENSEGGWMEDYDYVHLQGKEEFEKTQKELLEKGNIVRQGKGQLELQQLKQFERLEQEVSRPIDHDLANWTPAQPLVPGRTGGLGPSDRQLLLFYLEQCEANLTTLTDAVDAFFTAVATNQPPKIFVAHSKFVILSAHKLVFIGDTLSRQAKAADVRSKVTHYSNLLCDLLRGIVATTKAAALQYPSPSAAQDMVDRVKELGHSTQQFRRVLGQLAAA paxi_mouse Paxillin Pxn protein protein mouse Mus musculus Mouse MDDLDALLADLESTTSHISKRPVFLSEEPPYSYPTGNHTYQEIAVPPPVPPPPSSEALNGTVLDPLDQWQPSGSRYAHQQPPSPLPVYSSSAKNSSASNTQDGVGSLCSRAGEEEHVYSFPNKQKSAEPSPTVMSSSLGSNLSELDRLLLELNAVQHSPPGFPADEAESSPPLPGALSPLYGIPENNTPLGGKAGPLVKEKPKRNGGRGLEDVRPSVESLLDELESSVPSPVPAITVNQGEMSSPQRVTSSQQQTRISASSATRELDELMASLSDFKMQGLEQRVDGERPWAAGWPPSSRQSSPEGQDEGGFMAQGKTGSSSPPGGLSKPGSQLDSMLGSLQSDLNKLGVATVAKGVCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYHSLFSPRCYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDYFDMFAPKCGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCQSCFVKLFC bcar1_mouse Breast cancer anti-estrogen resistance protein 1 Bcar1 Cas Crkas p130cas CRK-associated substrate protein protein mouse Mus musculus Mouse MTVPNVLAKALYDNVAESPDELSFRKGDIMTVLERDTQGLDGWWLCSLHGRQGIVPGNRLKILVGMYDKKPVGPGPGPPATPPQPQPSLPQGVHAPVPPASQYSPMLPTAYQPQSDNVYLVPTPSKTQQGLYQAPGPNPQFQSPPAKQTSTFSKQTPHHSFPSPATDLYQVPPGPGSPAQDIYQVPPSAGIGHDIYQVPPSLDTRGWEGTKPPAKVVVPTRVGQGYVYEAAQTEQDEYDTPRHLLAPGPQDIYDVPPVRGLLPNQYGQEVYDTPPMAVKGPNGRDPLLDVYDVPPSVEKGLLSSSHHSVYDVPPSVSKDVPDGPLLREETYDVPPAFAKPKPFDPTRHPLILAAPPPDSPAAEDVYDVPPPAPDLYDVPPGLRRPGPGTLYDVPRERVLPPEVADGSVVDDGVYAVPPPAEREAPTDGKRLSASSTGSTRSSQSASSLEVVVPGREPLELEVAVESLARLQQGVSTTVAHLLDLVGSASGPGGWRGTSEPQEPPAQDLKAAVAAVHGAVHELLEFARGAVSNATHTSDRTLHAKLSRQLQKMEDVYQTLVVHGQVLDSGRGSPGFTPEDLDRLVACSRAVPEDAKQLASFLHGNASLLFRRTKAPGPGPEGSSSLHPNPTDKASSIQSRPLPSPPKFTSQDSPDGQYENSEGGWMEDYDYVHLQGKEEFEKTQKELLERGNIMRQGKGQLELQQLKQFERLEQEVSRPIDHDLANWTPAQPLVPGRTGGLGPSDRQLLLFYLEQCEANLTTLTDAVDAFFTAVATNQPPKIFVAHSKFVILSAHKLVFIGDTLSRQAKAADVRSQVTHYSNLLCDLLRGIVATTKAAALQYPSPSAAQDMVDRVKELGHSTQQFRRVLGQLAAA pxn-src-1 1351393 n/a 1351397 unspecified role unspecified role fluorescence donor fluorescence donor region cfp tag cyan fluorescent protein tag CFP cyan fluorescent protein cyan fluorescent protein CFP cfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1351398 unspecified role unspecified role fluorescence accept fluorescence acceptor fluorescence accept sh2 domain sufficient to bind sufficient binding region sufficient to bind range range range range false Two tandem repeats of the SH2 domain of pp60c-src fused to YFP was used as a PY reporter. The sequence range [156-253] is not directly referenced by the authors and is inferred from uniprot. region yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false proximity proximity close-contact colocalization neighbourhood interaction false false false Fig 1A, 1B, 1D, 2A, 3B, 5A, 6A, 6B, 6C, 8B. The FRET values betwwen CFP-Paxillin and YFP-Src-SH2 remained high in Y27632 (Rock inhibitor)-treated cells (Fig 6A) and in the presence of activated Rac (Figs 6B, 6C) and Rho (Fig 6C). bcar1-src-3 1351393 n/a 1351399 unspecified role unspecified role fluorescence accept fluorescence acceptor fluorescence accept region yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1351398 unspecified role unspecified role fluorescence donor fluorescence donor region cfp tag cyan fluorescent protein tag CFP cyan fluorescent protein cyan fluorescent protein CFP cfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false sh2 domain sufficient to bind sufficient binding region sufficient to bind range range range range false Tandem repeats of the pp60c-src fused to the CFP tag was used as a PY reporter. The sequence range [156-253] was not directly referenced by the author and was inferred from uniprot. proximity proximity close-contact colocalization neighbourhood interaction false false false Fig 3A, 3B. pxn-src-4 1351393 n/a 1351397 unspecified role unspecified role neutral component neutral component region yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false n/a 1351398 unspecified role unspecified role neutral component neutral component sh2 domain sufficient to bind sufficient binding region sufficient to bind range range range range false region cfp tag cyan fluorescent protein tag CFP cyan fluorescent protein cyan fluorescent protein CFP cfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false proximity proximity close-contact colocalization neighbourhood interaction false false false Fig 1A, 1B. src-pxn 1351394 n/a 1351400 unspecified role unspecified role prey prey n/a 1351398 unspecified role unspecified role bait bait region yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false sh2 domain sufficient to bind sufficient binding region sufficient to bind range range range range false Tandem repeats of the pp60c-src SH2 domain fused to YFP was used as PY reporter. The sequence range [156-253] was not directly referenced by the author and was inferred from uniprot. physical association physical association false false false Fig 1C (Right bottom panel). bcar1-src-2 1351395 n/a 1351398 unspecified role unspecified role prey prey region cfp tag cyan fluorescent protein tag CFP cyan fluorescent protein cyan fluorescent protein CFP cfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false sh2 domain sufficient to bind sufficient binding region sufficient to bind range range range range false Tandem repeats of pp60c-src SH2 domain fused to CFP, was used as PY reporter. The sequence range [156-253] was not directly referenced by the author and was inferred from uniprot. n/a 1351399 unspecified role unspecified role bait bait region yfp tag yellow fluorescent protein tag YFP yellow fluorescent protein yellow fluorescent protein YFP yfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false physical association physical association false false false Fig 3C (left). bcar1-pxn 1351396 n/a 1351400 unspecified role unspecified role neutral component neutral component n/a 1351401 unspecified role unspecified role neutral component neutral component colocalization colocalization false false false Fig 4I.