IntAct European Bioinformatics Institute IntAct intact http://www.ebi.ac.uk/ http://www.ebi.ac.uk/intact/query/${ac} EBI-[0-9]+|IA:[0-9]+ INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact European Bioinformatics Institute; Wellcome Trust Genome Campus; Hinxton, Cambridge; CB10 1SD; United Kingdom http://www.ebi.ac.uk/intact/ http://www.ebi.ac.uk/ kalogeropulou-2018-1 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 tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Kalogeropulou AF., Zhao J., Bolliger MF., Memou A., Narasimha S., Molitor TP., Wilson WH., Rideout HJ., Nichols RJ. Parkinsons - Interactions investigated in the context of Parkinsons disease No information is given regarding the species origin of the V5-Hsp27 construct so no interaction involving this construct has been annotated. The "V5-HSP90" construct ( - Addgene plasmid #22487) has an HA tag rather than the stated V5 tag. 293 or T-REX 293 cell lines. T-REX line exhibits extremely low basal protein expression levels in the repressed state and high expression upon induction with tetracycline. rjnichols@stanford.edu The Biochemical journal 2018 Only protein-protein interactions imex curation imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. kalogeropulou-2018-6 in vitro In vitro protein kinase assay protein kinase assay sequence tag sequence tag identification sequence tag Kalogeropulou AF., Zhao J., Bolliger MF., Memou A., Narasimha S., Molitor TP., Wilson WH., Rideout HJ., Nichols RJ. Parkinsons - Interactions investigated in the context of Parkinsons disease Only p62 phosphorylation sites with a high "A score" (probability) have been entered. rjnichols@stanford.edu The Biochemical journal 2018 Only protein-protein interactions imex curation imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. kalogeropulou-2018-7 in vitro In vitro protein kinase assay protein kinase assay experimental particp experimental participant identification experimental particp Kalogeropulou AF., Zhao J., Bolliger MF., Memou A., Narasimha S., Molitor TP., Wilson WH., Rideout HJ., Nichols RJ. Parkinsons - Interactions investigated in the context of Parkinsons disease rjnichols@stanford.edu The Biochemical journal 2018 Only protein-protein interactions imex curation imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. kalogeropulou-2018-2 human-a_549 Homo sapiens Caucasian lung carcinoma cell line a_549 Human Caucasian lung carcinoma anti bait coip anti bait coimmunoprecipitation anti bait coip western blot western blot Immuno blot Immuno blot Kalogeropulou AF., Zhao J., Bolliger MF., Memou A., Narasimha S., Molitor TP., Wilson WH., Rideout HJ., Nichols RJ. Parkinsons - Interactions investigated in the context of Parkinsons disease rjnichols@stanford.edu The Biochemical journal 2018 Only protein-protein interactions imex curation imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. kalogeropulou-2018-3 human-h1299 Homo sapiens lung lymph node carcinoma h1299 Human lung lymph node carcinoma p53 null. These cells have also been reported to secrete the peptide hormone neuromedin B (NMB), but not gastrin releasing peptide (GRP). Also known as NCI H1299 or CRL-5803. http://www.lgcpromochem.com/atcc/ ATCC number: CRL-5803. ATCC number of the cell line is CRL-5803. anti tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Kalogeropulou AF., Zhao J., Bolliger MF., Memou A., Narasimha S., Molitor TP., Wilson WH., Rideout HJ., Nichols RJ. Parkinsons - Interactions investigated in the context of Parkinsons disease The CRISPR/Cas9 system was used to insert a GFP tag into the LRRK2 locus of these cells. rjnichols@stanford.edu The Biochemical journal 2018 Only protein-protein interactions imex curation imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. kalogeropulou-2018-4 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 tag coip anti tag coimmunoprecipitation anti tag coip western blot western blot Immuno blot Immuno blot Kalogeropulou AF., Zhao J., Bolliger MF., Memou A., Narasimha S., Molitor TP., Wilson WH., Rideout HJ., Nichols RJ. Parkinsons - Interactions investigated in the context of Parkinsons disease rjnichols@stanford.edu The Biochemical journal 2018 Only protein-protein interactions imex curation imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. kalogeropulou-2018-5 in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Kalogeropulou AF., Zhao J., Bolliger MF., Memou A., Narasimha S., Molitor TP., Wilson WH., Rideout HJ., Nichols RJ. Parkinsons - Interactions investigated in the context of Parkinsons disease rjnichols@stanford.edu The Biochemical journal 2018 Only protein-protein interactions imex curation imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. kalogeropulou-2018-8 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. pla proximity ligation assay pELISA pELISA PLA antibody detection identification by antibody antibody detection Kalogeropulou AF., Zhao J., Bolliger MF., Memou A., Narasimha S., Molitor TP., Wilson WH., Rideout HJ., Nichols RJ. Parkinsons - Interactions investigated in the context of Parkinsons disease rjnichols@stanford.edu The Biochemical journal 2018 Only protein-protein interactions imex curation imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. kalogeropulou-2018-9 human-a_549 Homo sapiens Caucasian lung carcinoma cell line a_549 Human Caucasian lung carcinoma pla proximity ligation assay pELISA pELISA PLA antibody detection identification by antibody antibody detection Kalogeropulou AF., Zhao J., Bolliger MF., Memou A., Narasimha S., Molitor TP., Wilson WH., Rideout HJ., Nichols RJ. Parkinsons - Interactions investigated in the context of Parkinsons disease rjnichols@stanford.edu The Biochemical journal 2018 Only protein-protein interactions imex curation imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. kalogeropulou-2018-10 human-a_549 Homo sapiens Caucasian lung carcinoma cell line a_549 Human Caucasian lung carcinoma fluorescence imaging fluorescence microscopy fluorescence imaging immunocytochemistry immunocytochemistry Kalogeropulou AF., Zhao J., Bolliger MF., Memou A., Narasimha S., Molitor TP., Wilson WH., Rideout HJ., Nichols RJ. Parkinsons - Interactions investigated in the context of Parkinsons disease rjnichols@stanford.edu The Biochemical journal 2018 Only protein-protein interactions imex curation imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. dnjb6_human DnaJ homolog subfamily B member 6 Heat shock protein J2 MSJ-1 HHDJ1 DNAJB6 HSJ2 MSJ1 MRJ protein protein human Homo sapiens Human MVDYYEVLGVQRHASPEDIKKAYRKLALKWHPDKNPENKEEAERKFKQVAEAYEVLSDAKKRDIYDKYGKEGLNGGGGGGSHFDSPFEFGFTFRNPDDVFREFFGGRDPFSFDFFEDPFEDFFGNRRGPRGSRSRGTGSFFSAFSGFPSFGSGFSSFDTGFTSFGSLGHGGLTSFSSTSFGGSGMGNFKSISTSTKMVNGRKITTKRIVENGQERVEVEEDGQLKSLTINGVADDDALAEERMRRGQNALPAQPAGLRPPKPPRPASLLRHAPHCLSEEEGEQDRPRAPGPWDPLASAAGLKEGGKRKKQKQREESKKKKSTKGNH lrrk2_human Leucine-rich repeat serine/threonine-protein kinase 2 LRRK2 PARK8 Dardarin protein protein human Homo sapiens Human MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNIHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILKMLTVHNASVNLSVIGLKTLDLLLTSGKITLLILDEESDIFMLIFDAMHSFPANDEVQKLGCKALHVLFERVSEEQLTEFVENKDYMILLSALTNFKDEEEIVLHVLHCLHSLAIPCNNVEVLMSGNVRCYNIVVEAMKAFPMSERIQEVSCCLLHRLTLGNFFNILVLNEVHEFVVKAVQQYPENAALQISALSCLALLTETIFLNQDLEEKNENQENDDEGEEDKLFWLEACYKALTWHRKNKHVQEAACWALNNLLMYQNSLHEKIGDEDGHFPAHREVMLSMLMHSSSKEVFQASANALSTLLEQNVNFRKILLSKGIHLNVLELMQKHIHSPEVAESGCKMLNHLFEGSNTSLDIMAAVVPKILTVMKRHETSLPVQLEALRAILHFIVPGMPEESREDTEFHHKLNMVKKQCFKNDIHKLVLAALNRFIGNPGIQKCGLKVISSIVHFPDALEMLSLEGAMDSVLHTLQMYPDDQEIQCLGLSLIGYLITKKNVFIGTGHLLAKILVSSLYRFKDVAEIQTKGFQTILAILKLSASFSKLLVHHSFDLVIFHQMSSNIMEQKDQQFLNLCCKCFAKVAMDDYLKNVMLERACDQNNSIMVECLLLLGADANQAKEGSSLICQVCEKESSPKLVELLLNSGSREQDVRKALTISIGKGDSQIISLLLRRLALDVANNSICLGGFCIGKVEPSWLGPLFPDKTSNLRKQTNIASTLARMVIRYQMKSAVEEGTASGSDGNFSEDVLSKFDEWTFIPDSSMDSVFAQSDDLDSEGSEGSFLVKKKSNSISVGEFYRDAVLQRCSPNLQRHSNSLGPIFDHEDLLKRKRKILSSDDSLRSSKLQSHMRHSDSISSLASEREYITSLDLSANELRDIDALSQKCCISVHLEHLEKLELHQNALTSFPQQLCETLKSLTHLDLHSNKFTSFPSYLLKMSCIANLDVSRNDIGPSVVLDPTVKCPTLKQFNLSYNQLSFVPENLTDVVEKLEQLILEGNKISGICSPLRLKELKILNLSKNHISSLSENFLEACPKVESFSARMNFLAAMPFLPPSMTILKLSQNKFSCIPEAILNLPHLRSLDMSSNDIQYLPGPAHWKSLNLRELLFSHNQISILDLSEKAYLWSRVEKLHLSHNKLKEIPPEIGCLENLTSLDVSYNLELRSFPNEMGKLSKIWDLPLDELHLNFDFKHIGCKAKDIIRFLQQRLKKAVPYNRMKLMIVGNTGSGKTTLLQQLMKTKKSDLGMQSATVGIDVKDWPIQIRDKRKRDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQAEVDAMKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDYHFVNATEESDALAKLRKTIINESLNFKIRDQLVVGQLIPDCYVELEKIILSERKNVPIEFPVIDRKRLLQLVRENQLQLDENELPHAVHFLNESGVLLHFQDPALQLSDLYFVEPKWLCKIMAQILTVKVEGCPKHPKGIISRRDVEKFLSKKRKFPKNYMSQYFKLLEKFQIALPIGEEYLLVPSSLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPYMLSGRERALRPNRMYWRQGIYLNWSPEAYCLVGSEVLDNHPESFLKITVPSCRKGCILLGQVVDHIDSLMEEWFPGLLEIDICGEGETLLKKWALYSFNDGEEHQKILLDDLMKKAEEGDLLVNPDQPRLTIPISQIAPDLILADLPRNIMLNNDELEFEQAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNKHTSLRLLRQELVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQHRIALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKTSEGTPGFRAPEVARGNVIYNQQADVYSFGLLLYDILTTGGRIVEGLKFPNEFDELEIQGKLPDPVKEYGCAPWPMVEKLIKQCLKENPQERPTSAQVFDILNSAELVCLTRRILLPKNVIVECMVATHHNSRNASIWLGCGHTDRGQLSFLDLNTEGYTSEEVADSRILCLALVHLPVEKESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTCLYCNSFSKQSKQKNFLLVGTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSESTNSTERNVMWGGCGTKIFSFSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYIAKQNSPVVEVWDKKTEKLCGLIDCVHFLREVMVKENKESKHKMSYSGRVKTLCLQKNTALWIGTGGGHILLLDLSTRRLIRVIYNFCNSVRVMMTAQLGSLKNVMLVLGYNRKNTEGTQKQKEIQSCLTVWDINLPHEVQNLEKHIEVRKELAEKMRRTSVE dnjb8_human DnaJ homolog subfamily B member 8 DNAJB8 protein protein human Homo sapiens Human MANYYEVLGVQASASPEDIKKAYRKLALRWHPDKNPDNKEEAEKKFKLVSEAYEVLSDSKKRSLYDRAGCDSWRAGGGASTPYHSPFDTGYTFRNPEDIFREFFGGLDPFSFEFWDSPFNSDRGGRGHGLRGAFSAGFGEFPAFMEAFSSFNMLGCSGGSHTTFSSTSFGGSSSGSSGFKSVMSSTEMINGHKVTTKRIVENGQERVEVEEDGQLKSVTVNGKEQLKWMDSK hs71a_human Heat shock 70 kDa protein 1A HSPA1A HSPA1 HSX70 Heat shock 70 kDa protein 1 HSP72 protein protein human Homo sapiens Human MAKAAAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVALNPQNTVFDAKRLIGRKFGDPVVQSDMKHWPFQVINDGDKPKVQVSYKGETKAFYPEEISSMVLTKMKEIAEAYLGYPVTNAVITVPAYFNDSQRQATKDAGVIAGLNVLRIINEPTAAAIAYGLDRTGKGERNVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVNHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQASLEIDSLFEGIDFYTSITRARFEELCSDLFRSTLEPVEKALRDAKLDKAQIHDLVLVGGSTRIPKVQKLLQDFFNGRDLNKSINPDEAVAYGAAVQAAILMGDKSENVQDLLLLDVAPLSLGLETAGGVMTALIKRNSTIPTKQTQIFTTYSDNQPGVLIQVYEGERAMTKDNNLLGRFELSGIPPAPRGVPQIEVTFDIDANGILNVTATDKSTGKANKITITNDKGRLSKEEIERMVQEAEKYKAEDEVQRERVSAKNALESYAFNMKSAVEDEGLKGKISEADKKKVLDKCQEVISWLDANTLAEKDEFEHKRKELEQVCNPIISGLYQGAGGPGPGGFGAQGPKGGSGSGPTIEEVD hsp7c_human Heat shock cognate 71 kDa protein HSPA8 HSC70 HSP73 HSPA10 Heat shock 70 kDa protein 8 Lipopolysaccharide-associated protein 1 protein protein human Homo sapiens Human MSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGGFPGGGAPPSGGASSGPTIEEVD sqstm_human Sequestosome-1 SQSTM1 ORCA OSIL Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa Ubiquitin-binding protein p62 EBI3-associated protein of 60 kDa protein protein human Homo sapiens Human MASLTVKAYLLGKEDAAREIRRFSFCCSPEPEAEAEAAAGPGPCERLLSRVAALFPALRPGGFQAHYRDEDGDLVAFSSDEELTMAMSYVKDDIFRIYIKEKKECRRDHRPPCAQEAPRNMVHPNVICDGCNGPVVGTRYKCSVCPDYDLCSVCEGKGLHRGHTKLAFPSPFGHLSEGFSHSRWLRKVKHGHFGWPGWEMGPPGNWSPRPPRAGEARPGPTAESASGPSEDPSVNFLKNVGESVAAALSPLGIEVDIDVEHGGKRSRLTPVSPESSSTEEKSSSQPSSCCSDPSKPGGNVEGATQSLAEQMRKIALESEGRPEEQMESDNCSGGDDDWTHLSSKEVDPSTGELQSLQMPESEGPSSLDPSQEGPTGLKEAALYPHLPPEADPRLIESLSQMLSMGFSDEGGWLTRLLQTKNYDIGAALDTIQYSKHPPPL hdac6_human Histone deacetylase 6 HDAC6 KIAA0901 JM21 Tubulin-lysine deacetylase HDAC6 protein protein human Homo sapiens Human MTSTGQDSTTTRQRRSRQNPQSPPQDSSVTSKRNIKKGAVPRSIPNLAEVKKKGKMKKLGQAMEEDLIVGLQGMDLNLEAEALAGTGLVLDEQLNEFHCLWDDSFPEGPERLHAIKEQLIQEGLLDRCVSFQARFAEKEELMLVHSLEYIDLMETTQYMNEGELRVLADTYDSVYLHPNSYSCACLASGSVLRLVDAVLGAEIRNGMAIIRPPGHHAQHSLMDGYCMFNHVAVAARYAQQKHRIRRVLIVDWDVHHGQGTQFTFDQDPSVLYFSIHRYEQGRFWPHLKASNWSTTGFGQGQGYTINVPWNQVGMRDADYIAAFLHVLLPVALEFQPQLVLVAAGFDALQGDPKGEMAATPAGFAQLTHLLMGLAGGKLILSLEGGYNLRALAEGVSASLHTLLGDPCPMLESPGAPCRSAQASVSCALEALEPFWEVLVRSTETVERDNMEEDNVEESEEEGPWEPPVLPILTWPVLQSRTGLVYDQNMMNHCNLWDSHHPEVPQRILRIMCRLEELGLAGRCLTLTPRPATEAELLTCHSAEYVGHLRATEKMKTRELHRESSNFDSIYICPSTFACAQLATGAACRLVEAVLSGEVLNGAAVVRPPGHHAEQDAACGFCFFNSVAVAARHAQTISGHALRILIVDWDVHHGNGTQHMFEDDPSVLYVSLHRYDHGTFFPMGDEGASSQIGRAAGTGFTVNVAWNGPRMGDADYLAAWHRLVLPIAYEFNPELVLVSAGFDAARGDPLGGCQVSPEGYAHLTHLLMGLASGRIILILEGGYNLTSISESMAACTRSLLGDPPPLLTLPRPPLSGALASITETIQVHRRYWRSLRVMKVEDREGPSSSKLVTKKAPQPAKPRLAERMTTREKKVLEAGMGKVTSASFGEESTPGQTNSETAVVALTQDQPSEAATGGATLAQTISEAAIGGAMLGQTTSEEAVGGATPDQTTSEETVGGAILDQTTSEDAVGGATLGQTTSEEAVGGATLAQTTSEAAMEGATLDQTTSEEAPGGTELIQTPLASSTDHQTPPTSPVQGTTPQISPSTLIGSLRTLELGSESQGASESQAPGEENLLGEAAGGQDMADSMLMQGSRGLTDQAIFYAVTPLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNKFGEDMPHPH lrrk1_human Leucine-rich repeat serine/threonine-protein kinase 1 LRRK1 KIAA1790 protein protein human Homo sapiens Human MAGMSQRPPSMYWCVGPEESAVCPERAMETLNGAGDTGGKPSTRGGDPAARSRRTEGIRAAYRRGDRGGARDLLEEACDQCASQLEKGQLLSIPAAYGDLEMVRYLLSKRLVELPTEPTDDNPAVVAAYFGHTAVVQELLESLPGPCSPQRLLNWMLALACQRGHLGVVKLLVLTHGADPESYAVRKNEFPVIVRLPLYAAIKSGNEDIAIFLLRHGAYFCSYILLDSPDPSKHLLRKYFIEASPLPSSYPGKTALRVKWSHLRLPWVDLDWLIDISCQITELDLSANCLATLPSVIPWGLINLRKLNLSDNHLGELPGVQSSDEIICSRLLEIDISSNKLSHLPPGFLHLSKLQKLTASKNCLEKLFEEENATNWIGLRKLQELDISDNKLTELPALFLHSFKSLNSLNVSRNNLKVFPDPWACPLKCCKASRNALECLPDKMAVFWKNHLKDVDFSENALKEVPLGLFQLDALMFLRLQGNQLAALPPQEKWTCRQLKTLDLSRNQLGKNEDGLKTKRIAFFTTRGRQRSGTEAASVLEFPAFLSESLEVLCLNDNHLDTVPPSVCLLKSLSELYLGNNPGLRELPPELGQLGNLWQLDTEDLTISNVPAEIQKEGPKAMLSYLRAQLRKAEKCKLMKMIIVGPPRQGKSTLLEILQTGRAPQVVHGEATIRTTKWELQRPAGSRAKVESVEFNVWDIGGPASMATVNQCFFTDKALYVVVWNLALGEEAVANLQFWLLNIEAKAPNAVVLVVGTHLDLIEAKFRVERIATLRAYVLALCRSPSGSRATGFPDITFKHLHEISCKSLEGQEGLRQLIFHVTCSMKDVGSTIGCQRLAGRLIPRSYLSLQEAVLAEQQRRSRDDDVQYLTDRQLEQLVEQTPDNDIKDYEDLQSAISFLIETGTLLHFPDTSHGLRNLYFLDPIWLSECLQRIFNIKGSRSVAKNGVIRAEDLRMLLVGTGFTQQTEEQYFQFLAKFEIALPVANDSYLLPHLLPSKPGLDTHGMRHPTANTIQRVFKMSFVPVGFWQRFIARMLISLAEMDLQLFENKKNTKSRNRKVTIYSFTGNQRNRCSTFRVKRNQTIYWQEGLLVTFDGGYLSVESSDVNWKKKKSGGMKIVCQSEVRDFSAMAFITDHVNSLIDQWFPALTATESDGTPLMEQYVPCPVCETAWAQHTDPSEKSEDVQYFDMEDCVLTAIERDFISCPRHPDLPVPLQELVPELFMTDFPARLFLENSKLEHSEDEGSVLGQGGSGTVIYRARYQGQPVAVKRFHIKKFKNFANVPADTMLRHLRATDAMKNFSEFRQEASMLHALQHPCIVALIGISIHPLCFALELAPLSSLNTVLSENARDSSFIPLGHMLTQKIAYQIASGLAYLHKKNIIFCDLKSDNILVWSLDVKEHINIKLSDYGISRQSFHEGALGVEGTPGYQAPEIRPRIVYDEKVDMFSYGMVLYELLSGQRPALGHHQLQIAKKLSKGIRPVLGQPEEVQFRRLQALMMECWDTKPEKRPLALSVVSQMKDPTFATFMYELCCGKQTAFFSSQGQEYTVVFWDGKEESRNYTVVNTEKGLMEVQRMCCPGMKVSCQLQVQRSLWTATEDQKIYIYTLKGMCPLNTPQQALDTPAVVTCFLAVPVIKKNSYLVLAGLADGLVAVFPVVRGTPKDSCSYLCSHTANRSKFSIADEDARQNPYPVKAMEVVNSGSEVWYSNGPGLLVIDCASLEICRRLEPYMAPSMVTSVVCSSEGRGEEVVWCLDDKANSLVMYHSTTYQLCARYFCGVPSPLRDMFPVRPLDTEPPAASHTANPKVPEGDSIADVSIMYSEELGTQILIHQESLTDYCSMSSYSSSPPRQAARSPSSLPSSPASSSSVPFSTDCEDSDMLHTPGAASDRSEHDLTPMDGETFSQHLQAVKILAVRDLIWVPRRGGDVIVIGLEKDSGAQRGRVIAVLKARELTPHGVLVDAAVVAKDTVVCTFENENTEWCLAVWRGWGAREFDIFYQSYEELGRLEACTRKRR lrrk2-dnajb6-1 3632370 N/A 3632380 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed n-terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false N/A 3632381 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false 1A-2 lrrk2-dnajb6-2 3632370 N/A 3632382 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed n-terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false N/A 3632381 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false 1A-3 lrrk2-dnajb8-1 3632370 N/A 3632383 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed n-terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false N/A 3632381 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false 1A-4 lrrk2-hspa1a-1 3632370 N/A 3632384 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed n-terminus v5 tag v5 tag GKPIPNPLLGLDST epitope tag GKPIPNPLLGLDST epitope tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false N/A 3632381 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false 1A-5 lrrk2-sqstm1-1 3632370 N/A 3632385 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false N/A 3632381 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false 1A-7, 2 C/D lrrk2-sqstm1-2 3632370 N/A 3632386 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed C-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 3632381 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false 1A-8 lrrk2-sqstm1-3 3632370 N/A 3632385 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed c-terminus ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 3632381 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed n-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ser935 opser O-phospho-L-serine (2S)-2-amino-3-(phosphonooxy)propanoic acid 2-amino-3-hydroxypropanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)propanoic acid ACT_SITE Phosphoserine intermediate MOD_RES Phosphoserine O-phospho-L-serine O-phosphonoserine O-phosphorylated L-serine O3-phosphoserine serine phosphate ester OPSer Phospho Phospho Seryl Phosphorylation phosphorylations certain certain sequence position certain certain certain sequence position certain false Ser1292 opser O-phospho-L-serine (2S)-2-amino-3-(phosphonooxy)propanoic acid 2-amino-3-hydroxypropanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)propanoic acid ACT_SITE Phosphoserine intermediate MOD_RES Phosphoserine O-phospho-L-serine O-phosphonoserine O-phosphorylated L-serine O3-phosphoserine serine phosphate ester OPSer Phospho Phospho Seryl Phosphorylation phosphorylations certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false 1B GNE1023: p62 was highly enriched in LRRK2 immune- complexes, with a slight increase in the presence of LRRK2 inhibitor GNE1023. In the presence of LRRK2 inhibitor GNE1023, LRRK2 phosphorylation at residues S935 and S1292 was reduced. HSP90 was also detected but due to lack of antibody specificity the identity of the molecule(s) is not known. lrrk2-sqstm1-4 3632370 N/A 3632385 unspecified role unspecified role prey prey over-expressed over expressed level over-expressed c-terminus ha tag ha tag YPYDVPDYA epitope tag YPYDVPDYA epitope tag c-term range C-terminal range c-term range c-term range C-terminal range c-term range false N/A 3632387 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed n-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false 1B-2 HSP90 was also detected but due to lack of antibody specificity the identity of the molecule(s) is not known. sqstm1-lrrk2-1 3632371 N/A 3632385 enzyme target enzyme target substrate substrate neutral component neutral component purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false region phosres phosphorylated residue PhosRes Phospho Phosphorylation Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) N/A 3632381 enzyme enzyme neutral component neutral component purified purified n-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Q5S007:p.Gly2019Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false human Homo sapiens Human phosphorylation phosphorylation reaction phosphorylation false false false 3A, Supp. fig 3C. Several potential sites of phosphorylation were identified. lrrk2-sqstm1-16 3632371 N/A 3632385 enzyme target enzyme target substrate substrate neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Thr138 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 3632381 enzyme enzyme neutral component neutral component purified purified n-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Q5S007:p.Gly2019Ser mutation increasing rate mutation increasing interaction rate mutation increasing rate certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Asp1994Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false human Homo sapiens Human phosphorylation phosphorylation reaction phosphorylation false false false Supp. fig 3A. lrrk2-sqstm1-17 3632371 N/A 3632385 enzyme target enzyme target substrate substrate neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Thr138 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false region his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false N/A 3632381 enzyme enzyme neutral component neutral component purified purified n-terminus gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Q5S007:p.Gly2019Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false region 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) phosphorylation phosphorylation reaction phosphorylation false false false Supp. fig 3A-2 lrrk2-sqstm1-18 3632371 N/A 3632385 enzyme target enzyme target substrate substrate neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Thr138 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false n-terminus gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 3632381 enzyme enzyme neutral component neutral component purified purified n-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Q5S007:p.Gly2019Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false human Homo sapiens Human phosphorylation phosphorylation reaction phosphorylation false false false Supp. fig 3B. lrrk2-sqstm1-19 3632371 N/A 3632385 enzyme target enzyme target substrate substrate neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Thr138 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false n-terminus gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Thr176 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3632381 enzyme enzyme neutral component neutral component purified purified n-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Q5S007:p.Gly2019Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false human Homo sapiens Human phosphorylation phosphorylation reaction phosphorylation false false false Supp. fig 3B-2. lrrk2-sqstm1-20 3632371 N/A 3632385 enzyme target enzyme target substrate substrate neutral component neutral component region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Thr138 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false n-terminus gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Thr176 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3632381 enzyme enzyme neutral component neutral component purified purified n-terminus gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Q5S007:p.Gly2019Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false region 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) phosphorylation phosphorylation reaction phosphorylation false false false Supp. fig 3B-3. lrrk2-sqstm1-9 3632372 N/A 3632385 weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra western blot western blot Immuno blot Immuno blot enzyme target enzyme target substrate substrate neutral component neutral component purified purified region phosres phosphorylated residue PhosRes Phospho Phosphorylation Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false Thr138 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false Q13501:p.Thr138Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3632381 weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra western blot western blot Immuno blot Immuno blot enzyme enzyme neutral component neutral component purified purified n-terminus gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Q5S007:p.Gly2019Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false region 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) phosphorylation phosphorylation reaction phosphorylation false false false 3B-LHS LRRK2 inhibitor GNE1023 lrrk2-sqstm1-10 3632372 N/A 3632385 weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra western blot western blot Immuno blot Immuno blot enzyme target enzyme target substrate substrate neutral component neutral component purified purified region phosres phosphorylated residue PhosRes Phospho Phosphorylation Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false Thr138 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false Q13501:p.Thr138Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3632381 weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra western blot western blot Immuno blot Immuno blot enzyme enzyme neutral component neutral component purified purified Q5S007:p.Arg1441Gly mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Tyr1699Cys mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Gly2019Ser mutation increasing rate mutation increasing interaction rate mutation increasing rate certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Gly2385Arg mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Asp1994Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false n-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false human Homo sapiens Human phosphorylation phosphorylation reaction phosphorylation false false false 3B-RHS,6C Figure 3B:The image text states:-"Right panel, 3 PM recombinant wild type p62 or p62 [T138A] were reacted with 56nM full length LRRK2 1-2527 G2019S or kinase inactive LRRK2 1-2527 [D1994A];however the image itself gives "LRRK2 WT" -no mention of the G2019S mutation. lrrk2-sqstm1-11 3632372 N/A 3632381 weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra western blot western blot Immuno blot Immuno blot putative self putative self putative self putative self purified purified n-terminus gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Q5S007:p.Gly2019Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false thr1491 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false phosres phosres phosphorylated residue PhosRes Phospho Phosphorylation Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) phosphorylation phosphorylation reaction phosphorylation false true false 3B-LHSi, Supp. Fig 4A LRRK2 inhibitor GNE1023 lrrk2-sqstm1-12 3632372 N/A 3632381 weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra western blot western blot Immuno blot Immuno blot putative self putative self putative self putative self purified purified Q5S007:p.Tyr1699Cys mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Arg1441Gly mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Gly2385Arg mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Asp1994Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false thr1491 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false n-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false phosres phosres phosphorylated residue PhosRes Phospho Phosphorylation Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false Q5S007:p.Gly2019Ser mutation increasing rate mutation increasing interaction rate mutation increasing rate certain certain sequence position certain certain certain sequence position certain false human Homo sapiens Human phosphorylation phosphorylation reaction phosphorylation false true false 3B-RHSi,6C Figure 3B:The image text states:-"Right panel, 3 PM recombinant wild type p62 or p62 [T138A] were reacted with 56nM full length LRRK2 1-2527 G2019S or kinase inactive LRRK2 1-2527 [D1994A];however the image itself gives "LRRK2 WT" -no mention of the G2019S mutation. lrrk2-42 3632372 N/A 3632381 weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra western blot western blot Immuno blot Immuno blot putative self putative self putative self putative self purified purified Q5S007:p.Tyr1699Cys mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Arg1441Gly mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Gly2385Arg mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Asp1994Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false thr1491 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false n-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false phosres phosres phosphorylated residue PhosRes Phospho Phosphorylation Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false Q5S007:p.Gly2019Ser mutation increasing rate mutation increasing interaction rate mutation increasing rate certain certain sequence position certain certain certain sequence position certain false human Homo sapiens Human phosphorylation phosphorylation reaction phosphorylation false true false 6C Figure 3B:The image text states:-"Right panel, 3 PM recombinant wild type p62 or p62 [T138A] were reacted with 56nM full length LRRK2 1-2527 G2019S or kinase inactive LRRK2 1-2527 [D1994A];however the image itself gives "LRRK2 WT" -no mention of the G2019S mutation. lrrk2-sqstm1-21 3632372 N/A 3632385 weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra enzyme target enzyme target substrate substrate neutral component neutral component purified purified region phosres phosphorylated residue PhosRes Phospho Phosphorylation Phosphorylation (O of Serine, Threonine, Tyrosine and Aspartate, N epsilon of Lysine) undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false Thr138 opthr O-phospho-L-threonine (2S,3R)-2-amino-3-(phosphonooxy)butanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)butanoic acid MOD_RES Phosphothreonine O-phospho-L-threonine O-phosphorylated L-threonine O3-phosphothreonine threonine phosphate ester OPThr Phospho Phospho Threonyl Phosphorylation phosphorylationt certain certain sequence position certain certain certain sequence position certain false Q13501:p.Thr138Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false Q13501:p.Thr164Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q13501:p.[Thr138Ala;Thr164Ala] mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false Q13501:p.Ser176Ala mutation with no effect mutation with no effect mutation with no effect mutation not affecting interaction certain certain sequence position certain certain certain sequence position certain false Q13501:p.[Thr138Ala;Thr164Ala;Ser176Ala] mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 3632381 weight by comassie molecular weight estimation by coomasie staining weight by comassie weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra enzyme enzyme neutral component neutral component purified purified n-terminus gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Q5S007:p.Gly2019Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false region 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) phosphorylation phosphorylation reaction phosphorylation false false false Supp. fig. 4A lrrk2-sqstm1-5 3632373 N/A 3632385 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level N/A 3632381 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level ser935 opser O-phospho-L-serine (2S)-2-amino-3-(phosphonooxy)propanoic acid 2-amino-3-hydroxypropanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)propanoic acid ACT_SITE Phosphoserine intermediate MOD_RES Phosphoserine O-phospho-L-serine O-phosphonoserine O-phosphorylated L-serine O3-phosphoserine serine phosphate ester OPSer Phospho Phospho Seryl Phosphorylation phosphorylations certain certain sequence position certain certain certain sequence position certain false Ser1292 opser O-phospho-L-serine (2S)-2-amino-3-(phosphonooxy)propanoic acid 2-amino-3-hydroxypropanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)propanoic acid ACT_SITE Phosphoserine intermediate MOD_RES Phosphoserine O-phospho-L-serine O-phosphonoserine O-phosphorylated L-serine O3-phosphoserine serine phosphate ester OPSer Phospho Phospho Seryl Phosphorylation phosphorylations certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false 1C, Supp. figure 2C GNE1023: p62 was highly enriched in LRRK2 immune- complexes, with a slight increase in the presence of LRRK2 inhibitor GNE1023. In the presence of LRRK2 inhibitor GNE1023, LRRK2 phosphorylation at residues S935 and S1292 was reduced. LRRK2 inhibitor MLi2 (CHEBI:132484) lrrk2-sqstm1-7 3632374 N/A 3632385 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level N/A 3632381 unspecified role unspecified role bait bait physiological level physiological level endogenous level endogenous endogenous endogenous level ser935 opser O-phospho-L-serine (2S)-2-amino-3-(phosphonooxy)propanoic acid 2-amino-3-hydroxypropanoic acid 3-phosphate 2-azanyl-3-(phosphonooxy)propanoic acid ACT_SITE Phosphoserine intermediate MOD_RES Phosphoserine O-phospho-L-serine O-phosphonoserine O-phosphorylated L-serine O3-phosphoserine serine phosphate ester OPSer Phospho Phospho Seryl Phosphorylation phosphorylations certain certain sequence position certain certain certain sequence position certain false n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false physical association physical association false false false 1D HSP90 and 14-3-3 proteins were also detected but due to lack of antibody specificity the identity of the molecule(s) is not known. lrrk2-sqstm1-6 3632375 N/A 3632385 unspecified role unspecified role prey prey physiological level physiological level endogenous level endogenous endogenous endogenous level N/A 3632381 unspecified role unspecified role bait bait over-expressed over expressed level over-expressed n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false physical association physical association false false false 2A/B lrrk2-sqstm1-8 3632376 N/A 3632385 unspecified role unspecified role bait bait purified purified region sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n-terminus gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 3632381 unspecified role unspecified role prey prey purified purified n-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false Q5S007:p.Gly2019Ser mutation mutation certain certain sequence position certain certain certain sequence position certain false human Homo sapiens Human direct interaction direct interaction false false false 2E weak binding FLAG-LRRK2 has been assumed to have been purified, as the same construct was used in figure 3A. Similarly FLAG-LRRK2 is stated in Fig 3A to have been expressed from a mammalian cell line, presumably a human one. lrrk2-sqstm1-13 3632377 N/A 3632381 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false N/A 3632385 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed n-terminus flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged n-term range n-terminal range n-term range n-term range n-terminal range n-term range false proximity proximity close-contact colocalization neighbourhood interaction false false false Supp. fig 2 lrrk2-sqstm1-14 3632378 N/A 3632385 unspecified role unspecified role neutral component neutral component physiological level physiological level endogenous level endogenous endogenous endogenous level N/A 3632381 unspecified role unspecified role neutral component neutral component physiological level physiological level endogenous level endogenous endogenous endogenous level proximity proximity close-contact colocalization neighbourhood interaction false false false Supp. figure 2D LRRK2 inhibitor: GNE1023 lrrk2-sqstm1-15 3632379 N/A 3632385 unspecified role unspecified role neutral component neutral component physiological level physiological level endogenous level endogenous endogenous endogenous level N/A 3632381 unspecified role unspecified role neutral component neutral component over-expressed over expressed level over-expressed n-terminus gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false colocalization colocalization false false false Supp. figure 2E LRRK2 forms skein or punctate structures in the cytoplasm of cells.