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/ reynolds-2014-1 LRRK2 kinase activity and biology are not uniformly predicted by its autophosphorylation and cellular phosphorylation site status. in vitro In vitro protein kinase assay protein kinase assay tag visualisation tag visualisation Reynolds A., Doggett E.A., Riddle S.M., Lebakken C.S., Nichols R.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. For Figure 1(A) it is stated that:- "We next employed full length recombinant LRRK2 [wild-type, Gly2019Ser, Arg1441Cys, and Asp1994Ala] (LifeTechnologies)". However Life Technologies do not sell full length R1441C nor D1994A mutants, so all these mutants have been entered as having FLAG tags, as these tags are stated to be used for the detection of reaction products - see Figures 1 D-G and Methods section. The authors have not replied to a clarification request. Results have not been annotated when LRRK2 has only been purified by IP alone. jnichols@parkinsonsinstitute.org Front Mol Neurosci 2014 Only protein-protein interactions imex curation Parkinsons - Interactions investigated in the context of Parkinsons disease The authors confirm that " all of the LRRK2 constructs, as used in Figure 1, are FULL length, FLAG tagged, and Human in origin. The variants used in figure 1 were supplied in a collaboration (with LifeTech), and appear to be no longer available. reynolds-2014-2 LRRK2 kinase activity and biology are not uniformly predicted by its autophosphorylation and cellular phosphorylation site status. in vitro In vitro protein kinase assay protein kinase assay antibody detection identification by antibody antibody detection Reynolds A., Doggett E.A., Riddle S.M., Lebakken C.S., Nichols R.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. For Figure 1(A) it is stated that:- "We next employed full length recombinant LRRK2 [wild-type, Gly2019Ser, Arg1441Cys, and Asp1994Ala] (LifeTechnologies)". However Life Technologies do not sell full length R1441C nor D1994A mutants, so all these mutants have been entered as having FLAG tags, as these tags are stated to be used for the detection of reaction products - see Figures 1 D-G and Methods section. The authors have not replied to a clarification request. Results have not been annotated when LRRK2 has only been purified by IP alone. jnichols@parkinsonsinstitute.org Front Mol Neurosci 2014 Only protein-protein interactions imex curation Parkinsons - Interactions investigated in the context of Parkinsons disease The authors confirm that " all of the LRRK2 constructs, as used in Figure 1, are FULL length, FLAG tagged, and Human in origin. The variants used in figure 1 were supplied in a collaboration (with LifeTech), and appear to be no longer available. moes_human Moesin Membrane-organizing extension spike protein MSN protein protein human Homo sapiens Human MPKTISVRVTTMDAELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKESPLLFKFRAKFYPEDVSEELIQDITQRLFFLQVKEGILNDDIYCPPETAVLLASYAVQSKYGDFNKEVHKSGYLAGDKLLPQRVLEQHKLNKDQWEERIQVWHEEHRGMLREDAVLEYLKIAQDLEMYGVNYFSIKNKKGSELWLGVDALGLNIYEQNDRLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRINKRILALCMGNHELYMRRRKPDTIEVQQMKAQAREEKHQKQMERAMLENEKKKREMAEKEKEKIEREKEELMERLKQIEEQTKKAQQELEEQTRRALELEQERKRAQSEAEKLAKERQEAEEAKEALLQASRDQKKTQEQLALEMAELTARISQLEMARQKKESEAVEWQQKAQMVQEDLEKTRAELKTAMSTPHVAEPAENEQDEQDENGAEASADLRADAMAKDRSEEERTTEAEKNERVQKHLKALTSELANARDESKKTANDMIHAENMRLGRDKYKTLRQIRQGNTKQRIDEFESM lrrk2_human Leucine-rich repeat serine/threonine-protein kinase 2 LRRK2 PARK8 Dardarin protein protein human Homo sapiens Human MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNIHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILKMLTVHNASVNLSVIGLKTLDLLLTSGKITLLILDEESDIFMLIFDAMHSFPANDEVQKLGCKALHVLFERVSEEQLTEFVENKDYMILLSALTNFKDEEEIVLHVLHCLHSLAIPCNNVEVLMSGNVRCYNIVVEAMKAFPMSERIQEVSCCLLHRLTLGNFFNILVLNEVHEFVVKAVQQYPENAALQISALSCLALLTETIFLNQDLEEKNENQENDDEGEEDKLFWLEACYKALTWHRKNKHVQEAACWALNNLLMYQNSLHEKIGDEDGHFPAHREVMLSMLMHSSSKEVFQASANALSTLLEQNVNFRKILLSKGIHLNVLELMQKHIHSPEVAESGCKMLNHLFEGSNTSLDIMAAVVPKILTVMKRHETSLPVQLEALRAILHFIVPGMPEESREDTEFHHKLNMVKKQCFKNDIHKLVLAALNRFIGNPGIQKCGLKVISSIVHFPDALEMLSLEGAMDSVLHTLQMYPDDQEIQCLGLSLIGYLITKKNVFIGTGHLLAKILVSSLYRFKDVAEIQTKGFQTILAILKLSASFSKLLVHHSFDLVIFHQMSSNIMEQKDQQFLNLCCKCFAKVAMDDYLKNVMLERACDQNNSIMVECLLLLGADANQAKEGSSLICQVCEKESSPKLVELLLNSGSREQDVRKALTISIGKGDSQIISLLLRRLALDVANNSICLGGFCIGKVEPSWLGPLFPDKTSNLRKQTNIASTLARMVIRYQMKSAVEEGTASGSDGNFSEDVLSKFDEWTFIPDSSMDSVFAQSDDLDSEGSEGSFLVKKKSNSISVGEFYRDAVLQRCSPNLQRHSNSLGPIFDHEDLLKRKRKILSSDDSLRSSKLQSHMRHSDSISSLASEREYITSLDLSANELRDIDALSQKCCISVHLEHLEKLELHQNALTSFPQQLCETLKSLTHLDLHSNKFTSFPSYLLKMSCIANLDVSRNDIGPSVVLDPTVKCPTLKQFNLSYNQLSFVPENLTDVVEKLEQLILEGNKISGICSPLRLKELKILNLSKNHISSLSENFLEACPKVESFSARMNFLAAMPFLPPSMTILKLSQNKFSCIPEAILNLPHLRSLDMSSNDIQYLPGPAHWKSLNLRELLFSHNQISILDLSEKAYLWSRVEKLHLSHNKLKEIPPEIGCLENLTSLDVSYNLELRSFPNEMGKLSKIWDLPLDELHLNFDFKHIGCKAKDIIRFLQQRLKKAVPYNRMKLMIVGNTGSGKTTLLQQLMKTKKSDLGMQSATVGIDVKDWPIQIRDKRKRDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQAEVDAMKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDYHFVNATEESDALAKLRKTIINESLNFKIRDQLVVGQLIPDCYVELEKIILSERKNVPIEFPVIDRKRLLQLVRENQLQLDENELPHAVHFLNESGVLLHFQDPALQLSDLYFVEPKWLCKIMAQILTVKVEGCPKHPKGIISRRDVEKFLSKKRKFPKNYMSQYFKLLEKFQIALPIGEEYLLVPSSLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPYMLSGRERALRPNRMYWRQGIYLNWSPEAYCLVGSEVLDNHPESFLKITVPSCRKGCILLGQVVDHIDSLMEEWFPGLLEIDICGEGETLLKKWALYSFNDGEEHQKILLDDLMKKAEEGDLLVNPDQPRLTIPISQIAPDLILADLPRNIMLNNDELEFEQAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNKHTSLRLLRQELVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQHRIALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKTSEGTPGFRAPEVARGNVIYNQQADVYSFGLLLYDILTTGGRIVEGLKFPNEFDELEIQGKLPDPVKEYGCAPWPMVEKLIKQCLKENPQERPTSAQVFDILNSAELVCLTRRILLPKNVIVECMVATHHNSRNASIWLGCGHTDRGQLSFLDLNTEGYTSEEVADSRILCLALVHLPVEKESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTCLYCNSFSKQSKQKNFLLVGTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSESTNSTERNVMWGGCGTKIFSFSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYIAKQNSPVVEVWDKKTEKLCGLIDCVHFLREVMVKENKESKHKMSYSGRVKTLCLQKNTALWIGTGGGHILLLDLSTRRLIRVIYNFCNSVRVMMTAQLGSLKNVMLVLGYNRKNTEGTQKQKEIQSCLTVWDINLPHEVQNLEKHIEVRKELAEKMRRTSVE lrrk2-msn-14 1563115 n/a 1563117 enzyme target enzyme target substrate substrate neutral component neutral component region_lrrktide sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1563118 enzyme enzyme neutral component neutral component region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false phosphorylation phosphorylation reaction phosphorylation false false false 1C P26038 opser Specific Activity of WT LRRK2 =52 nmol/mg/min, R1441C mutant - 64 nmol/mg/min, G2019S mutant = 128 nmol/mg/min, (Kinase Dead mutant = not detected). lrrk2-msn-15 1563115 n/a 1563118 enzyme enzyme neutral component neutral component region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged 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 Q5S007:p.Arg1441Cys 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 n/a 1563117 enzyme target enzyme target substrate substrate neutral component neutral component region_lrrktide sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false chemical synthesis Chemical synthesis (Chemical synthesis) phosphorylation phosphorylation reaction phosphorylation false false false 1Ci P26038 opser Specific Activity of WT LRRK2 =52 nmol/mg/min, R1441C mutant - 64 nmol/mg/min, G2019S mutant = 128 nmol/mg/min, (Kinase Dead mutant = not detected). lrrk2-3 1563116 n/a 1563118 self self self self Q5S007:p.Arg1441Cys mutation increasing rate mutation increasing interaction rate mutation increasing rate 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.Asp1994Ala mutation disrupting rate mutation disrupting interaction rate mutation disrupting rate certain certain sequence position certain certain certain sequence position certain false region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false phosphorylation phosphorylation reaction phosphorylation false true false 1D-G Q5S007 ser-1292 O-phospho-L-serine Q5S007 thr-1503 O-phospho-L-serine Q5S007 thr-1491 O-phospho-L-serine Q5S007 thr-2483 O-phospho-L-serine For the Gly2019Ser and Arg1441Cys LRRK2 mutants, Ser1292 is already phosphorylated at the beginning of the reaction. A twofold increase in autophosphorylation can be seen using the Gly2019Ser mutant; the autophosphorylation activity of the Arg1441Cys mutant is increased relative to wild-type. lrrk2-3 1563116 n/a 1563118 self self self self region flag tag flag tag FLAG-tagged FLAG DYKDDDDKV epitope tag DYKDDDDKV epitope tag FLAG FLAG-tagged undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false phosphorylation phosphorylation reaction phosphorylation false true false 1D-G Q5S007 ser-1292 O-phospho-L-serine Q5S007 thr-1503 O-phospho-L-serine Q5S007 thr-1491 O-phospho-L-serine Q5S007 thr-2483 O-phospho-L-serine Q5S007 increases activity of Q5S007