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/ liao-2014-1 Parkinson disease-associated mutation R1441H in LRRK2 prolongs the "active state" of its GTPase domain. ecoli Escherichia coli (strain K12) molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Liao J., Wu C.X., Burlak C., Zhang S., Sahm H., Wang M., Zhang Z.Y., Vogel K.W., Federici M., Riddle S.M., Nichols R.J., Liu D., Cookson M.R., Stone T.A., Hoang Q.Q. Parkinsons - Interactions investigated in the context of Parkinsons disease qqhoang@iu.edu Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2014 imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Only protein-protein interactions liao-2014-2 Parkinson disease-associated mutation R1441H in LRRK2 prolongs the "active state" of its GTPase domain. ecoli Escherichia coli (strain K12) light scattering light scattering predetermined predetermined participant predetermined Liao J., Wu C.X., Burlak C., Zhang S., Sahm H., Wang M., Zhang Z.Y., Vogel K.W., Federici M., Riddle S.M., Nichols R.J., Liu D., Cookson M.R., Stone T.A., Hoang Q.Q. Parkinsons - Interactions investigated in the context of Parkinsons disease SEC-MALS (Size-Exclusion Chromatography+ Multi-Angle Static Light Scattering) qqhoang@iu.edu Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2014 imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Only protein-protein interactions liao-2014-4 Parkinson disease-associated mutation R1441H in LRRK2 prolongs the "active state" of its GTPase domain. in vitro In vitro fps fluorescence polarization spectroscopy Fluorescence anisotropy FPS FPS Fluorescence anisotropy fps tag fluorescence tag visualisation by fluorescence tag fluorescence Liao J., Wu C.X., Burlak C., Zhang S., Sahm H., Wang M., Zhang Z.Y., Vogel K.W., Federici M., Riddle S.M., Nichols R.J., Liu D., Cookson M.R., Stone T.A., Hoang Q.Q. Parkinsons - Interactions investigated in the context of Parkinsons disease The fluorescence of BODIPY FL GTP-gamma-S is quenched ~90% relative to that of the free dye, but may be recovered on binding to G-proteins. qqhoang@iu.edu Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2014 imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Only protein-protein interactions liao-2014-5 Parkinson disease-associated mutation R1441H in LRRK2 prolongs the "active state" of its GTPase domain. in vitro In vitro gtpase assay gtpase assay GTPase gtp hydrolisis gtp hydrolisis GTPase predetermined predetermined participant predetermined Liao J., Wu C.X., Burlak C., Zhang S., Sahm H., Wang M., Zhang Z.Y., Vogel K.W., Federici M., Riddle S.M., Nichols R.J., Liu D., Cookson M.R., Stone T.A., Hoang Q.Q. Parkinsons - Interactions investigated in the context of Parkinsons disease Participant Detection was by Normal-phase hydrophilic interaction liquid chromatography (HILIC) HPLC coupled to electrospray mass-spectrometry (LC/MS) after incubation, denaturation and centrifugation of protein samples. qqhoang@iu.edu Proc. Natl. Acad. Sci. U.S.A. (0027-8424) 2014 imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Only protein-protein interactions lrrk2_human Leucine-rich repeat serine/threonine-protein kinase 2 LRRK2 PARK8 Dardarin protein protein human Homo sapiens Human MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNIHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILKMLTVHNASVNLSVIGLKTLDLLLTSGKITLLILDEESDIFMLIFDAMHSFPANDEVQKLGCKALHVLFERVSEEQLTEFVENKDYMILLSALTNFKDEEEIVLHVLHCLHSLAIPCNNVEVLMSGNVRCYNIVVEAMKAFPMSERIQEVSCCLLHRLTLGNFFNILVLNEVHEFVVKAVQQYPENAALQISALSCLALLTETIFLNQDLEEKNENQENDDEGEEDKLFWLEACYKALTWHRKNKHVQEAACWALNNLLMYQNSLHEKIGDEDGHFPAHREVMLSMLMHSSSKEVFQASANALSTLLEQNVNFRKILLSKGIHLNVLELMQKHIHSPEVAESGCKMLNHLFEGSNTSLDIMAAVVPKILTVMKRHETSLPVQLEALRAILHFIVPGMPEESREDTEFHHKLNMVKKQCFKNDIHKLVLAALNRFIGNPGIQKCGLKVISSIVHFPDALEMLSLEGAMDSVLHTLQMYPDDQEIQCLGLSLIGYLITKKNVFIGTGHLLAKILVSSLYRFKDVAEIQTKGFQTILAILKLSASFSKLLVHHSFDLVIFHQMSSNIMEQKDQQFLNLCCKCFAKVAMDDYLKNVMLERACDQNNSIMVECLLLLGADANQAKEGSSLICQVCEKESSPKLVELLLNSGSREQDVRKALTISIGKGDSQIISLLLRRLALDVANNSICLGGFCIGKVEPSWLGPLFPDKTSNLRKQTNIASTLARMVIRYQMKSAVEEGTASGSDGNFSEDVLSKFDEWTFIPDSSMDSVFAQSDDLDSEGSEGSFLVKKKSNSISVGEFYRDAVLQRCSPNLQRHSNSLGPIFDHEDLLKRKRKILSSDDSLRSSKLQSHMRHSDSISSLASEREYITSLDLSANELRDIDALSQKCCISVHLEHLEKLELHQNALTSFPQQLCETLKSLTHLDLHSNKFTSFPSYLLKMSCIANLDVSRNDIGPSVVLDPTVKCPTLKQFNLSYNQLSFVPENLTDVVEKLEQLILEGNKISGICSPLRLKELKILNLSKNHISSLSENFLEACPKVESFSARMNFLAAMPFLPPSMTILKLSQNKFSCIPEAILNLPHLRSLDMSSNDIQYLPGPAHWKSLNLRELLFSHNQISILDLSEKAYLWSRVEKLHLSHNKLKEIPPEIGCLENLTSLDVSYNLELRSFPNEMGKLSKIWDLPLDELHLNFDFKHIGCKAKDIIRFLQQRLKKAVPYNRMKLMIVGNTGSGKTTLLQQLMKTKKSDLGMQSATVGIDVKDWPIQIRDKRKRDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQAEVDAMKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDYHFVNATEESDALAKLRKTIINESLNFKIRDQLVVGQLIPDCYVELEKIILSERKNVPIEFPVIDRKRLLQLVRENQLQLDENELPHAVHFLNESGVLLHFQDPALQLSDLYFVEPKWLCKIMAQILTVKVEGCPKHPKGIISRRDVEKFLSKKRKFPKNYMSQYFKLLEKFQIALPIGEEYLLVPSSLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPYMLSGRERALRPNRMYWRQGIYLNWSPEAYCLVGSEVLDNHPESFLKITVPSCRKGCILLGQVVDHIDSLMEEWFPGLLEIDICGEGETLLKKWALYSFNDGEEHQKILLDDLMKKAEEGDLLVNPDQPRLTIPISQIAPDLILADLPRNIMLNNDELEFEQAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNKHTSLRLLRQELVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQHRIALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKTSEGTPGFRAPEVARGNVIYNQQADVYSFGLLLYDILTTGGRIVEGLKFPNEFDELEIQGKLPDPVKEYGCAPWPMVEKLIKQCLKENPQERPTSAQVFDILNSAELVCLTRRILLPKNVIVECMVATHHNSRNASIWLGCGHTDRGQLSFLDLNTEGYTSEEVADSRILCLALVHLPVEKESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTCLYCNSFSKQSKQKNFLLVGTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSESTNSTERNVMWGGCGTKIFSFSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYIAKQNSPVVEVWDKKTEKLCGLIDCVHFLREVMVKENKESKHKMSYSGRVKTLCLQKNTALWIGTGGGHILLLDLSTRRLIRVIYNFCNSVRVMMTAQLGSLKNVMLVLGYNRKNTEGTQKQKEIQSCLTVWDINLPHEVQNLEKHIEVRKELAEKMRRTSVE gdp guanosine 5-diphosphate small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) gppnhp Guanosine 5'-[beta,gamma-imido]triphosphate trisodium salt hydrate small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) guanosine 5'-[gamma-thio]triphosphate GTP-gamma-S small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) gtp guanosine triphosphate - GTP 5'-GTP GTP Guanosine 5'-triphosphate guanosine 5'-triphosphoric acid guanosine triphosphate GUANOSINE-5'-TRIPHOSPHATE H4gtp guanosine 5'-(tetrahydrogen triphosphate) small molecule small molecule chemical synthesis Chemical synthesis (Chemical synthesis) InChI=1/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1/f/h14,19-20,22,24H,11H2 lrrk2-1 1512965 n/a 1512969 unspecified role unspecified role neutral component neutral component n_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false extended_roc_domain 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) Stoichiometry: 2.0 direct interaction direct interaction false false false 2A gdp-lrrk2 1512965 n/a 1512969 unspecified role unspecified role neutral component neutral component n_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false extended_roc_domain 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) Stoichiometry: 2.0 n/a 1512970 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction false false false 3A The Roc48 peak (molecular weight ~48kDa) is converted into a Roc24 peak (molecular weight ~24kDa) upon binding to either GDP or GTP. gdp-lrrk2-2 1512965 n/a 1512971 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1512969 unspecified role unspecified role neutral component neutral component extended_roc_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-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) Stoichiometry: 2.0 direct interaction direct interaction false false false 3A The Roc48 peak (molecular weight ~48kDa) is converted into a Roc24 peak (molecular weight ~24kDa) upon binding to either GDP or GTP. lrrk2-1 1512966 n/a 1512969 unspecified role unspecified role neutral component neutral component extended_roc_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-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) Stoichiometry: 2.0 direct interaction direct interaction false false false 2D gdp-lrrk2-1 1512966 n/a 1512969 unspecified role unspecified role neutral component neutral component n_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false extended_roc_domain 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) Stoichiometry: 2.0 n/a 1512971 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction false false false 3B The Roc48 peak (molecular weight ~48kDa) is converted into a Roc24 peak (molecular weight ~24kDa) upon binding to either GDP or GTP. gppnhp-lrrk2 1512966 n/a 1512969 unspecified role unspecified role neutral component neutral component n_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false extended_roc_domain 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) Stoichiometry: 2.0 n/a 1512970 unspecified role unspecified role neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction false false false 3B The Roc48 peak (molecular weight ~48kDa) is converted into a Roc24 peak (molecular weight ~24kDa) upon binding to either GDP or GTP. gtp-lrrk2-19 1512967 n/a 1512972 enzyme target enzyme target substrate substrate neutral component neutral component gamma_thiol_linked bodipy label bodipy label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1512969 enzyme enzyme neutral component neutral component n_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false extended_roc_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Arg1441His mutation increasing mutation increasing interaction mutation increasing certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1512967 5A/B/C The GTPgamma-S-binding affinity of RocR1414H is twofold higher than that of Roc-ext, Kd = 3.39 vs. 7.85 µM (WT), gtp-guanosine_5___gamma_thio_triphosphate 1512967 n/a 1512973 competitor competitor competitor neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1512972 unspecified role unspecified role neutral component neutral component gamma_thiol_linked bodipy label bodipy label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1512969 unspecified role unspecified role neutral component neutral component n_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false extended_roc_domain 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) physical association physical association false false false 5B guanosine_5___gamma_thio_triphosphate-lrrk2 1512967 n/a 1512970 enzyme target enzyme target substrate substrate neutral component neutral component gamma_thiol_linked bodipy label bodipy label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1512969 enzyme enzyme neutral component neutral component extended_roc_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false n_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-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) direct interaction direct interaction false false false 1512967 5D The GDP binding affinity of RocR1414H is Kd = 0.55 uM. WT Kd =0.47uM.) gtp-lrrk2-20 1512968 n/a 1512973 enzyme target enzyme target substrate substrate neutral component neutral component chemical synthesis Chemical synthesis (Chemical synthesis) n/a 1512969 enzyme enzyme neutral component neutral component n_terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false extended_roc_domain sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false Q5S007:p.Arg1441His mutation decreasing rate mutation decreasing interaction rate mutation decreasing rate certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) gtpase reaction gtpase reaction false false false 1512968 1512968 4 and 7 The low turnover rate and high Km indicate that the isolated extended Roc domain is a slow enzyme. R1441H mutant has a Km of 0.112 mM and a Kcat = 0.009 /min (0.00015/sec). These figures show the mutant is less active than the wild type.