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/ Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Biochemistry (0006-2960) 2010 imex curation Berger Z., Smith K.A., Lavoie M.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... email sent 22/10/12 Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions human-293ft Homo sapiens HEK293FT cell line 293ft HEK293FT cell line molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column anti tag western anti tag western blot anti tag western Berger Z., Smith K.A., Lavoie M.J. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu Accepted 2012-DEC-14 by ORCHARD 18-Dec-2012: Contacted by IntAct-Help. Biochemistry (0006-2960) 2010 Only protein-protein interactions imex curation Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Biochemistry (0006-2960) 2010 imex curation Berger Z., Smith K.A., Lavoie M.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... email sent 22/10/12 Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions rat-mes23_5 Rat -Mouse interspecies hybrid MES23.5; dopaminergic neuroblastoma/glioma cell line mes23_5 Rat -Mouse interspecies hybrid MES23.5; dopaminergic neuroblastoma/glioma cell line This line expresses GHS-R1a. It was hybridised from the murine neuroblastoma-glioma N18TG2 with rat mesencephalic neurons. It is a stable inter-species hybrid. density sedimentation cosedimentation through density gradient density sedimentation anti tag western anti tag western blot anti tag western Berger Z., Smith K.A., Lavoie M.J. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu Accepted 2012-DEC-14 by ORCHARD 18-Dec-2012: Contacted by IntAct-Help. Biochemistry (0006-2960) 2010 Only protein-protein interactions imex curation Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Biochemistry (0006-2960) 2010 imex curation Berger Z., Smith K.A., Lavoie M.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... email sent 22/10/12 Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions human-293ft Homo sapiens HEK293FT cell line 293ft HEK293FT cell line anti tag coip anti tag coimmunoprecipitation anti tag coip anti tag western anti tag western blot anti tag western Berger Z., Smith K.A., Lavoie M.J. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu Accepted 2012-DEC-14 by ORCHARD 18-Dec-2012: Contacted by IntAct-Help. Biochemistry (0006-2960) 2010 Only protein-protein interactions imex curation Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Biochemistry (0006-2960) 2010 imex curation Berger Z., Smith K.A., Lavoie M.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... email sent 22/10/12 Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions rat-mes23_5 Rat -Mouse interspecies hybrid MES23.5; dopaminergic neuroblastoma/glioma cell line mes23_5 Rat -Mouse interspecies hybrid MES23.5; dopaminergic neuroblastoma/glioma cell line This line expresses GHS-R1a. It was hybridised from the murine neuroblastoma-glioma N18TG2 with rat mesencephalic neurons. It is a stable inter-species hybrid. crosslink cross-linking study crosslink anti tag western anti tag western blot anti tag western Berger Z., Smith K.A., Lavoie M.J. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu Accepted 2012-DEC-14 by ORCHARD 18-Dec-2012: Contacted by IntAct-Help. Biochemistry (0006-2960) 2010 Only protein-protein interactions imex curation Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Biochemistry (0006-2960) 2010 imex curation Berger Z., Smith K.A., Lavoie M.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... email sent 22/10/12 Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro protein kinase assay protein kinase assay weight autoradiogra molecular weight estimation by autoradiography weight autoradiogra Berger Z., Smith K.A., Lavoie M.J. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu Accepted 2012-DEC-14 by ORCHARD 18-Dec-2012: Contacted by IntAct-Help. Biochemistry (0006-2960) 2010 Only protein-protein interactions imex curation Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Biochemistry (0006-2960) 2010 imex curation Berger Z., Smith K.A., Lavoie M.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... email sent 22/10/12 Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro affinity chrom affinity chromatography technology Affinity purification Affinity purification affinity chrom western blot western blot Immuno blot Immuno blot Berger Z., Smith K.A., Lavoie M.J. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu Accepted 2012-DEC-14 by ORCHARD 18-Dec-2012: Contacted by IntAct-Help. Biochemistry (0006-2960) 2010 Only protein-protein interactions imex curation Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Biochemistry (0006-2960) 2010 imex curation Berger Z., Smith K.A., Lavoie M.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... email sent 22/10/12 Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions in vitro In vitro affinity chrom affinity chromatography technology Affinity purification Affinity purification affinity chrom anti tag western anti tag western blot anti tag western Berger Z., Smith K.A., Lavoie M.J. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu Accepted 2012-DEC-14 by ORCHARD 18-Dec-2012: Contacted by IntAct-Help. Biochemistry (0006-2960) 2010 Only protein-protein interactions imex curation Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Biochemistry (0006-2960) 2010 imex curation Berger Z., Smith K.A., Lavoie M.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... email sent 22/10/12 Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions human-lymphoblast Homo sapiens, lymphoblast lymphoblast Transformed lymphocytes; Blast cell; Lymphoblastoid crosslink cross-linking study crosslink western blot western blot Immuno blot Immuno blot Berger Z., Smith K.A., Lavoie M.J. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu Accepted 2012-DEC-14 by ORCHARD 18-Dec-2012: Contacted by IntAct-Help. Biochemistry (0006-2960) 2010 Only protein-protein interactions imex curation Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Biochemistry (0006-2960) 2010 imex curation Berger Z., Smith K.A., Lavoie M.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... email sent 22/10/12 Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions human-293ft Homo sapiens HEK293FT cell line 293ft HEK293FT cell line crosslink cross-linking study crosslink western blot western blot Immuno blot Immuno blot Berger Z., Smith K.A., Lavoie M.J. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu Accepted 2012-DEC-14 by ORCHARD 18-Dec-2012: Contacted by IntAct-Help. Biochemistry (0006-2960) 2010 Only protein-protein interactions imex curation Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Biochemistry (0006-2960) 2010 imex curation Berger Z., Smith K.A., Lavoie M.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... email sent 22/10/12 Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions human-293ft Homo sapiens HEK293FT cell line 293ft HEK293FT cell line density sedimentation cosedimentation through density gradient density sedimentation anti tag western anti tag western blot anti tag western Berger Z., Smith K.A., Lavoie M.J. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu Accepted 2012-DEC-14 by ORCHARD 18-Dec-2012: Contacted by IntAct-Help. Biochemistry (0006-2960) 2010 Only protein-protein interactions imex curation Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Membrane localization of LRRK2 is associated with increased formation of the highly active LRRK2 dimer and changes in its phosphorylation. Biochemistry (0006-2960) 2010 imex curation Berger Z., Smith K.A., Lavoie M.J. Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... email sent 22/10/12 Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu 18-Dec-2012: Contacted by IntAct-Help. Only protein-protein interactions human-lymphoblast Homo sapiens, lymphoblast lymphoblast Transformed lymphocytes; Blast cell; Lymphoblastoid density sedimentation cosedimentation through density gradient density sedimentation western blot western blot Immuno blot Immuno blot Berger Z., Smith K.A., Lavoie M.J. Parkinsons - Interactions investigated in the context of Parkinsons disease Fig 4/6/S4A - these might be "mice" cells -cytosolic/membrane fractions - see section just above "RESULTS". But as similar cell fractions are used from many sources it is hard to know... Cell lysates were separated using glycerol gradients and low and high molecular weight fractions used for cross linking with DSS. (disuccinimidyl suberate). Live cells were also used for cross linking. As the authors have not replied to email communications:- Interactions involving cells originating from "non-human primates" have not been entered as the identity of the proteins involved is unknown. No origin of the cells used in Figure 4/6/S4A is given (-Heterologous co-IP and Blue-Native PAGE), so these results have not been entered. mlavoie@rics.bwh.harvard.edu Accepted 2012-DEC-14 by ORCHARD 18-Dec-2012: Contacted by IntAct-Help. Biochemistry (0006-2960) 2010 Only protein-protein interactions imex curation nica_human Nicastrin NCSTN KIAA0253 UNQ1874/PRO4317 protein protein human Homo sapiens Human MATAGGGSGADPGSRGLLRLLSFCVLLAGLCRGNSVERKIYIPLNKTAPCVRLLNATHQIGCQSSISGDTGVIHVVEKEEDLQWVLTDGPNPPYMVLLESKHFTRDLMEKLKGRTSRIAGLAVSLTKPSPASGFSPSVQCPNDGFGVYSNSYGPEFAHCREIQWNSLGNGLAYEDFSFPIFLLEDENETKVIKQCYQDHNLSQNGSAPTFPLCAMQLFSHMHAVISTATCMRRSSIQSTFSINPEIVCDPLSDYNVWSMLKPINTTGTLKPDDRVVVAATRLDSRSFFWNVAPGAESAVASFVTQLAAAEALQKAPDVTTLPRNVMFVFFQGETFDYIGSSRMVYDMEKGKFPVQLENVDSFVELGQVALRTSLELWMHTDPVSQKNESVRNQVEDLLATLEKSGAGVPAVILRRPNQSQPLPPSSLQRFLRARNISGVVLADHSGAFHNKYYQSIYDTAENINVSYPEWLSPEEDLNFVTDTAKALADVATVLGRALYELAGGTNFSDTVQADPQTVTRLLYGFLIKANNSWFQSILRQDLRSYLGDGPLQHYIAVSSPTNTTYVVQYALANLTGTVVNLTREQCQDPSKVPSENKDLYEYSWVQGPLHSNETDRLPRCVRSTARLARALSPAFELSQWSSTEYSTWTESRWKDIRARIFLIASKELELITLTVGFGILIFSLIVTYCINAKADVLFIAPREPGAVSY DIP protein Q92542 original sequence version: 74 DIP protein Q92542 original sequence version: 146 C8C0EAEAD89E976A 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 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_human Leucine-rich repeat serine/threonine-protein kinase 2 LRRK2 PARK8 Dardarin protein protein human Homo sapiens Human MASGSCQGCEEDEETLKKLIVRLNNVQEGKQIETLVQILEDLLVFTYSERASKLFQGKNIHVPLLIVLDSYMRVASVQQVGWSLLCKLIEVCPGTMQSLMGPQDVGNDWEVLGVHQLILKMLTVHNASVNLSVIGLKTLDLLLTSGKITLLILDEESDIFMLIFDAMHSFPANDEVQKLGCKALHVLFERVSEEQLTEFVENKDYMILLSALTNFKDEEEIVLHVLHCLHSLAIPCNNVEVLMSGNVRCYNIVVEAMKAFPMSERIQEVSCCLLHRLTLGNFFNILVLNEVHEFVVKAVQQYPENAALQISALSCLALLTETIFLNQDLEEKNENQENDDEGEEDKLFWLEACYKALTWHRKNKHVQEAACWALNNLLMYQNSLHEKIGDEDGHFPAHREVMLSMLMHSSSKEVFQASANALSTLLEQNVNFRKILLSKGIHLNVLELMQKHIHSPEVAESGCKMLNHLFEGSNTSLDIMAAVVPKILTVMKRHETSLPVQLEALRAILHFIVPGMPEESREDTEFHHKLNMVKKQCFKNDIHKLVLAALNRFIGNPGIQKCGLKVISSIVHFPDALEMLSLEGAMDSVLHTLQMYPDDQEIQCLGLSLIGYLITKKNVFIGTGHLLAKILVSSLYRFKDVAEIQTKGFQTILAILKLSASFSKLLVHHSFDLVIFHQMSSNIMEQKDQQFLNLCCKCFAKVAMDDYLKNVMLERACDQNNSIMVECLLLLGADANQAKEGSSLICQVCEKESSPKLVELLLNSGSREQDVRKALTISIGKGDSQIISLLLRRLALDVANNSICLGGFCIGKVEPSWLGPLFPDKTSNLRKQTNIASTLARMVIRYQMKSAVEEGTASGSDGNFSEDVLSKFDEWTFIPDSSMDSVFAQSDDLDSEGSEGSFLVKKKSNSISVGEFYRDAVLQRCSPNLQRHSNSLGPIFDHEDLLKRKRKILSSDDSLRSSKLQSHMRHSDSISSLASEREYITSLDLSANELRDIDALSQKCCISVHLEHLEKLELHQNALTSFPQQLCETLKSLTHLDLHSNKFTSFPSYLLKMSCIANLDVSRNDIGPSVVLDPTVKCPTLKQFNLSYNQLSFVPENLTDVVEKLEQLILEGNKISGICSPLRLKELKILNLSKNHISSLSENFLEACPKVESFSARMNFLAAMPFLPPSMTILKLSQNKFSCIPEAILNLPHLRSLDMSSNDIQYLPGPAHWKSLNLRELLFSHNQISILDLSEKAYLWSRVEKLHLSHNKLKEIPPEIGCLENLTSLDVSYNLELRSFPNEMGKLSKIWDLPLDELHLNFDFKHIGCKAKDIIRFLQQRLKKAVPYNRMKLMIVGNTGSGKTTLLQQLMKTKKSDLGMQSATVGIDVKDWPIQIRDKRKRDLVLNVWDFAGREEFYSTHPHFMTQRALYLAVYDLSKGQAEVDAMKPWLFNIKARASSSPVILVGTHLDVSDEKQRKACMSKITKELLNKRGFPAIRDYHFVNATEESDALAKLRKTIINESLNFKIRDQLVVGQLIPDCYVELEKIILSERKNVPIEFPVIDRKRLLQLVRENQLQLDENELPHAVHFLNESGVLLHFQDPALQLSDLYFVEPKWLCKIMAQILTVKVEGCPKHPKGIISRRDVEKFLSKKRKFPKNYMSQYFKLLEKFQIALPIGEEYLLVPSSLSDHRPVIELPHCENSEIIIRLYEMPYFPMGFWSRLINRLLEISPYMLSGRERALRPNRMYWRQGIYLNWSPEAYCLVGSEVLDNHPESFLKITVPSCRKGCILLGQVVDHIDSLMEEWFPGLLEIDICGEGETLLKKWALYSFNDGEEHQKILLDDLMKKAEEGDLLVNPDQPRLTIPISQIAPDLILADLPRNIMLNNDELEFEQAPEFLLGDGSFGSVYRAAYEGEEVAVKIFNKHTSLRLLRQELVVLCHLHHPSLISLLAAGIRPRMLVMELASKGSLDRLLQQDKASLTRTLQHRIALHVADGLRYLHSAMIIYRDLKPHNVLLFTLYPNAAIIAKIADYGIAQYCCRMGIKTSEGTPGFRAPEVARGNVIYNQQADVYSFGLLLYDILTTGGRIVEGLKFPNEFDELEIQGKLPDPVKEYGCAPWPMVEKLIKQCLKENPQERPTSAQVFDILNSAELVCLTRRILLPKNVIVECMVATHHNSRNASIWLGCGHTDRGQLSFLDLNTEGYTSEEVADSRILCLALVHLPVEKESWIVSGTQSGTLLVINTEDGKKRHTLEKMTDSVTCLYCNSFSKQSKQKNFLLVGTADGKLAIFEDKTVKLKGAAPLKILNIGNVSTPLMCLSESTNSTERNVMWGGCGTKIFSFSNDFTIQKLIETRTSQLFSYAAFSDSNIITVVVDTALYIAKQNSPVVEVWDKKTEKLCGLIDCVHFLREVMVKENKESKHKMSYSGRVKTLCLQKNTALWIGTGGGHILLLDLSTRRLIRVIYNFCNSVRVMMTAQLGSLKNVMLVLGYNRKNTEGTQKQKEIQSCLTVWDINLPHEVQNLEKHIEVRKELAEKMRRTSVE DIP protein Q5S007 original sequence version: 36 DIP protein Q5S007 original sequence version: 68 DIP protein Q5S007 original sequence version: 64 26142A0CECBBC3F4 q92542-pro_0000019681 Nicastrin NCSTN KIAA0253 UNQ1874/PRO4317 protein protein human Homo sapiens Human NSVERKIYIPLNKTAPCVRLLNATHQIGCQSSISGDTGVIHVVEKEEDLQWVLTDGPNPPYMVLLESKHFTRDLMEKLKGRTSRIAGLAVSLTKPSPASGFSPSVQCPNDGFGVYSNSYGPEFAHCREIQWNSLGNGLAYEDFSFPIFLLEDENETKVIKQCYQDHNLSQNGSAPTFPLCAMQLFSHMHAVISTATCMRRSSIQSTFSINPEIVCDPLSDYNVWSMLKPINTTGTLKPDDRVVVAATRLDSRSFFWNVAPGAESAVASFVTQLAAAEALQKAPDVTTLPRNVMFVFFQGETFDYIGSSRMVYDMEKGKFPVQLENVDSFVELGQVALRTSLELWMHTDPVSQKNESVRNQVEDLLATLEKSGAGVPAVILRRPNQSQPLPPSSLQRFLRARNISGVVLADHSGAFHNKYYQSIYDTAENINVSYPEWLSPEEDLNFVTDTAKALADVATVLGRALYELAGGTNFSDTVQADPQTVTRLLYGFLIKANNSWFQSILRQDLRSYLGDGPLQHYIAVSSPTNTTYVVQYALANLTGTVVNLTREQCQDPSKVPSENKDLYEYSWVQGPLHSNETDRLPRCVRSTARLARALSPAFELSQWSSTEYSTWTESRWKDIRARIFLIASKELELITLTVGFGILIFSLIVTYCINAKADVLFIAPREPGAVSY 34 709 91A1D4466910E100 ndua9_human NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial NADH-ubiquinone oxidoreductase 39 kDa subunit Complex I-39kD NDUFA9 NDUFS2L protein protein human Homo sapiens Human MAAAAQSRVVRVLSMSRSAITAIATSVCHGPPCRQLHHALMPHGKGGRSSVSGIVATVFGATGFLGRYVVNHLGRMGSQVIIPYRCDKYDIMHLRPMGDLGQLLFLEWDARDKDSIRRVVQHSNVVINLIGRDWETKNFDFEDVFVKIPQAIAQLSKEAGVEKFIHVSHLNANIKSSSRYLRNKAVGEKVVRDAFPEAIIVKPSDIFGREDRFLNSFASMHRFGPIPLGSLGWKTVKQPVYVVDVSKGIVNAVKDPDANGKSFAFVGPSRYLLFHLVKYIFAVAHRLFLPFPLPLFAYRWVARVFEISPFEPWITRDKVERMHITDMKLPHLPGLEDLGIQATPLELKAIEVLRRHRTYRWLSAEIEDVKPAKTVNI DIP protein Q16795 original sequence version: 88 66A1CC7FCE86DD0E p49768-pro_0000025591 Presenilin-1 NTF subunit PSEN1 AD3 PS1 PSNL1 Protein S182 protein protein human Homo sapiens Human MTELPAPLSYFQNAQMSEDNHLSNTVRSQNDNRERQEHNDRRSLGHPEPLSNGRPQGNSRQVVEQDEEEDEELTLKYGAKHVIMLFVPVTLCMVVVVATIKSVSFYTRKDGQLIYTPFTEDTETVGQRALHSILNAAIMISVIVVMTILLVVLYKYRCYKVIHAWLIISSLLLLFFFSFIYLGEVFKTYNVAVDYITVALLIWNFGVVGMISIHWKGPLRLQQAYLIMISALMALVFIKYLPEWTAWLILAVISVYDLVAVLCPKGPLRMLVETAQERNETLFPALIYSSTMVWLVNM 1 298 58C420367AAEC20B lrrk2-1 10 14 unspecified role unspecified role neutral component neutral component region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined colocalization colocalization Fig 1A, 2B, 3B 0.5% SDS A 20-fold enrichment of HMW LRRK2 at the membrane was found compared to the cytosol. The distribution of LMW and HMW LRRK2 in either cytosol or membrane fractions is not significantly changed by the introduction of PD-linked LRRK2 mutations (G2019S, R1441C, Y1699C). lrrk2-1 11 14 unspecified role unspecified role neutral component neutral component colocalization colocalization Fig 1B, 2C 0.5% SDS A 15-fold enrichment of HMW LRRK2 at the membrane was found compared to the cytosol. lrrk2-1 2 14 unspecified role unspecified role neutral component neutral component region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined colocalization colocalization Fig S 1B lrrk2-lrrk2-21 3 14 unspecified role unspecified role bait bait region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 14 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Fig S1C lrrk2-lrrk2-22 3 14 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 14 unspecified role unspecified role prey prey region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Figs 4C, S1C Higher levels of GFP-LRRK2 are pulled down from membrane extracts (lane 7), despite lower levels of myc-LRRK2 in the same IP, suggesting an enrichment of LRRK2 dimer at the membrane. lrrk2-lrrk2-23 3 14 unspecified role unspecified role prey prey region gfp tag green fluorescent protein tag GFP green fluorescent protein GFP green fluorescent protein gfp tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 14 unspecified role unspecified role bait bait region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Fig S1D Substantially more GFP-LRRK2 was co-IPed from the HMW than from the LMW fractions. lrrk2-1 8 14 unspecified role unspecified role neutral component neutral component physical association physical association Fig S2A,1D, 5A LRRK2 from HMW fractions was more efficiently cross linked than from LMW fractions. No cross linking was observed from cytosolic fractions wheras membrane fractions were effectively cross linked. lrrk2-lrrk2-24 4 14 unspecified role unspecified role neutral component neutral component region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association Fig S 2 A/B/C LRRK2 from HMW fractions was more efficiently cross linked than from LMW fractions lrrk2-1 5 14 putative self putative self putative self putative self purified purified Q5S007:p.Gly2019Ser mutation increasing rate mutation increasing interaction rate mutation increasing rate certain certain sequence position certain certain certain sequence position certain G S Wed May 02 18:12:37 BST 2018 This feature has been corrected as a result of our quality control procedures. The original label was 'gly2019ser' Tue Jun 30 17:38:40 BST 2020 This feature has been corrected as a result of our quality control procedures. The original label was 'p.Gly2019Ser' region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined human-293ft Homo sapiens HEK293FT cell line 293ft HEK293FT cell line phosphorylation phosphorylation reaction phosphorylation true Fig S2D, 1E, 7A, S5A An X8 increase in relative LRRK2 activity was seen in the HMW fractions. Membrane fractions showed X3 greater kinase activity than cytosol fractions. lrrk2-1 9 14 unspecified role unspecified role neutral component neutral component region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association 5B Efficient crosslinking of LRRK2 into HMW complexes was also observed in membrane extracts from HEK293FT cells transfected with LRRK2. lrrk2-1 1 14 unspecified role unspecified role neutral component neutral component region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined physical association physical association S4B Addition of the detergent leads to a broader elution peak for LRRK2, thus changing its estimated molecular weight. gtp-lrrk2-2 6 13 unspecified role unspecified role bait bait chemical synthesis Chemical synthesis (Chemical synthesis) 14 unspecified role unspecified role prey prey human-lymphoblast Homo sapiens, lymphoblast lymphoblast Transformed lymphocytes; Blast cell; Lymphoblastoid physical association physical association 7B, S5C Membrane-associated LRRK2 binds GTP more efficiently than cytosolic LRRK2. gtp-lrrk2-4 7 14 unspecified role unspecified role prey prey region myc tag myc tag EUKLISEED epitope tag EUKLISEED epitope tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined rat-mes23_5 Rat -Mouse interspecies hybrid MES23.5; dopaminergic neuroblastoma/glioma cell line mes23_5 Rat -Mouse interspecies hybrid MES23.5; dopaminergic neuroblastoma/glioma cell line This line expresses GHS-R1a. It was hybridised from the murine neuroblastoma-glioma N18TG2 with rat mesencephalic neurons. It is a stable inter-species hybrid. 13 unspecified role unspecified role bait bait chemical synthesis Chemical synthesis (Chemical synthesis) physical association physical association S5E Membrane-associated LRRK2 binds GTP more efficiently than cytosolic LRRK2. ncstn-ncstn-1 10 16 unspecified role unspecified role neutral component neutral component 17 unspecified role unspecified role neutral component neutral component 12 unspecified role unspecified role neutral component neutral component 15 unspecified role unspecified role neutral component neutral component colocalization colocalization 1C