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/ Dequalinium-induced protofibril formation of alpha-synuclein. Dequalinium-induced protofibril formation of alpha-synuclein. J. Biol. Chem. (0021-9258) 2006 imex curation Lee CH., Kim HJ., Lee JH., Cho HJ., Kim J., Chung KC., Jung S., Paik SR. BioCreative - Critical Assessment of Information Extraction systems in Biology Revisit when small molecule editor in place - has been in place since June Yes Jyoti but no-one has been shown how to use it - and put it in the manual ! Alpha-synuclein was incubated with for 30 minutes at 37C with various concetrations of Dequalinium (C10-DQ) or dequalinium analogue with C14-linker (C14-DQ) prior to cross-linking. srpaik@snu.ac.kr 24-JAN-2007: Contacted by JYOTI. Only protein-protein interactions in vitro In vitro tem transmission electron microscopy tem predetermined predetermined participant predetermined Lee CH., Kim HJ., Lee JH., Cho HJ., Kim J., Chung KC., Jung S., Paik SR. BioCreative - Critical Assessment of Information Extraction systems in Biology Revisit when small molecule editor in place - has been in place since June Yes Jyoti but no-one has been shown how to use it - and put it in the manual ! Alpha-synuclein was incubated with for 30 minutes at 37C with various concetrations of Dequalinium (C10-DQ) or dequalinium analogue with C14-linker (C14-DQ) prior to cross-linking. srpaik@snu.ac.kr Accepted 2006-SEP-14 by JYOTI. 24-JAN-2007: Contacted by JYOTI. J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Dequalinium-induced protofibril formation of alpha-synuclein. Dequalinium-induced protofibril formation of alpha-synuclein. J. Biol. Chem. (0021-9258) 2006 imex curation Lee CH., Kim HJ., Lee JH., Cho HJ., Kim J., Chung KC., Jung S., Paik SR. BioCreative - Critical Assessment of Information Extraction systems in Biology Revisit when small molecule editor in place - has been in place since June Yes Jyoti but no-one has been shown how to use it - and put it in the manual ! Alpha-synuclein was incubated with for 30 minutes at 37C with various concetrations of Dequalinium (C10-DQ) or dequalinium analogue with C14-linker (C14-DQ) prior to cross-linking. srpaik@snu.ac.kr 24-JAN-2007: Contacted by JYOTI. Only protein-protein interactions in vitro In vitro fluorescence spectr classical fluorescence spectroscopy fluorescence spectr predetermined predetermined participant predetermined Lee CH., Kim HJ., Lee JH., Cho HJ., Kim J., Chung KC., Jung S., Paik SR. BioCreative - Critical Assessment of Information Extraction systems in Biology Revisit when small molecule editor in place - has been in place since June Yes Jyoti but no-one has been shown how to use it - and put it in the manual ! Alpha-synuclein was incubated with for 30 minutes at 37C with various concetrations of Dequalinium (C10-DQ) or dequalinium analogue with C14-linker (C14-DQ) prior to cross-linking. srpaik@snu.ac.kr Accepted 2006-SEP-14 by JYOTI. 24-JAN-2007: Contacted by JYOTI. J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Dequalinium-induced protofibril formation of alpha-synuclein. Dequalinium-induced protofibril formation of alpha-synuclein. J. Biol. Chem. (0021-9258) 2006 imex curation Lee CH., Kim HJ., Lee JH., Cho HJ., Kim J., Chung KC., Jung S., Paik SR. BioCreative - Critical Assessment of Information Extraction systems in Biology Revisit when small molecule editor in place - has been in place since June Yes Jyoti but no-one has been shown how to use it - and put it in the manual ! Alpha-synuclein was incubated with for 30 minutes at 37C with various concetrations of Dequalinium (C10-DQ) or dequalinium analogue with C14-linker (C14-DQ) prior to cross-linking. srpaik@snu.ac.kr 24-JAN-2007: Contacted by JYOTI. Only protein-protein interactions in vitro In vitro biophysical biophysical predetermined predetermined participant predetermined Lee CH., Kim HJ., Lee JH., Cho HJ., Kim J., Chung KC., Jung S., Paik SR. BioCreative - Critical Assessment of Information Extraction systems in Biology Revisit when small molecule editor in place - has been in place since June Yes Jyoti but no-one has been shown how to use it - and put it in the manual ! Alpha-synuclein was incubated with for 30 minutes at 37C with various concetrations of Dequalinium (C10-DQ) or dequalinium analogue with C14-linker (C14-DQ) prior to cross-linking. srpaik@snu.ac.kr Accepted 2006-SEP-14 by JYOTI. 24-JAN-2007: Contacted by JYOTI. J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Dequalinium-induced protofibril formation of alpha-synuclein. Dequalinium-induced protofibril formation of alpha-synuclein. J. Biol. Chem. (0021-9258) 2006 imex curation Lee CH., Kim HJ., Lee JH., Cho HJ., Kim J., Chung KC., Jung S., Paik SR. BioCreative - Critical Assessment of Information Extraction systems in Biology Revisit when small molecule editor in place - has been in place since June Yes Jyoti but no-one has been shown how to use it - and put it in the manual ! Alpha-synuclein was incubated with for 30 minutes at 37C with various concetrations of Dequalinium (C10-DQ) or dequalinium analogue with C14-linker (C14-DQ) prior to cross-linking. srpaik@snu.ac.kr 24-JAN-2007: Contacted by JYOTI. Only protein-protein interactions in vitro In vitro 3d-em 3D electron microscopy 3D-EM electron tomog predetermined predetermined participant predetermined Lee CH., Kim HJ., Lee JH., Cho HJ., Kim J., Chung KC., Jung S., Paik SR. BioCreative - Critical Assessment of Information Extraction systems in Biology Revisit when small molecule editor in place - has been in place since June Yes Jyoti but no-one has been shown how to use it - and put it in the manual ! Alpha-synuclein was incubated with for 30 minutes at 37C with various concetrations of Dequalinium (C10-DQ) or dequalinium analogue with C14-linker (C14-DQ) prior to cross-linking. srpaik@snu.ac.kr Accepted 2006-SEP-14 by JYOTI. 24-JAN-2007: Contacted by JYOTI. J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Dequalinium-induced protofibril formation of alpha-synuclein. Dequalinium-induced protofibril formation of alpha-synuclein. J. Biol. Chem. (0021-9258) 2006 imex curation Lee CH., Kim HJ., Lee JH., Cho HJ., Kim J., Chung KC., Jung S., Paik SR. BioCreative - Critical Assessment of Information Extraction systems in Biology Revisit when small molecule editor in place - has been in place since June Yes Jyoti but no-one has been shown how to use it - and put it in the manual ! Alpha-synuclein was incubated with for 30 minutes at 37C with various concetrations of Dequalinium (C10-DQ) or dequalinium analogue with C14-linker (C14-DQ) prior to cross-linking. srpaik@snu.ac.kr 24-JAN-2007: Contacted by JYOTI. Only protein-protein interactions in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Lee CH., Kim HJ., Lee JH., Cho HJ., Kim J., Chung KC., Jung S., Paik SR. BioCreative - Critical Assessment of Information Extraction systems in Biology Revisit when small molecule editor in place - has been in place since June Yes Jyoti but no-one has been shown how to use it - and put it in the manual ! Alpha-synuclein was incubated with for 30 minutes at 37C with various concetrations of Dequalinium (C10-DQ) or dequalinium analogue with C14-linker (C14-DQ) prior to cross-linking. srpaik@snu.ac.kr Accepted 2006-SEP-14 by JYOTI. 24-JAN-2007: Contacted by JYOTI. J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Dequalinium-induced protofibril formation of alpha-synuclein. Dequalinium-induced protofibril formation of alpha-synuclein. J. Biol. Chem. (0021-9258) 2006 imex curation Lee CH., Kim HJ., Lee JH., Cho HJ., Kim J., Chung KC., Jung S., Paik SR. BioCreative - Critical Assessment of Information Extraction systems in Biology Revisit when small molecule editor in place - has been in place since June Yes Jyoti but no-one has been shown how to use it - and put it in the manual ! Alpha-synuclein was incubated with for 30 minutes at 37C with various concetrations of Dequalinium (C10-DQ) or dequalinium analogue with C14-linker (C14-DQ) prior to cross-linking. srpaik@snu.ac.kr 24-JAN-2007: Contacted by JYOTI. Only protein-protein interactions in vitro In vitro comig non denat gel comigration in non denaturing gel electrophoresis comig non denat gel predetermined predetermined participant predetermined Lee CH., Kim HJ., Lee JH., Cho HJ., Kim J., Chung KC., Jung S., Paik SR. BioCreative - Critical Assessment of Information Extraction systems in Biology Revisit when small molecule editor in place - has been in place since June Yes Jyoti but no-one has been shown how to use it - and put it in the manual ! Alpha-synuclein was incubated with for 30 minutes at 37C with various concetrations of Dequalinium (C10-DQ) or dequalinium analogue with C14-linker (C14-DQ) prior to cross-linking. srpaik@snu.ac.kr Accepted 2006-SEP-14 by JYOTI. J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation syua_human Alpha-synuclein Non-A beta component of AD amyloid Non-A4 component of amyloid precursor SNCA NACP PARK1 protein protein human Homo sapiens Human MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQDYEPEA DIP protein P37840 original sequence version: 124 DIP protein P37840 original sequence version: 175 DIP protein P37840 original sequence version: 178 6BB2F12128931663 scna 1 7 unspecified role unspecified role neutral component neutral component direct interaction direct interaction Figure 9 Oligomer formation of -synuclein in the presence of dequalinium. In the presence of 50micro molar dequalinium, the highest peak due to the oligomeric protein aggregates was obtained at the void volume, although the condition caused most rapid protein aggregation with the highest final turbidity scna-1 3 7 unspecified role unspecified role neutral component neutral component direct interaction direct interaction Figure 7A and 7C Aggregation kinetics of alpha -synuclein with various concentrations of dequalinium As dequalinium concentrations increased (1.4, 14, and 140micro molar) the final turbidities were also increased. As the length of hydrocarbon chain was varied among C4, C6, and C10 at a fixed concentration of 50 micro molar, the final turbidity was increased with apparent reduction in the lag period. scna-2 2 7 unspecified role unspecified role neutral component neutral component c terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain direct interaction direct interaction Figure 7B and 7D Amyloid formation was also evaluated with thioflavin-T biniding fluorescence The final thioflavin-T binding fluorescence obtained in the presence of the analogues of alpha-synclein was lower than that of the aggregates prepared with alpha-synuclein alone scna-3 6 7 unspecified role unspecified role neutral component neutral component c terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain direct interaction direct interaction dequalinium The protein was self-oligomerized by dequalinium, which gave rise to the ladder formation on N-[2-hydroxy-1,1- bis(hydroxymethyl)ethyl]glycine/SDS-PAGE in the presence of a coupling reagent of N-(ethoxycarbonyl)-2-ethoxy-1,2-dihydroquinoline. Figure 2, 3 and 4 Self-oligomerization of alpha-synclein in the presence of various amounts of dequalinium (C10-DQ) and C14-DQ. scna-4 4 7 unspecified role unspecified role neutral component neutral component direct interaction direct interaction Figure 8 and 10 The protein aggregates obtained in the absence and presence of the compound were also observed with AFM. By measuring various granular structures revealed under AFM, their average diameters were estimated as 39 nm (SE = 9), scna-5 5 7 unspecified role unspecified role neutral component neutral component direct interaction direct interaction Figure 9 The deqyalinium-mediated oligomeric intermediate formation od alpha-synuclein was examined with size exclusion chromotography The authors state that "Intriguingly, the oligomer- containing peak was increased as dequalinium level was raised. In the presence of 50 micro molar dequalinium, the highest peak due to the oligomeric protein aggregates was obtained at the void volume, although the condition caused most rapid protein aggregation with the highest final turbidity (Fig. 9). This finding data clearly indicated that dequalinium favored the oligomer formation and also prevented further development into the amyloids."