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/ gobbi-2006-4 Gerstmann-Straussler-Scheinker disease amyloid protein polymerizes according to the "dock-and-lock" model. in vitro In vitro molecular sieving molecular sieving Gel Filtration Size Exclusion Chromatography Size Exclusion Chromatography Gel Filtration Sizing column predetermined predetermined participant predetermined Gobbi M., Colombo L., Morbin M., Mazzoleni G., Accardo E., Vanoni M., Del Favero E., Cantu L., Kirschner DA., Manzoni C., Beeg M., Ceci P., Ubezio P., Forloni G., Tagliavini F., Salmona M. BioCreative - Critical Assessment of Information Extraction systems in Biology The assay used immunogold labelling. Gobbi@marionegri.it J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Apoptosis - Interactions involving proteins with a function related to apoptosis Synapse - Interactions of proteins with an established role in the presynapse. gobbi-2006-5 Gerstmann-Straussler-Scheinker disease amyloid protein polymerizes according to the "dock-and-lock" model. in vitro In vitro spr surface plasmon resonance Optical biosensor BIAcore(r) BIAcore(r) Optical biosensor spr predetermined predetermined participant predetermined Gobbi M., Colombo L., Morbin M., Mazzoleni G., Accardo E., Vanoni M., Del Favero E., Cantu L., Kirschner DA., Manzoni C., Beeg M., Ceci P., Ubezio P., Forloni G., Tagliavini F., Salmona M. BioCreative - Critical Assessment of Information Extraction systems in Biology The assay used immunogold labelling. Gobbi@marionegri.it J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Apoptosis - Interactions involving proteins with a function related to apoptosis Synapse - Interactions of proteins with an established role in the presynapse. gobbi-2006-2 Gerstmann-Straussler-Scheinker disease amyloid protein polymerizes according to the "dock-and-lock" model. in vitro In vitro electron microscopy electron microscopy Electron crystallography Electron cryomicroscopy Electron crystallography Electron cryomicroscopy predetermined predetermined participant predetermined Gobbi M., Colombo L., Morbin M., Mazzoleni G., Accardo E., Vanoni M., Del Favero E., Cantu L., Kirschner DA., Manzoni C., Beeg M., Ceci P., Ubezio P., Forloni G., Tagliavini F., Salmona M. BioCreative - Critical Assessment of Information Extraction systems in Biology The assay used immunogold labelling. Gobbi@marionegri.it J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Apoptosis - Interactions involving proteins with a function related to apoptosis Synapse - Interactions of proteins with an established role in the presynapse. gobbi-2006-3 Gerstmann-Straussler-Scheinker disease amyloid protein polymerizes according to the "dock-and-lock" model. in vitro In vitro light scattering light scattering predetermined predetermined participant predetermined Gobbi M., Colombo L., Morbin M., Mazzoleni G., Accardo E., Vanoni M., Del Favero E., Cantu L., Kirschner DA., Manzoni C., Beeg M., Ceci P., Ubezio P., Forloni G., Tagliavini F., Salmona M. BioCreative - Critical Assessment of Information Extraction systems in Biology The assay used immunogold labelling. Gobbi@marionegri.it J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Apoptosis - Interactions involving proteins with a function related to apoptosis Synapse - Interactions of proteins with an established role in the presynapse. gobbi-2006-1 Gerstmann-Straussler-Scheinker disease amyloid protein polymerizes according to the "dock-and-lock" model. in vitro In vitro electron microscopy electron microscopy Electron crystallography Electron cryomicroscopy Electron crystallography Electron cryomicroscopy immunostaining immunostaining Gobbi M., Colombo L., Morbin M., Mazzoleni G., Accardo E., Vanoni M., Del Favero E., Cantu L., Kirschner DA., Manzoni C., Beeg M., Ceci P., Ubezio P., Forloni G., Tagliavini F., Salmona M. BioCreative - Critical Assessment of Information Extraction systems in Biology The assay used immunogold labelling. Gobbi@marionegri.it J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Apoptosis - Interactions involving proteins with a function related to apoptosis Synapse - Interactions of proteins with an established role in the presynapse. prio_human Major prion protein PrP27-30 PrP33-35C ASCR PRNP PRIP PRP ALTPRP protein protein human Homo sapiens Human MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVG prp82_human_peptide Prp82-146 peptide - scrambled sequence peptide peptide polypeptide oligopeptide oligopeptide polypeptide human Homo sapiens Human EADQFALGGSKHGNGMQQVAGHGGSMGAKAWGANGHPSGTGIPTAKMVPYKIYGGGWAGMGRPSS Similar to Q27H91 An amino acid sequence which is not represented in UniProt a4_human Amyloid-beta precursor protein APP A4 AD1 Alzheimer disease amyloid protein ABPP PreA4 Cerebral vascular amyloid peptide Protease nexin-II APPI Amyloid precursor protein Amyloid-beta A4 protein Alzheimer disease amyloid A4 protein homolog Amyloid-beta (A4) precursor protein protein protein human Homo sapiens Human MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQERMDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPLAEESDNVDSADAEEDDSDVWWGGADTDYADGSEDKVVEVAEEEEVAEVEEEEADDDEDDEDGDEVEEEAEEPYEEATERTTSIATTTTTTTESVEEVVREVCSEQAETGPCRAMISRWYFDVTEGKCAPFFYGGCGGNRNNFDTEEYCMAVCGSAMSQSLLKTTQEPLARDPVKLPTTAASTPDAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPRHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMISEPRISYGNDALMPSLTETKTTVELLPVNGEFSLDDLQPWHSFGADSVPANTENEVEPVDARPAADRGLTTRPGSGLTNIKTEEISEVKMDAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKKQYTSIHHGVVEVDAAVTPEERHLSKMQQNGYENPTYKFFEQMQN prnp-prnp-5 dimer formation 501387 N/A 501392 unspecified role unspecified role neutral component neutral component region integral part of minimal sequence that sustains prion replication 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) Stoichiometry: 2.0 physical association physical association false false false 2B Dimers of PrP82-146 were formed. SDS-PAGE on both the PrP82�146 solutions, without any irradiation, showed monomers to trimers (Fig. 2B, lanes 1, 2, 5, and 6).Dimers and trimers are therefore very stable, being resistant to a procedure involving boiling in SDS. For comparison, in the same experimental conditions Abeta40 was detected as monomers only, as previously described (25, 26). PrP82�146 monomers-to-trimers are presumably in dynamic equilibrium, as indicated by preliminary data showing that isolation of the monomers promptly results in the formation of dimers and trimers. For comparison, in the same experimental conditions Abeta40 was detected as monomers only, as previously described (25, 26). Prp82-146 is a chemically synthesised peptide. prnp-prnp-6 trimer formation 501387 N/A 501392 unspecified role unspecified role neutral component neutral component region integral part of minimal sequence that sustains prion replication 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) Stoichiometry: 3.0 physical association physical association false false false 2B Trimers of PrP82-146 were formed. SDS-PAGE on both the PrP82�146 solutions, without any irradiation, showed monomers to trimers (Fig. 2B, lanes 1, 2, 5, and 6).Dimers and trimers are therefore very stable, being resistant to a procedure involving boiling in SDS. For comparison, in the same experimental conditions Abeta40 was detected as monomers only, as previously described (25, 26). PrP82�146 monomers-to-trimers are presumably in dynamic equilibrium, as indicated by preliminary data showing that isolation of the monomers promptly results in the formation of dimers and trimers. Photo-induced cross-linking of unmodified proteins followed by SDS-PAGE. Lanes 1-4 were obtained using the flowing PrP solution (25 M), and lanes 5-8 were obtained with the PrP solution used for immobilization. Prp82-146 is a chemically synthesised peptide. prnp-prnp-7 tetramer formation 501387 N/A 501392 unspecified role unspecified role neutral component neutral component region integral part of minimal sequence that sustains prion replication 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) Stoichiometry: 4.0 physical association physical association false false false 2 B Tetramers of PrP82-146 were formed maily in the lanes with photo-induced cross-linking. Photo-induced cross-linking of unmodified proteins followed by SDS-PAGE. Lanes 1-4 were obtained using the flowing PrP solution (25 M), and lanes 5-8 were obtained with the PrP solution used for immobilization. Prp82-146 is a chemically synthesised peptide. prnp-prnp-8 pentamer formation 501387 N/A 501392 unspecified role unspecified role neutral component neutral component region integral part of minimal sequence that sustains prion replication 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) Stoichiometry: 5.0 physical association physical association false false false 2 B (lanes 3,4, 7 and 8) Pentamers of PrP82-146 were formed in the lanes with photo-induced cross-linking. Photo-induced cross-linking of unmodified proteins followed by SDS-PAGE. Lanes 1-4 were obtained using the flowing PrP solution (25 M), and lanes 5-8 were obtained with the PrP solution used for immobilization. Prp82-146 is a chemically synthesised peptide. prnp-prnp-9 heavy form formation 501387 N/A 501392 unspecified role unspecified role neutral component neutral component region integral part of minimal sequence that sustains prion replication 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) physical association physical association false false false 2 B (lanes 3,4, 7 and 8) photo-induced cross-linking of unmodified proteins followed by SDS-PAGE. Lanes 1-4 were obtained using the flowing PrP solution (25 M), and lanes 5-8 were obtained with the PrP solution used for immobilization. There do seem to be some heavy forms in lanes 3 and 4 corresponding to the irradiated flowing solution. Prp82-146 is a chemically synthesised peptide. prnp-prnp-10 501388 N/A 501392 unspecified role unspecified role prey prey region integral part of minimal sequence that sustains prion replication 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 501392 unspecified role unspecified role bait bait region integral part of minimal sequence that sustains prion replication 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) physical association physical association false false false 3, 5 and Table 1 the cumulative amount of peptide remaining pseudo-irreversibly bound after consecutive cycles of injections could greatly exceed (up to 30 times) the amount of peptide that had been initially immobilized on the chip, strongly suggesting an aggregation/elongation process. In the three step model: k1 (per M per s) is 3.9 plus or minus 0.2 E2, k-1 (per s) is 4.0 plus or minus 1.0 E-2, k2 (per s) is 2.3 plus or minus 0.3 E-2, k-2 is 2.3 plus or minus 1.0 E-3, k3 is 4.4 plus or minus 1.0 E-3, k-3 is 7.2 plus or minus 3.3 E-5. The apparent Kd for the initial binding step is 105 E-6 M. The absolute amount of PrP82-146 remaining pseudo-irreversibly bound to (incorporated into) the immobilized peptide structures was proportional to the concentration of both the injected and the immobilized peptide. In all cases this amounted to 68.1 plus or minus 2.7% of the maximal PrP82-146 binding measured at the end of the 2-min injection (mean plus or minus S.E. n equal 11). The proportion was significantly higher (77.7 plus or minus 2.7%, n equal 6, p 0.05, Student's t test) when the association time was increased to 8 min. According to the triple exponential fitting shown in the inset of Fig. 5, 9 plus or minus 5% (n equals 8) of the bound PrP82-146 dissociates with a very short half-life (0.05 plus or minus 0.02 min), 9 plus or minus5% dissociates with a longer half-life (1.1 plus or minus 0.9 min), and 12 plus or minus 5% dissociates with an even longer half-life (6 plus or minus 5 min). The remaining fraction appears to be irreversibly bound. Prp82-146 is a chemically synthesised peptide. prnp-prnp-11 501388 N/A 501392 unspecified role unspecified role prey prey region integral part of minimal sequence that sustains prion replication 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 501392 unspecified role unspecified role bait bait region integral part of minimal sequence that sustains prion replication 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) physical association physical association false false false 6 The PrP82�146 prefibrillar aggregates, unlike PrP82-146 small oligomers, concentrate on the chip matrix, quite likely by weak electrostatic forces. Despite this "preconcentration" on the sensor surface, the specific binding of these aggregates to immobilized structures (obtained by subtracting the signal in the empty cell) was much smaller than the signal obtained after injection of 20 M of the small PrP82-146 oligomers. Prp82-146 is a chemically synthesised peptide. Immobilised PrP82-146 was the bait and the injected solution of prefibrillar aggregates of PrP82-146 was the prey. prnp-prnp-12 Binding to PrP82-146scr 501388 N/A 501393 unspecified role unspecified role bait bait chemical synthesis Chemical synthesis (Chemical synthesis) N/A 501392 unspecified role unspecified role prey prey region integral part of minimal sequence that sustains prion replication 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) physical association physical association false false false 4 Much lower binding levels were also found when PrP82-146 was injected on flow cells in which PrP82-146scr or A42 prefibrillar aggregates had been immobilized (Fig. 4); furthermore PrP82-146 binding to PrP82-146scr and A42 dissociated rapidly and completely, whereas most of its binding to PrP82-146 did not dissociate (Figs. 4 and 5), suggesting pseudo-irreversible elongation/aggregation. PrP82-146scr is a scrambled version of Prp82-146scr. Prp82-146 and PrP82-146scr are chemically synthesised peptides. prnp-app Binding to Abeta42 501388 N/A 501394 unspecified role unspecified role bait bait n-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false N/A 501392 unspecified role unspecified role prey prey region integral part of minimal sequence that sustains prion replication 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) physical association physical association false false false 4 Much lower binding levels were also found when PrP82-146 was injected on flow cells in which PrP82-146scr or A42 prefibrillar aggregates had been immobilized (Fig. 4); furthermore PrP82-146 binding to PrP82-146scr and A42 dissociated rapidly and completely, whereas most of its binding to PrP82-146 did not dissociate (Figs. 4 and 5), suggesting pseudo-irreversible elongation/aggregation. The company from which the Abeta1-42 peptide was purchased does not have a website but their tel. no. is available. The accession number for the human amyloid protein that causes Alzheimer's has been entered but it was not possible to check this nor the method of generation of the peptide. Prp82-146 is a chemically synthesised peptide. prnp-prnp-1 501389 N/A 501392 unspecified role unspecified role neutral component neutral component region integral part of minimal sequence that sustains prion replication 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 501392 unspecified role unspecified role neutral component neutral component region integral part of minimal sequence that sustains prion replication 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) colocalization colocalization false false false 1 A It is not possible to determine stoichiometry from the structures seen. I have presumed the protein to be the one identified based on the text of the report, as a solution of PrP82-146 was used. Globular structures were seen when viewing the flowing solution whereas a loose meshwork of little chains formed by small round particles as well as a few straight short filaments were seen when viewing the immobilization solution. PrP82-146 is a chemically synthesised peptide. app-app 501389 N/A 501394 unspecified role unspecified role neutral component neutral component n-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false N/A 501394 unspecified role unspecified role neutral component neutral component n-terminal sufficient to bind sufficient binding region sufficient to bind certain certain sequence position certain certain certain sequence position certain false colocalization colocalization false false false There are a number of different forms of Abeta but it is not clear which form has been used. Thus the main accession number is used. The company from which this peptide was purchased does not have a website but their tel. no. is available. The accession number for the human amyloid protein that causes Alzheimer's has been entered but it was not possible to check this nor the method of generation of the peptide. 1 D Small round shaped material, often organized to form little chains, was present in the solution of Abeta42 immobilized on sensor chip as an internal control, however, the globular units appeared smaller. The company from which the Abeta1-42 peptide was purchased does not have a website but their tel. no. is available. The accession number for the human amyloid protein that causes Alzheimer's has been entered but it was not possible to check this nor the method of generation of the peptide. prnp-prnp-4 501389 N/A 501392 unspecified role unspecified role neutral component neutral component region integral part of minimal sequence that sustains prion replication 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) Stoichiometry: 2.0 colocalization colocalization false false false 1 C It is not possible to determine stoichiometry from the structures seen but must be 2 or greater. I have presumed the protein to be the one identified based on the text of the report, as a solution of PrP82-146 was used. Globular structures were seen when viewing the flowing solution whereas a loose meshwork of little chains formed by small round particles as well as a few straight short filaments were seen when viewing the immobilization solution. Prp82-146 is a chemically synthesised peptide. prnp-prnp-2 501390 N/A 501392 unspecified role unspecified role neutral component neutral component region integral part of minimal sequence that sustains prion replication 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 501392 unspecified role unspecified role neutral component neutral component region integral part of minimal sequence that sustains prion replication 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) physical association physical association false false false 2 A No specific means of identifying the constituents of the species was used. The flowing solution contained much smaller species than the immobilization solution. The stoichiometry of these species has not been determined. For the flowing solution multiexponential analysis of the correlation function decay (Fig. 2A) showed that most of these species (99% by number) had average RH =12 nm, corresponding to small oligomers. PrP82-146 is a chemically synthesised peptide. prnp-prnp-3 501390 N/A 501392 unspecified role unspecified role neutral component neutral component region integral part of minimal sequence that sustains prion replication 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) physical association physical association false false false 2 A No specific means of identifying the constituents of the species were used. The solution used for immobilisation contained much larger species than the flowing solution. The stoichiometry of these species has not been determined. Much larger species (average RH = 1700 nm) were found in the PrP82-146 solution used for immobilization on the sensor surfaces. Prp82-146 is a chemically synthesised peptide. prnp-prnp 501391 N/A 501392 unspecified role unspecified role 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 chemical synthesis Chemical synthesis (Chemical synthesis) N/A 501392 unspecified role unspecified role neutral component neutral component region integral part of minimal sequence that sustains prion replication 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) colocalization colocalization false false false 1 B Poorly defined sphere shapes were seen. These are aggregates of PrP82-146. It is not possible to determine stoichiometry. PrP82-146 is a chemically synthesised peptide.