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/ The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions. The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions. J. Biol. Chem. (0021-9258) 2006 imex curation Leliveld SR., Dame RT., Wuite GJ., Stitz L., Korth C. BioCreative - Critical Assessment of Information Extraction systems in Biology ckorth@uni-duesseldorf.de 24-JAN-2007: Contacted by JYOTI. Only protein-protein interactions in vitro In vitro pull down pull down western blot western blot Immuno blot Immuno blot Leliveld SR., Dame RT., Wuite GJ., Stitz L., Korth C. BioCreative - Critical Assessment of Information Extraction systems in Biology ckorth@uni-duesseldorf.de Accepted 2006-AUG-29 by JYOTI. J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions. The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions. J. Biol. Chem. (0021-9258) 2006 imex curation Leliveld SR., Dame RT., Wuite GJ., Stitz L., Korth C. BioCreative - Critical Assessment of Information Extraction systems in Biology ckorth@uni-duesseldorf.de 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 Leliveld SR., Dame RT., Wuite GJ., Stitz L., Korth C. BioCreative - Critical Assessment of Information Extraction systems in Biology Complexes were fractionated on a HiPrep 16/60 Sephacryl S-200 HR column ckorth@uni-duesseldorf.de Accepted 2006-AUG-29 by JYOTI. 24-JAN-2007: Contacted by JYOTI. J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions. The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions. J. Biol. Chem. (0021-9258) 2006 imex curation Leliveld SR., Dame RT., Wuite GJ., Stitz L., Korth C. BioCreative - Critical Assessment of Information Extraction systems in Biology ckorth@uni-duesseldorf.de 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 Leliveld SR., Dame RT., Wuite GJ., Stitz L., Korth C. BioCreative - Critical Assessment of Information Extraction systems in Biology GST�OR fusions were deposited on a freshly cleaved mica surface and images were acquired on a Nanoscope IIIa (Digital Instruments Inc.), operating in tapping mode in air with a type E scanner using silicon tips from Digital Instruments. ckorth@uni-duesseldorf.de Accepted 2006-AUG-29 by JYOTI. 24-JAN-2007: Contacted by JYOTI. J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions. The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions. J. Biol. Chem. (0021-9258) 2006 imex curation Leliveld SR., Dame RT., Wuite GJ., Stitz L., Korth C. BioCreative - Critical Assessment of Information Extraction systems in Biology ckorth@uni-duesseldorf.de 24-JAN-2007: Contacted by JYOTI. Only protein-protein interactions in vitro In vitro dls dynamic light scattering dls predetermined predetermined participant predetermined Leliveld SR., Dame RT., Wuite GJ., Stitz L., Korth C. BioCreative - Critical Assessment of Information Extraction systems in Biology Dynamic light scattering (DLS) measurements were performed on a DynaPro-MS/X machine. peptides linked to BSA. ckorth@uni-duesseldorf.de Accepted 2006-AUG-29 by JYOTI. 24-JAN-2007: Contacted by JYOTI. J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation prio_mesau Major prion protein PrP27-30 PrP33-35C PRNP PRP protein protein mesau Mesocricetus auratus (Golden hamster) Golden hamster MANLSYWLLALFVAMWTDVGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGTWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHNQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPMMHFGNDWEDRYYRENMNRYPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGENFTETDIKIMERVVEQMCTTQYQKESQAYYDGRRSSAVLFSSPPVILLISFLIFLMVG DIP protein P04273 original sequence version: 95 DIP protein P04273 original sequence version: 100 DIP protein P04273-1 original sequence version: 104 442C0E3ED4D20672 prion_or_construct Synthetic octarepeat contruct peptide peptide polypeptide oligopeptide oligopeptide polypeptide in vitro In vitro An amino acid sequence which is not represented in UniProt prnp-prnp-13 1 5 unspecified role unspecified role prey prey mesau-brain Mesocricetus auratus brain brain Brain [cerebrum] 5 unspecified role unspecified role bait bait region gst tag glutathione s tranferase tag glutathione S-tranferase tag glutathione S-tranferase tag gst tag undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined 4or region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain ecobb Escherichia coli (strain B / BL21) direct interaction direct interaction Paper describes prey construct as having 4 octarepeats between residues 52-98. UniProtKB entry contains 5. Interaction requires the presence of copper or zinc. A synthetic contruct containing 16 octarepeats (sequence not given) does not require a divalent metal ion to be present. 1 When incubated with brain extract from normal, non-infected hamsters (NHa) in sarkosyl-containing buffer (0.3%), both the GST�4OR and GST�16OR captured PrPC in the presence of copper ions at pH 7.5 with a half-maximal effect between 75 and 125 �M (Fig. 1A). prnp-prnp-14 4 5 unspecified role unspecified role neutral component neutral component 4or region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction Paper describes prey construct as having 4 octarepeats between residues 52-98. UniProtKB entry contains 5. Peptides form multimeric comlexes, interaction requires the presence of copper or zinc. Synthetic contructs containing 10-16 octarepeats (sequence not given) do not require a divalent metal ion to be present. Table 1 To establish whether OR domains could interact directly in solution and to analyze the critical OR length needed for such an interaction, we covalently linked synthetic 1OR (residues 55�67) and 4OR (residues 55�98) peptides via amine linkage to BSA and analyzed copper-dependent OR-OR interactions in vitro by DLS prnp-prnp-15 1 5 unspecified role unspecified role prey prey mesau-brain Mesocricetus auratus brain brain Brain [cerebrum] 6 unspecified role unspecified role bait bait direct interaction direct interaction A minimum octarepeat construct of 10 ORs was required to bind the pathological conformer of the prion protein. The interaction was inhibited by the addition of copper or zinc ions. Complex binding is resistant to SDS. 3 & 4 When we incubated Sepharose-immobilized GST�OR fusion proteins with brain extract from ScHa in the presence of sarkosyl-containing buffer, we observed that only GST�16OR captured PrPSc at pH 7.5 in the absence of copper ions (Fig. 3, A and B), demonstrating selective interaction of the expanded OR domain with PrPSc. Scrapie prnp-prnp-16 2 5 unspecified role unspecified role neutral component neutral component 4or region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction Paper describes prey construct as having 4 octarepeats between residues 52-98. UniProtKB entry contains 5. Peptides form multimeric comlexes, interaction requires the presence of copper or zinc. Synthetic contructs containing 10-16 octarepeats (sequence not given) do not require a divalent metal ion to be present. 2B Our DLS findings on multimerization of expanded OR domains were confirmed by scanning force microscopy and SEC (Fig. 2, A and B, respectively). prnp-prnp-17 3 5 unspecified role unspecified role neutral component neutral component 4or region sufficient to bind sufficient binding region sufficient to bind deletion analysis deletion analysis certain certain sequence position certain certain certain sequence position certain chemical synthesis Chemical synthesis (Chemical synthesis) direct interaction direct interaction Paper describes prey construct as having 4 octarepeats between residues 52-98. UniProtKB entry contains 5. Peptides form multimeric comlexes, interaction requires the presence of copper or zinc. Synthetic contructs containing 10-16 octarepeats (sequence not given) do not require a divalent metal ion to be present. 2B Our DLS findings on multimerization of expanded OR domains were confirmed by scanning force microscopy and SEC (Fig. 2, A and B, respectively).