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/ he-2006-2 Deficiency of disulfide bonds facilitating fibrillogenesis of endostatin. in vitro In vitro electron microscopy electron microscopy Electron crystallography Electron cryomicroscopy Electron crystallography Electron cryomicroscopy predetermined predetermined participant predetermined He Y., Zhou H., Tang H., Luo Y. BioCreative - Critical Assessment of Information Extraction systems in Biology The enhancement in the fluorescence intensity of ThT upon binding to ordered protein aggregates is a rapid and sensitive method to show the presence of fibrils A ThT Binding Assay�Fluorescence was measured with a Hitachi FL-4500 fluorescence spectrophotometer using cuvettes that have an optical path length of 1 cm. protein@tsinghua.edu.cn J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Alzheimers - Interactions investigated in the context of Alzheimers disease he-2006-3 Deficiency of disulfide bonds facilitating fibrillogenesis of endostatin. in vitro In vitro cd circular dichroism CD CD cd predetermined predetermined participant predetermined He Y., Zhou H., Tang H., Luo Y. BioCreative - Critical Assessment of Information Extraction systems in Biology The enhancement in the fluorescence intensity of ThT upon binding to ordered protein aggregates is a rapid and sensitive method to show the presence of fibrils A ThT Binding Assay�Fluorescence was measured with a Hitachi FL-4500 fluorescence spectrophotometer using cuvettes that have an optical path length of 1 cm. protein@tsinghua.edu.cn J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Alzheimers - Interactions investigated in the context of Alzheimers disease he-2006-1 Deficiency of disulfide bonds facilitating fibrillogenesis of endostatin. in vitro In vitro fluorescence spectr classical fluorescence spectroscopy fluorescence spectr predetermined predetermined participant predetermined He Y., Zhou H., Tang H., Luo Y. BioCreative - Critical Assessment of Information Extraction systems in Biology The enhancement in the fluorescence intensity of ThT upon binding to ordered protein aggregates is a rapid and sensitive method to show the presence of fibrils A ThT Binding Assay�Fluorescence was measured with a Hitachi FL-4500 fluorescence spectrophotometer using cuvettes that have an optical path length of 1 cm. protein@tsinghua.edu.cn J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Alzheimers - Interactions investigated in the context of Alzheimers disease he-2006-4 Deficiency of disulfide bonds facilitating fibrillogenesis of endostatin. in vitro In vitro biophysical biophysical predetermined predetermined participant predetermined He Y., Zhou H., Tang H., Luo Y. BioCreative - Critical Assessment of Information Extraction systems in Biology The enhancement in the fluorescence intensity of ThT upon binding to ordered protein aggregates is a rapid and sensitive method to show the presence of fibrils A ThT Binding Assay�Fluorescence was measured with a Hitachi FL-4500 fluorescence spectrophotometer using cuvettes that have an optical path length of 1 cm. protein@tsinghua.edu.cn J. Biol. Chem. (0021-9258) 2006 Only protein-protein interactions imex curation Neurodegeneration - Publications depicting interactions involved in neurodegenerative diseases. Alzheimers - Interactions investigated in the context of Alzheimers disease p39060-pro_0000005794 Endostatin COL18A1 protein protein human Homo sapiens Human HSHRDFQPVLHLVALNSPLSGGMRGIRGADFQCFQQARAVGLAGTFRAFLSSRLQDLYSIVRRADRAAVPIVNLKDELLFPSWEALFSGSEGPLKPGARIFSFDGKDVLRHPTWPQKSVWHGSDPNGRRLTESYCETWRTEAPSATGQASSLLGGRLLGQSAASCHHAYIVLCIENSFMTASK 1572 1754 endo_all_ala-1 Tht Binding assay of mutated endostatin fibril formation 503354 N/A 503358 unspecified role unspecified role neutral component neutral component P39060-PRO_0000005794:p.[Cys33Ala;Cys135Ala;Cys165Ala;Cys173Ala] mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 503358 unspecified role unspecified role neutral component neutral component P39060-PRO_0000005794:p.[Cys33Ala;Cys135Ala;Cys165Ala;Cys173Ala] mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Figure 2 The coordinates for the mutated cysteine residues were taken from the UniProt entry Q8WXI5 It was shown that amorphous granular aggregates composed of spherical particles predominated immediately after the pH was adjusted (Fig. 2A). Eleven hours later, short fibrils emanated from the globular granules, which indicated that fibrillar protein aggregates were beginning to form (Fig. 2B). In a similar sample recovered at 41 h, the fibrillar material was clearly evident, and the fibril extension continued (Fig. 2C). This fibrillar type resembles the protofilaments observed in other fibrillogenic systems, according to the size and characteristics of the aggregates (33). After prolonged incubation for 81 h, the AFM image showed that the fibrils produced were long, smooth, and unbranched and possessed a rope-like structure with a width of 30�40 nm (Fig. 2D). When endo-WT was incubated under the same conditions for 81 h, there were only small spherical particles, which were probably the protein monomer molecules in appearance, with no evidence for extended fibrils characteristic of fibril formation (Fig. 2E). endostatin-2 Tht Binding assay of chemically induced endostatin fibril formation 503354 N/A 503358 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) N/A 503358 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Figure 4 The coordinates for the mutated cysteine residues were taken from the UniProt entry Q8WXI5 Fibril formation was seen in in 30% TFE and endostatin displayed long, twisted, and rope-like fibrils 2, 2, 2 Trifluoroethanol (TFE) endo_all_ala-2 Tht Binding assay of mutated endostatin fibril formation 503355 N/A 503358 unspecified role unspecified role neutral component neutral component P39060-PRO_0000005794:p.[Cys33Ala;Cys135Ala;Cys165Ala;Cys173Ala] Cys37Ala Cys139Ala Cys169Ala Cys177Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 503358 unspecified role unspecified role neutral component neutral component P39060-PRO_0000005794:p.[Cys33Ala;Cys135Ala;Cys165Ala;Cys173Ala] Cys37Ala Cys139Ala Cys169Ala Cys177Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Figure 3 The coordinates for the mutated cysteine residues were taken from the UniProt entry Q8WXI5 The difference of the spectra between endo-all- Ala before and after being incubated for 81 h showed a negative peak at 215 nm, which is a diagnostic mark for the presence of beta-structure The secondary structure of endo-WT did not alter after the incubation. endostatin-1 Tht Binding assay of chemically induced endostatin fibril formation 503355 N/A 503358 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) N/A 503358 unspecified role unspecified role neutral component neutral component ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Figure 8A The coordinates for the mutated cysteine residues were taken from the UniProt entry Q8WXI5 Alpha-helical structure of endo-WT increased with TFE concentrations from 0 to 30% at pH 6.0, according to the two negative peaks at 208 and 222 nm in the spectra. 2, 2, 2 Trifluoroethanol (TFE) endo_all_ala-4 Tht Binding assay of mutated endostatin fibril formation 503356 N/A 503358 unspecified role unspecified role neutral component neutral component P39060-PRO_0000005794:p.[Cys33Ala;Cys135Ala;Cys165Ala;Cys173Ala] mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 503358 unspecified role unspecified role neutral component neutral component P39060-PRO_0000005794:p.[Cys33Ala;Cys135Ala;Cys165Ala;Cys173Ala] mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Figure 1 Figure 7 In the case of endo-WT, no increased fluorescence was observed regardless of various pH values. The fluorescence for endo-all- Ala, however, increased rapidly from pH 4.3 to 6.0 and reached a maximum at pH 6.0. The coordinates for the mutated cysteine residues were taken from the UniProt entry Q8WXI5 endo_all_ala-3 Tht Binding assay of mutated endostatin fibril formation 503357 N/A 503358 unspecified role unspecified role neutral component neutral component P39060-PRO_0000005794:p.[Cys33Ala;Cys135Ala;Cys165Ala;Cys173Ala] Cys37Ala Cys139Ala Cys169Ala Cys177Ala mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 503358 unspecified role unspecified role neutral component neutral component P39060-PRO_0000005794:p.[Cys33Ala;Cys135Ala;Cys165Ala;Cys173Ala] mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false Figure 4 The coordinates for the mutated cysteine residues were taken from the UniProt entry Q8WXI5 Stoichiometry was not determined in this assay The FTIR spectrum of endo-WT after the incubation did not make any change compared with that of the protein incubated before