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/ semerdzhiev-2021-3 in vitro In vitro fcs fluorescence correlation spectroscopy FCS FCS fcs predetermined predetermined participant predetermined Semerdzhiev SA., Fakhree MAA., Segers-Nolten I., Blum C., Claessens MMAE. Virus - Publications including interactions involving viral proteins c.blum@utwente.nl,m.m.a.e.claessens@utwente.nl ACS chemical neuroscience 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus semerdzhiev-2021-1 in vitro In vitro aggregation aggregation assay aggregation predetermined predetermined participant predetermined Semerdzhiev SA., Fakhree MAA., Segers-Nolten I., Blum C., Claessens MMAE. Virus - Publications including interactions involving viral proteins The aggregation process is followed by recording the fluorescence of the amyloid-binding dye ThT;the fluorescence of the dye ThT increases upon binding to amyloid fibrils. c.blum@utwente.nl,m.m.a.e.claessens@utwente.nl ACS chemical neuroscience 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus semerdzhiev-2021-2 in vitro In vitro mst microscale thermophoresis mst predetermined predetermined participant predetermined Semerdzhiev SA., Fakhree MAA., Segers-Nolten I., Blum C., Claessens MMAE. Virus - Publications including interactions involving viral proteins c.blum@utwente.nl,m.m.a.e.claessens@utwente.nl ACS chemical neuroscience 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus semerdzhiev-2021-4 in vitro In vitro atomic force microsc atomic force microscopy AFM AFM atomic force microsc predetermined predetermined participant predetermined Semerdzhiev SA., Fakhree MAA., Segers-Nolten I., Blum C., Claessens MMAE. Virus - Publications including interactions involving viral proteins c.blum@utwente.nl,m.m.a.e.claessens@utwente.nl ACS chemical neuroscience 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus semerdzhiev-2021-5 human-sh_sy5y Homo sapiens SH-SY5Y cell line sh_sy5y Human neuroblastoma cells fret fluorescent resonance energy transfer FRET RET FRET analysis FRET RET FRET analysis fret tag fluorescence tag visualisation by fluorescence tag fluorescence Semerdzhiev SA., Fakhree MAA., Segers-Nolten I., Blum C., Claessens MMAE. Virus - Publications including interactions involving viral proteins A FRET Probe is labelled with Alexa 488 (donor) and Alexa 568(acceptor) at mutated residues -either Cys 9 or Cys 69. Purification ensured that the final sample only contained both the AF488 and AF568 FRET labeled alpha-S and some alpha-S with two AF568. Membrane-bound alpha-syn assumes an alpha-helical conformation. In the antiparallel alpha-helical form of alpha-syn residues 6 and 69 are very close and thus show high FRET, while in the unstructured form the average distance between the residues is larger, resulting in lower FRET; thus low FRET values indicate cytosolic localisation, high FRET - vesicle bound. The observed FRET is a result of a specific protein conformation rather than a signature of inter -alphaSyn interactions. c.blum@utwente.nl,m.m.a.e.claessens@utwente.nl ACS chemical neuroscience 2021 Only protein-protein interactions imex curation imex curation Coronavirus - Interactions investigated in the context of Coronavirus 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 ncap_sars2 Nucleoprotein N Nucleocapsid protein protein protein SARS-CoV-2 SARS-CoV-2 SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 2019-nCoV MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQGLPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAALALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTVTLLPAADLDDFSKQLQQSMSSADSTQA snca-snca-32 4113005 N/A 4113010 unspecified role unspecified role neutral component neutral component purified purified cys140 alexa label alexa label certain certain sequence position certain certain certain sequence position certain false P37840:p.Ala140Cys mutation mutation certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 4113010 unspecified role unspecified role neutral component neutral component purified purified cys140 alexa label alexa label certain certain sequence position certain certain certain sequence position certain false P37840:p.Ala140Cys mutation mutation certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 2 B-D n-snca-2 4113005 N/A 4113010 unspecified role unspecified role neutral component neutral component purified purified cys140 alexa label alexa label certain certain sequence position certain certain certain sequence position certain false P37840:p.Ala140Cys mutation mutation certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) N/A 4113011 unspecified role unspecified role neutral component neutral component purified purified n-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 4113005 2 B On average, 3 to 4 alpha-S proteins are present in an alpha-S/N-protein complex. snca-snca-30 4113006 N/A 4113010 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) N/A 4113010 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 1, 3 In the absence of additional proteins the onset of aggregation of alpha-S is observed at time scales >240 h. In the presence of the N protein aggregation time was reduced to <24 h. In the presence of N-protein, aggregation of alpha-S proceeds in two steps, represented by two plateaus in the observed ThT fluorescence. P0DTC9 - N protein increasing NaCl concentration. n-snca-1 4113007 N/A 4113011 unspecified role unspecified role neutral component neutral component purified purified n-terminus his tag his tag Hexa-His-tag 6-His-tag Histidine-tag Hexa-His-tag Histidine-tag 6-His-tag n-term range n-terminal range n-term range n-term range n-terminal range n-term range false ecoli Escherichia coli (strain K12) N/A 4113010 unspecified role unspecified role neutral component neutral component purified purified cys140 alexa 488 label alexa 488 label certain certain sequence position certain certain certain sequence position certain false P37840:p.Ala140Cys mutation mutation certain certain sequence position certain certain certain sequence position certain false ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 4113007 2A The lines indicate binding with a Hill coefficient of 1 (orange) and 4 (blue) indicating binding is cooperative. snca-snca-31 4113008 N/A 4113010 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) N/A 4113010 unspecified role unspecified role neutral component neutral component purified purified ecoli Escherichia coli (strain K12) direct interaction direct interaction false false false 3 Two distinctly different fibril populations, with different morphologies, can be discriminated. The N-protein speeds up the formation of alpha-S fibrils but does not change the morphology of fibrils observed after long time incubation. snca-snca-33 4113009 N/A 4113010 unspecified role unspecified role putative self putative self purified purified cys9 or cys69 alexa 488 label alexa 488 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false P37840:p.[Ser9Cys;Ala69Cys] mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false cys9 or cys69 alexa 568 label alexa 568 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) N/A 4113010 unspecified role unspecified role putative self putative self purified purified cys9 or cys69 alexa 488 label alexa 488 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false P37840:p.[Ser9Cys;Ala69Cys] mutation mutation certain certain sequence position certain certain certain sequence position certain false certain certain sequence position certain certain certain sequence position certain false cys9 or cys69 alexa 568 label alexa 568 label undetermined undetermined sequence position undetermined undetermined undetermined sequence position undetermined false ecoli Escherichia coli (strain K12) proximity proximity close-contact colocalization neighbourhood interaction false false false 4 In the cells that were microinjected with N-protein, less high FRET (orange) signal was seen compared to the control group, which indicates there is less vesicle-bound alpha-Syn in N-treated cells.