title: Selectivity of aggregation-determining interactions.
abstract: Protein aggregation is sequence specific, favoring self-assembly over cross-seeding with non-homologous sequences. Still, as the majority of proteins in a proteome are aggregation prone, the high level of homogeneity of protein inclusions in vivo both during recombinant overexpression and in disease remains surprising. To investigate the selectivity of protein aggregation in a proteomic context, we here compared the selectivity of aggregation-determined interactions with antibody binding. To that purpose, we synthesized biotin-labeled peptides, corresponding to aggregation-determining sequences of the bacterial protein β-galactosidase and two human disease biomarkers: C-reactive protein and prostate-specific antigen. We analyzed the selectivity of their interactions in Escherichia coli lysate, human serum and human seminal plasma, respectively, using a Western blot-like approach in which the aggregating peptides replace the conventional antibody. We observed specific peptide accumulation in the same bands detected by antibody staining. Combined spectroscopic and mutagenic studies confirmed accumulation resulted from binding of the peptide on the identical sequence of the immobilized target protein. Further, we analyzed the sequence redundancy of aggregating sequences and found that about 90% of them are unique within their proteome. As a result, the combined specificity and low sequence redundancy of aggregating sequences therefore contribute to the observed homogeneity of protein aggregation in vivo. This suggests that these intrinsic proteomic properties naturally compartmentalize aggregation events in sequence space. In the event of physiological stress, this might benefit the ability of cells to respond to proteostatic stress by allowing chaperones to focus on specific aggregation events rather than having to face systemic proteostatic failure.
authors.affiliation: VIB Switch Laboratory, VIB, B-3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium.
authors.forename: Ashok
authors.initials: A
authors.lastname: Ganesan
authors.affiliation: VIB Switch Laboratory, VIB, B-3000 Leuven, Belgium; Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
authors.forename: Maja
authors.initials: M
authors.lastname: Debulpaep
authors.affiliation: VIB Switch Laboratory, VIB, B-3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium.
authors.forename: Hannah
authors.initials: H
authors.lastname: Wilkinson
authors.affiliation: VIB Switch Laboratory, VIB, B-3000 Leuven, Belgium; Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
authors.forename: Joost
authors.initials: J
authors.lastname: Van Durme
authors.affiliation: VIB Switch Laboratory, VIB, B-3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium.
authors.forename: Greet
authors.initials: G
authors.lastname: De Baets
authors.affiliation: VIB Switch Laboratory, VIB, B-3000 Leuven, Belgium; Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
authors.forename: Wim
authors.initials: W
authors.lastname: Jonckheere
authors.affiliation: VIB Switch Laboratory, VIB, B-3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium.
authors.forename: Meine
authors.initials: M
authors.lastname: Ramakers
authors.affiliation: Department of Human Genetics, KU Leuven, B-3000 Leuven, Belgium; Department of Chemistry-BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden.
authors.forename: Ylva
authors.initials: Y
authors.lastname: Ivarsson
authors.affiliation: Department of Human Genetics, KU Leuven, B-3000 Leuven, Belgium.
authors.forename: Pascale
authors.initials: P
authors.lastname: Zimmermann
authors.affiliation: Department of Medical Diagnostic Sciences, KU Leuven, B-3000 Leuven, Belgium.
authors.forename: Johan
authors.initials: J
authors.lastname: Van Eldere
authors.affiliation: VIB Switch Laboratory, VIB, B-3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium. Electronic address: joost.schymkowitz@switch-vib.kuleuven.be.
authors.forename: Joost
authors.initials: J
authors.lastname: Schymkowitz
authors.affiliation: VIB Switch Laboratory, VIB, B-3000 Leuven, Belgium; Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium. Electronic address: Frederic.Rousseau@switch-vib.kuleuven.be.
authors.forename: Frederic
authors.initials: F
authors.lastname: Rousseau
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D002097:C-Reactive Protein / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008297:Male; D018832:Molecular Chaperones / Q000235:genetics / Q000378:metabolism; D010455:Peptides / Q000378:metabolism; D017430:Prostate-Specific Antigen / Q000097:blood / Q000235:genetics; D066329:Protein Aggregates; D011485:Protein Binding / Q000235:genetics; D060066:Protein Interaction Maps; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D017550:Spectroscopy, Fourier Transform Infrared; D001616:beta-Galactosidase / Q000235:genetics* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D018832:Molecular Chaperones; D010455:Peptides; D066329:Protein Aggregates; D020543:Proteome; D002097:C-Reactive Protein; D001616:beta-Galactosidase; D017430:Prostate-Specific Antigen
keywords: amyloid; detection; interaction; protein aggregation; specificity