ATP modulates self-perpetuating conformational conversion generating structurally distinct yeast prion amyloids that limit autocatalytic amplification

Prion-like self-perpetuating conformational conversion of proteins into amyloid aggregates is associated with both transmissible neurodegenerative diseases and non-Mendelian inheritance. The cellular energy currency ATP is known to indirectly regulate the formation, dissolution, or transmission of amyloid-like aggregates by providing energy to the molecular chaperones that maintain protein homeostasis. In this work, we demonstrate that ATP molecules, independent of any chaperones, modulate the formation and dissolution of amyloids from a yeast prion domain (NM domain of Saccharomyces cerevisiae Sup35) and restricts autocatalytic amplification by controlling the amount of fragmentable and seeding-competent aggregates. ATP, at (high) physiological concentrations in the presence of Mg2+, kinetically accelerates NM aggregation. Interestingly, ATP also promotes phase separation–mediated aggregation of a human protein harboring a yeast prion-like domain. We also show that ATP disaggregates preformed NM fibrils in a dose-independent manner. Our results indicate that ATP-mediated disaggregation, unlike the disaggregation by the disaggregase Hsp104, yields no oligomers that are considered one of the critical species for amyloid transmission. Furthermore, high concentrations of ATP delimited the number of seeds by giving rise to compact ATP-bound NM fibrils that exhibited nominal fragmentation by either free ATP or Hsp104 disaggregase to generate lower molecular weight amyloids. In addition, (low) pathologically relevant ATP concentrations restricted autocatalytic amplification by forming structurally distinct amyloids that are found seeding inefficient because of their reduced β-content. Our results provide key mechanistic underpinnings of concentration-dependent chemical chaperoning by ATP against prion-like transmissions of amyloids. Prion-like self-perpetuating conformational conversion of proteins into amyloid aggregates is associated with both transmissible neurodegenerative diseases and non-Mendelian inheritance. The cellular energy currency ATP is known to indirectly regulate the formation, dissolution, or transmission of amyloid-like aggregates by providing energy to the molecular chaperones that maintain protein homeostasis. In this work, we demonstrate that ATP molecules, independent of any chaperones, modulate the formation and dissolution of amyloids from a yeast prion domain (NM domain of Saccharomyces cerevisiae Sup35) and restricts autocatalytic amplification by controlling the amount of fragmentable and seeding-competent aggregates. ATP, at (high) physiological concentrations in the presence of Mg2+, kinetically accelerates NM aggregation. Interestingly, ATP also promotes phase separation–mediated aggregation of a human protein harboring a yeast prion-like domain. We also show that ATP disaggregates preformed NM fibrils in a dose-independent manner. Our results indicate that ATP-mediated disaggregation, unlike the disaggregation by the disaggregase Hsp104, yields no oligomers that are considered one of the critical species for amyloid transmission. Furthermore, high concentrations of ATP delimited the number of seeds by giving rise to compact ATP-bound NM fibrils that exhibited nominal fragmentation by either free ATP or Hsp104 disaggregase to generate lower molecular weight amyloids. In addition, (low) pathologically relevant ATP concentrations restricted autocatalytic amplification by forming structurally distinct amyloids that are found seeding inefficient because of their reduced β-content. Our results provide key mechanistic underpinnings of concentration-dependent chemical chaperoning by ATP against prion-like transmissions of amyloids. Amyloids are proteinaceous β-sheet-rich ordered assemblies of misfolded proteins that bypass all the surveillance of the protein quality control (PQC) machinery and are often linked with some of the deadly neurodegenerative diseases such as Alzheimer’s, Parkinson’s, prion diseases, amyotrophic lateral sclerosis, and so on (1Chiti F. Dobson C.M. Protein misfolding, amyloid formation, and human disease: a summary of progress over the last decade.Annu. Rev. Biochem. 2017; 86: 27-68Crossref PubMed Scopus (1536) Google Scholar, 2Ke P.C. Zhou R. Serpell L.C. Riek R. Knowles T.P.J. Lashuel H.A. et al.Half a century of amyloids: past, present and future.Chem. Soc. Rev. 2020; 49: 5473-5509Crossref PubMed Google Scholar, 3Iadanza M.G. Jackson M.P. Hewitt E.W. Ranson N.A. Radford S.E. A new era for understanding amyloid structures and disease.Nat. Rev. Mol. Cell Biol. 2018; 19: 755-773Crossref PubMed Scopus (487) Google Scholar). The PQC system is a network of proteins devoted to countering protein misfolding and aggregation, where ATP plays an indirect, yet important, role by providing energy to the chaperones involved in protein homeostasis (4Hipp M.S. The proteostasis(definition) network and its decline in ageing.Nat. Rev. Mol. Cell Biol. 2019; 20: 421-435Crossref PubMed Scopus (590) Google Scholar). Although only micromolar concentrations of ATP are required for the function of enzymes that include this PQC machinery, the question as to why cells maintain a multifold higher concentration of ATP fascinated researchers to investigate the molecular role of ATP in cells apart from just being the cellular energy currency (5Patel A. Malinovska L. Saha S. Wang J. Alberti S. Krishnan Y. et al.Biochemistry: ATP as a biological hydrotrope.Science. 2017; 356: 753-756Crossref PubMed Scopus (508) Google Scholar, 6Moran U. Phillips R. Milo R. SnapShot: key numbers in biology.Cell. 2010; 141: 1-2Abstract Full Text PDF Scopus (135) Google Scholar). Intriguingly, in the amyloid deposits isolated from the brain tissues of patients with neurodegenerative diseases, biologically relevant polyanions such as nucleic acids, heparin, and glycosaminoglycans were detected. These reports hinted at a direct interaction proteins and the polyanions such as ATP and a of molecular ATP in prote