Abstract
Amyloid fibrils represent a pathological state of protein polymer that is closely associated with various neurodegenerative diseases. Polysaccharides have a prominent role in recognizing amyloid fibrils and mediating their pathogenicity. However, the mechanism underlying the amyloid–polysaccharide interaction remains elusive. We also do not know its impact on the structure and pathology of formed fibrils. Here, we used cryo-electron microscopy to analyze the atomic structures of mature α-synuclein (α-syn) fibrils upon binding with polymeric heparin and heparin-like oligosaccharides. The fibril structure, including the helical twist and conformation of α-syn, changed over time upon the binding of heparin but not oligosaccharides. The sulfation pattern and numbers of saccharide units are important for the binding. Similarly, negatively charged biopolymers typically interact with amyloid fibrils, including tau and various α-syn polymorphs, leading to alterations in their conformation. Moreover, we show that heparin-like oligosaccharides can not only block neuronal uptake and propagation of formed α-syn fibrils but also inhibit α-syn fibrillation. This work demonstrates a distinctive activity of heparin and biopolymers in remodeling amyloid fibrils and suggests the pharmaceutical potential of heparin-like oligosaccharides.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$32.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Data availability
Cryo-EM maps were deposited to the EM Data Bank under accession numbers EMD-35087 for Hep-remod-1 (1 h) α-syn fibrils, EMD-35088 for Hep-remod-2 (1 h) α-syn fibrils, EMD-35090 for Hep-remod-3 (3 days) α-syn fibrils, EMD-60527 for heparin-bound E46K α-syn fibrils, EMD-60539 for heparin-bound tau fibrils polymorph 1 (PHF), EMD-60531 for heparin-bound tau fibrils polymorph 2 (THF), EMD-60532 for heparin-bound tau fibrils polymorph 3, EMD-60533 for heparin-bound tau fibrils polymorph 4, EMD-60529 for poly(A)–α-syn polymorph 1, EMD-60530 for poly(A)–α-syn polymorph 2, EMD-60528 for CS-bound α-syn fibrils and EMD-60637 for poly(P)-bound α-syn fibrils. The corresponding atomic models were deposited to the PDB under accession numbers 8HZB for Hep-remod-1 (1 h) α-syn fibrils, 8HZC for Hep-remod-2 (1 h) α-syn fibrils, 8HZS for Hep-remod-3 (3 days) α-syn fibrils, 8ZWH for heparin-bound E46K α-syn fibrils, 8ZX6 for heparin-bound tau fibrils polymorph 1 (PHF), 8ZWL for heparin-bound tau fibrils polymorph 3, 8ZWM for heparin-bound tau fibrils polymorph 4, 8ZWJ for poly(A)–α-syn polymorph 1, 8ZWK for poly(A)–α-syn polymorph 2, 8ZWI for CS-bound α-syn fibrils and 9IJP for poly(P)-bound α-syn fibrils. The following initial models used in this study are available from the PDB: α-syn polymorph 1a fibrils (6A6B), E46K α-syn fibrils (6L4S), tau PHF (5O3L) and tau AD-MIA1 (8Q27). Source data are provided with this paper.
References
Tarutani, A. et al. Ultrastructural and biochemical classification of pathogenic tau, α-synuclein and TDP-43. Acta Neuropathol. 143, 613–640 (2022).
Spillantini, M. G. et al. α-Synuclein in Lewy bodies. Nature 388, 839–840 (1997).
Ballatore, C., Lee, V. M.-Y. & Trojanowski, J. Q. Tau-mediated neurodegeneration in Alzheimer’s disease and related disorders. Nat. Rev. Neurosci. 8, 663–672 (2007).
Iwatsubo, T. et al. Visualization of Aβ42(43) and Aβ40 in senile plaques with end-specific Aβ monoclonals: evidence that an initially deposited species is Aβ42(43). Neuron 13, 45–53 (1994).
Neumann, M. et al. Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Science 314, 130–133 (2006).
Goedert, M. et al. Assembly of microtubule-associated protein tau into Alzheimer-like filaments induced by sulphated glycosaminoglycans. Nature 383, 550–553 (1996).
Miura, T., Suzuki, K., Kohata, N. & Takeuchi, H. Metal binding modes of Alzheimer’s amyloid β-peptide in insoluble aggregates and soluble complexes. Biochemistry 39, 7024–7031 (2000).
Kampers, T., Friedhoff, P., Biernat, J., Mandelkow, E.-M. & Mandelkow, E. RNA stimulates aggregation of microtubule‐associated protein tau into Alzheimer‐like paired helical filaments. FEBS Lett. 399, 344–349 (1996).
Soares Da Costa, D., Reis, R. L. & Pashkuleva, I. Sulfation of glycosaminoglycans and its implications in human health and disorders. Annu. Rev. Biomed. Eng. 19, 1–26 (2017).
Xu, D. & Esko, J. D. Demystifying heparan sulfate–protein interactions. Annu. Rev. Biochem. 83, 129 (2014).
Watanabe, N. et al. Glypican‐1 as an Aβ binding HSPG in the human brain: its localization in DIG domains and possible roles in the pathogenesis of Alzheimer’s disease. FASEB J. 18, 1013–1015 (2004).
Liu, C.-C. et al. Neuronal heparan sulfates promote amyloid pathology by modulating brain amyloid-β clearance and aggregation in Alzheimer’s disease. Sci. Transl. Med. 8, 332ra44 (2016).
Perry, G. et al. Basic fibroblast growth factor binds to filamentous inclusions of neurodegenerative diseases. Brain Res. 579, 350–352 (1992).
Snow, A. et al. Early accumulation of heparan sulfate in neurons and in the β-amyloid protein-containing lesions of Alzheimer’s disease and Down’s syndrome. Am. J. Pathol. 137, 1253 (1990).
Su, J., Cummings, B. & Cotman, C. Localization of heparan sulfate glycosaminoglycan and proteoglycan core protein in aged brain and Alzheimer’s disease. Neuroscience 51, 801–813 (1992).
Cohlberg, J. A., Li, J., Uversky, V. N. & Fink, A. L. Heparin and other glycosaminoglycans stimulate the formation of amyloid fibrils from α-synuclein in vitro. Biochemistry 41, 1502–1511 (2002).
Mehra, S. et al. Glycosaminoglycans have variable effects on α-synuclein aggregation and differentially affect the activities of the resulting amyloid fibrils. J. Biol. Chem. 293, 12975–12991 (2018).
Snow, A. D., Cummings, J. A. & Lake, T.The unifying hypothesis of Alzheimer’s disease: heparan sulfate proteoglycans/glycosaminoglycans are key as first hypothesized over 30 years ago. Front. Aging Neurosci. 13, 710683 (2021).
Garg, D. K. & Bhat, R.Modulation of assembly of TDP-43 low-complexity domain by heparin: from droplets to amyloid fibrils. Biophys. J. 121, 2568–2582 (2022).
Holmes, B. B. et al. Heparan sulfate proteoglycans mediate internalization and propagation of specific proteopathic seeds. Proc. Natl Acad. Sci. USA 110, E3138–E3147 (2013).
Stewart, K. L. et al. Atomic details of the interactions of glycosaminoglycans with amyloid-β fibrils. J. Am. Chem. Soc. 138, 8328–8331 (2016).
Zhao, J. et al. 3‐O‐sulfation of heparan sulfate enhances tau interaction and cellular uptake. Angew. Chem. Int. Ed. 59, 1818–1827 (2020).
Zhang, Q. et al. A myosin-7B-dependent endocytosis pathway mediates cellular entry of α-synuclein fibrils and polycation-bearing cargos. Proc. Natl Acad. Sci. USA 117, 10865–10875 (2020).
Yin, Y. et al. in 2019 IEEE 16th International Symposium on Biomedical Imaging (eds Linguraru, M. G. & Grisan, E.) (IEEE, 2019).
Tao, Y. et al. Heparin induces α-synuclein to form new fibril polymorphs with attenuated neuropathology. Nat. Commun. 13, 1–9 (2022).
Schweighauser, M. et al. Structures of α-synuclein filaments from multiple system atrophy. Nature 585, 464–469 (2020).
Zhao, K. et al. Parkinson’s disease associated mutation E46K of α-synuclein triggers the formation of a distinct fibril structure. Nat. Commun. 11, 2643 (2020).
Lovestam, S. et al. Assembly of recombinant tau into filaments identical to those of Alzheimer’s disease and chronic traumatic encephalopathy. eLife 11, e76494 (2022).
Xu, P., Xu, W., Dai, Y., Yang, Y. & Yu, B. Efficient synthesis of a library of heparin tri- and tetrasaccharides relevant to the substrate of heparanase. Org. Chem. Front. 1, 405–414 (2014).
Xu, P., Laval, S., Guo, Z. & Yu, B. Microwave-assisted simultaneous O,N-sulfonation in the synthesis of heparin-like oligosaccharides. Org. Chem. Front. 3, 103–109 (2016).
Weiss, R. J., Esko, J. D. & Tor, Y. Targeting heparin and heparan sulfate protein interactions. Org. Biomol. Chem. 15, 5656–5668 (2017).
Tao, Y. Q. et al. Structural mechanism for specific binding of chemical compounds to amyloid fibrils. Nat. Chem. Biol. 19, 1235 (2023).
Yang, Y. et al. Structures of α-synuclein filaments from human brains with Lewy pathology. Nature 610, 791–795 (2022).
Zhang, W. et al. Novel tau filament fold in corticobasal degeneration. Nature 580, 283–287 (2020).
Zhang, W. et al. Heparin-induced tau filaments are polymorphic and differ from those in Alzheimer’s and Pick’s diseases. eLife 8, e43584 (2019).
Abskharon, R. et al. Cryo-EM structure of RNA-induced tau fibrils reveals a small C-terminal core that may nucleate fibril formation. Proc. Natl Acad. Sci. USA 119, e2119952119 (2022).
Peng, C. et al. Cellular milieu imparts distinct pathological α-synuclein strains in α-synucleinopathies. Nature 557, 558–563 (2018).
Li, D. & Liu, C. Conformational strains of pathogenic amyloid proteins in neurodegenerative diseases. Nat. Rev. Neurosci. 23, 523–534 (2022).
Fan, Y. Conformational change of α-synuclein fibrils in cerebrospinal fluid from different clinical phases of Parkinson’s disease. Structure 31, 78–87 (2023).
Chakraborty, P. et al. Co-factor-free aggregation of tau into seeding-competent RNA-sequestering amyloid fibrils. Nat. Commun. 12, 1–12 (2021).
Li, X. et al. Subtle change of fibrillation condition leads to substantial alteration of recombinant tau fibril structure. iScience 25, 105645 (2022).
Clausen, T. M. et al. SARS-CoV-2 infection depends on cellular heparan sulfate and ACE2. Cell 183, 1043–1057 (2020).
Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
Scheres, S. H. Amyloid structure determination in RELION-3.1. Acta Crystallogr. D 76, 94–101 (2020).
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
Li, Y. et al. Amyloid fibril structure of α-synuclein determined by cryo-electron microscopy. Cell Res. 28, 897–903 (2018).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
Volpicelli-Daley, L. A., Luk, K. C. & Lee, V. M. Addition of exogenous α-synuclein preformed fibrils to primary neuronal cultures to seed recruitment of endogenous α-synuclein to Lewy body and Lewy neurite-like aggregates. Nat. Protoc. 9, 2135–2146 (2014).
Acknowledgements
We thank the Cryo-EM center at the IRCBC, Shanghai Institute of Organic Chemistry for help with cryo-EM data collection. We would also like to thank the Bio-EM Facility of ShanghaiTech University for help with cryo-EM data collection. This work was supported by the National Natural Science Foundation of China (82188101 and 32171236 to C.L.; 22177125 and 92253301 to P.X.; 92353302 and 32170683 to D.L.), National Key R&D Program of China (2022YFA1304700 to B.Y.), the Key Research Program of Frontier Sciences of the Chinese Academy of Sciences (ZDBS-LY-SLH030 to B.Y.), the Science and Technology Commission of Shanghai Municipality (22JC1410400 to C.L.), Shanghai Basic Research Pioneer Project to C.L., the Shanghai Pilot Program for Basic Research—CAS, Shanghai Branch (CYJ-SHFY-2022-005 to C.L.) and the CAS Project for Young Scientists in Basic Research (YSBR-095 to C.L. and P.X.).
Author information
Authors and Affiliations
Contributions
Y.T., P.X., B.Y. and C.L. designed the project. Y.T., Y.S., X.L. and Q.Z. prepared heparin-bound and oligosaccharide-bound α-syn fibril cryo-EM samples and performed cryo-EM data collection and processing. P.X., W.S. and B.Y. synthesized the heparin-like oligosaccharide library. Y.T., K.L. and Q.Z. performed the screening for oligosaccharides to replace heparin activity. S.Z. performed the SPR assays and neuronal assays. G.Y. assisted with revising the manuscript. All authors were involved in analyzing the data and contributed to manuscript discussion and editing. Y.T., P.X., D.L., B.Y. and C.L. wrote the manuscript.
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
Nature Structural & Molecular Biology thanks Antonio Molinaro and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available. Primary Handling Editors: Sara Osman and Dimitris Typas, in collaboration with the Nature Structural & Molecular Biology team.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Extended data
Extended Data Fig. 1 Cryo-EM 2D averages, 3D density maps, and resolution estimation of the apo and heparin-remodelled α-syn fibrils.
a. Cryo-EM 2D class averages of the apo α-syn fibrils and heparin-remodelled α-syn fibrils. The lengths of half pitch for each fibril are indicated. b. Central slices of the cryo-EM 3D maps of the apo and heparin-remodelled α-syn fibrils. c. The overall resolution estimates are calculated based on the gold-standard 0.143 Fourier shell correlation (FSC) of the two independently refined half-maps. d. Top views (left) and side views (right) of the local resolution plots of the recombinant density maps.
Extended Data Fig. 2 Additional proteinaceous fragment in different heparin-remodelled α-syn fibril polymorphs and conformational changes of the Hep-remod-3 fibril.
a. Local structures of heparin-remodelled α-syn fibril polymorphs. Models near fragment 14-22/25 are shown in sticks. b. Structural comparison of apo and Hep-remod-3. Flipped residues are shown in sticks.
Extended Data Fig. 3 Conserved additional densities on the ex vivo α-syn fibrils from MSA and heparin-remodeled α-syn fibrils.
a, The structural models of the MSA α-syn fibril fitted in the density map. α-Syn is colored in gray. The additional densities adjacent to lysine residues are shown in red and zoomed in. b, Overlay of the α-syn subunit structures in the heparin-remodeled α-syn fibrils (blue) and ex vivo MSA α-syn fibrils (grey). Residues K58 and K60 are shown in sticks. The conserved additional densities are indicated by pink ovals. Root Mean Square Deviations (RMSDs) are shown at the bottom.
Extended Data Fig. 4 Cryo-EM structures of amyloid fibrils in complex with heparin and other biopolymers.
a, Central slices of the cryo-EM 3D maps of the apo- (top) and heparin-bound (bottom) E46K α-syn and Tau fibrils. b, Central slices of the cryo-EM 3D maps of the PolyA, CS, and PolyP bound α-syn fibrils. Additional densities are indicated with arrow heads. The length of half pitches (180° helical turn) are indicated.
Extended Data Fig. 5 Cryo-EM structures of E46K α-syn fibrils and Tau fibrils in complex with heparin.
a, Top view and side views of the cryo-EM density map of the heparin-bound E46K α-syn fibrils. The additional densities for heparin are colored in red. b, Cross-section view of the structural model of heparin-bound E46K α-syn fibrils fitted in the density maps. The model is colored in grey. The density maps are restricted to areas within 2-Å radius of the E46K α-syn model, and combined with the heparin densities colored in red. The models and maps at heparin binding sites are zoomed-in. c, Top views and side views of the density maps of the heparin-bound Tau PHFs (Polymorph 1). d, Cross-section views of the structural models of heparin-bound Tau PHFs. e, Cross-section view of the structural model of Tau PHFs extracted from AD brains (PDB ID: 5O3L) fitted in the density map (EMDB ID: EMD-3741). The additional densities for heparin are colored in red. Other additional densities are colored in pink. f, Structural comparison of 1layer models of heparin bound (red) and EGCG bound (blue, PDB ID: 7UPG) Tau PHFs. The RMSD between two models are 1.296 Å over 150 C-α atoms. g, Density map of the heparin-bound Tau THFs (Polymorph 2). h, Density map of the heparin-bound Tau Polymorph 3. i, Model of Polymorph 3 fitted in the density map. The model is colored in grey. The density map is restricted to areas within 2-Å radius of the Tau models, and combined with the heparin densities colored in red. The model and additional densities at each heparin binding sites are zoomed-in. j, Top, density map of the heparin-bound Tau Polymorph 4 fibrils. The additional densities for heparin are colored in red. Bottom, model of Polymorph 4 fitted in the density map, shown as in panel i. k, Half pitch changes of α-syn (red) and Tau (blue) polymorphs. The 110 nm half pitch is indicated by grey dashed line.
Extended Data Fig. 6 Cryo-EM structure of the α-syn fibrils in complex with RNA PolyA.
a, Top and side views of the cryo-EM density map of the PolyA-Polymorph 1 fibril. The PolyA densities are colored in orange. b, Cross-section view of the structural models of PolyA-Polymorph 1 fitted in the density map. Structural model is colored in grey. The density map is restricted to areas within 2-Å radius of the α-syn model, and combined with the PolyA densities colored in orange. The PolyA binding site is zoomed-in. c, Zoomed-in view of the interactions between PolyA and α-syn at the binding sites of PolyA-Polymorph 1. d, Density map of PolyA-Polymorph 2 fibril, shown as in panel a. e, Structural model of PolyA-polymorph 2 fitted in the density map, shown as in panel b. f, Interactions between PolyA and α-syn in PolyA-polymorph 2.
Extended Data Fig. 7 Cryo-EM structures of the α-syn fibrils in complex with CS and PolyP.
a, Top view and side views of the cryo-EM density maps of the CS-bound α-syn fibrils. The additional densities for CS are colored in orange. b, Cross-section view of the structural model of CS-bound α-syn fibrils fitted in the density maps. The model is colored in grey. The density maps are restricted to areas within 2-Å radius of the α-syn model, and combined with the CS densities colored in orange. The models and maps at heparin binding sites are zoomed-in. c, Overlay of 1-layer α-syn structures in the apo- (grey) and CS-bound α-syn fibrils (pink). The structural models are shown in sticks. Flipped residues are zoomed-in. d, Top view and side views of the cryo-EM density maps of the PolyP-bound α-syn fibrils. The additional densities for PolyP are colored in orange. e, Cross-section view of the structural model of PolyP-bound α-syn fibrils fitted in the density maps. The model is colored in grey. The density maps are restricted to areas within 2-Å radius of the α-syn model, and combined with the PolyP densities colored in orange. The models and maps at heparin binding sites are zoomed-in.
Extended Data Fig. 8 Heparin-like oligosaccharides library.
a, The chemical structures of oligosaccharides are shown. 2-O-sulfate and 6-O-sulfate are coloured in red. 2-N-sulfate and 2-Ac-N are coloured in blue. The Symbol Nomenclature for Glycans (SNFG) are shown under each chemical structure. b, Chemical structures of oligo-30 and oligo-31.
Extended Data Fig. 9 Cryo-EM structures of the oligosaccharide-bound α-syn fibrils.
a. Cryo-EM 2D class averages (left) and central slices of the 3D maps of the oligo-22-bound and oligo-26-bound α-syn fibrils. The lengths of half pitch for each fibril are indicated. b. Cryo-EM density maps of the oligo-22-bound and oligo-26-bound α-syn fibrils. Extra densities for fragment 14-22/25 are coloured in blue. Extra densities for oligosaccharides are coloured in orange. The maps are displayed with the contour level of σ = 0.0036 for oligo-22-bound α-syn fibril, and σ = 0.0068 for oligo-22-bound α-syn fibril. c. Cross-section view of the structural models of oligo-22-bound (left) and oligo-26-bound (right) α-syn fibrils fitted in the corresponding density maps. The density maps are restricted to areas within 2-Å radius of the α-syn models, and combined with the oligosaccharide densities coloured in orange and indicated by arrows. d. Global structural comparison of oligo-22-bound and oligo-26-bound α-syn fibril models.
Extended Data Fig. 10 Structural models of heparin induced α-syn fibrils and heparin biopolymer remodeled α-syn fibrils and heparin induced α-syn fibrils.
a, Structural models of heparin induced α-syn fibrils. The heparin molecules are indicated by orange ovals. b, Structural models of apo, heparin remodeled, CS bound, and polyA remodeled α-syn fibrils. Heparin, CS, and polyA molecules are indicated by orange, yellow, and purple ovals, respectively. Residues involved in the interactions with biopolymers are shown in blue sticks. K58-K60 surface on each fibril is indicated as dash box.
Supplementary information
Supplementary Information
Supplementary Figs. 1–5 and methods.
Supplementary Data 1
Source data for Supplementary Fig. 2b.
Supplementary Data 2
Source data for Supplementary Fig. 3.
Supplementary Data 3
Source data for Supplementary Fig. 4.
Source data
Source Data Fig. 2
Statistical source data.
Source Data Fig. 4
Statistical source data.
Source Data Fig. 5
Statistical source data.
Source Data Extended Data Fig. 5
Statistical source data.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Tao, Y., Xu, P., Zhang, S. et al. Time-course remodeling and pathology intervention of α-synuclein amyloid fibril by heparin and heparin-like oligosaccharides. Nat Struct Mol Biol 32, 369–380 (2025). https://doi.org/10.1038/s41594-024-01407-2
Received:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/s41594-024-01407-2
This article is cited by
-
Amyloid-forming property of the N-terminal 1−70 residues of human apolipoprotein A-IV
Scientific Reports (2025)
