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Exploring the locking stage of NFGAILS amyloid fibrillation via transition manifold analysis

Author

Listed:
  • Andreas Bittracher

    (Freie Universität Berlin)

  • Johann Moschner

    (Freie Universität Berlin)

  • Beate Koksch

    (Freie Universität Berlin)

  • Roland Netz

    (Freie Universität Berlin)

  • Christof Schütte

    (Freie Universität Berlin
    Zuse Institute Berlin)

Abstract

We demonstrate the application of the transition manifold framework to the late-stage fibrillation process of the NFGAILS peptide, a amyloidogenic fragment of the human islet amyloid polypeptide (hIAPP). This framework formulates machine learning methods for the analysis of multi-scale stochastic systems from short, massively parallel molecular dynamical simulations. We identify key intermediate states and dominant pathways of the process. Furthermore, we identify the optimally timescale-preserving reaction coordinate for the dock-lock process to a fixed pre-formed fibril and show that it exhibits strong correlation with the mean native hydrogen-bond distance. These results pave the way for a comprehensive model reduction and multi-scale analysis of amyloid fibrillation processes. Graphic Abstract

Suggested Citation

  • Andreas Bittracher & Johann Moschner & Beate Koksch & Roland Netz & Christof Schütte, 2021. "Exploring the locking stage of NFGAILS amyloid fibrillation via transition manifold analysis," The European Physical Journal B: Condensed Matter and Complex Systems, Springer;EDP Sciences, vol. 94(10), pages 1-12, October.
    • Handle: RePEc:spr:eurphb:v:94:y:2021:i:10:d:10.1140_epjb_s10051-021-00200-0
    DOI: 10.1140/epjb/s10051-021-00200-0
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    References listed on IDEAS

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    1. Michael R. Sawaya & Shilpa Sambashivan & Rebecca Nelson & Magdalena I. Ivanova & Stuart A. Sievers & Marcin I. Apostol & Michael J. Thompson & Melinda Balbirnie & Jed J. W. Wiltzius & Heather T. McFar, 2007. "Atomic structures of amyloid cross-β spines reveal varied steric zippers," Nature, Nature, vol. 447(7143), pages 453-457, May.
    2. J. Kruskal, 1964. "Nonmetric multidimensional scaling: A numerical method," Psychometrika, Springer;The Psychometric Society, vol. 29(2), pages 115-129, June.
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