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

Andreas Bittracher (), Johann Moschner, Beate Koksch, Roland Netz and Christof Schütte
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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

The European Physical Journal B: Condensed Matter and Complex Systems, 2021, vol. 94, issue 10, 1-12

Abstract: 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

Date: 2021
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DOI: 10.1140/epjb/s10051-021-00200-0

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