IDEAS home Printed from https://ideas.repec.org/a/spr/eurphb/v94y2021i10d10.1140_epjb_s10051-021-00200-0.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1140/epjb/s10051-021-00200-0
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.

    File URL: https://libkey.io/10.1140/epjb/s10051-021-00200-0?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Beniaich, Adnane & Guimarães, Danielle Vieira & Avanzi, Junior Cesar & Silva, Bruno Montoani & Acuña-Guzman, Salvador Francisco & dos Santos, Wharley Pereira & Silva, Marx Leandro Naves, 2023. "Spontaneous vegetation as an alternative to cover crops in olive orchards reduces water erosion and improves soil physical properties under tropical conditions," Agricultural Water Management, Elsevier, vol. 279(C).
    2. Giuseppe Arbia & Giovanni Lafratta, 2002. "Anisotropic spatial sampling designs for urban pollution," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 51(2), pages 223-234, May.
    3. Samuel Shye, 2010. "The Motivation to Volunteer: A Systemic Quality of Life Theory," Social Indicators Research: An International and Interdisciplinary Journal for Quality-of-Life Measurement, Springer, vol. 98(2), pages 183-200, September.
    4. Muñoz-Mas, Rafael & Vezza, Paolo & Alcaraz-Hernández, Juan Diego & Martínez-Capel, Francisco, 2016. "Risk of invasion predicted with support vector machines: A case study on northern pike (Esox Lucius, L.) and bleak (Alburnus alburnus, L.)," Ecological Modelling, Elsevier, vol. 342(C), pages 123-134.
    5. la Grange, Anthony & le Roux, Niël & Gardner-Lubbe, Sugnet, 2009. "BiplotGUI: Interactive Biplots in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 30(i12).
    6. Simensen, Trond & Halvorsen, Rune & Erikstad, Lars, 2018. "Methods for landscape characterisation and mapping: A systematic review," Land Use Policy, Elsevier, vol. 75(C), pages 557-569.
    7. Silvia Vilčeková & Ilija Zoran Apostoloski & Ľudmila Mečiarová & Eva Krídlová Burdová & Jozef Kiseľák, 2017. "Investigation of Indoor Air Quality in Houses of Macedonia," IJERPH, MDPI, vol. 14(1), pages 1-12, January.
    8. Funk, Patrick & Davis, Alex & Vaishnav, Parth & Dewitt, Barry & Fuchs, Erica, 2020. "Individual inconsistency and aggregate rationality: Overcoming inconsistencies in expert judgment at the technical frontier," Technological Forecasting and Social Change, Elsevier, vol. 155(C).
    9. Moris Triventi, 2014. "Higher education regimes: an empirical classification of higher education systems and its relationship with student accessibility," Quality & Quantity: International Journal of Methodology, Springer, vol. 48(3), pages 1685-1703, May.
    10. Jessica Dafflon & Pedro F. Da Costa & František Váša & Ricardo Pio Monti & Danilo Bzdok & Peter J. Hellyer & Federico Turkheimer & Jonathan Smallwood & Emily Jones & Robert Leech, 2022. "A guided multiverse study of neuroimaging analyses," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    11. Karim Abou-Moustafa & Frank P. Ferrie, 2018. "Local generalized quadratic distance metrics: application to the k-nearest neighbors classifier," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 12(2), pages 341-363, June.
    12. Camacho, Maximo & Perez-Quiros, Gabriel & Saiz, Lorena, 2006. "Are European business cycles close enough to be just one?," Journal of Economic Dynamics and Control, Elsevier, vol. 30(9-10), pages 1687-1706.
    13. Mingxu Zhao & Nalaka Geekiyanage & Jianchu Xu & Myo Myo Khin & Dian Ridwan Nurdiana & Ekananda Paudel & Rhett Daniel Harrison, 2015. "Structure of the Epiphyte Community in a Tropical Montane Forest in SW China," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-19, April.
    14. Willem Heiser, 1991. "A generalized majorization method for least souares multidimensional scaling of pseudodistances that may be negative," Psychometrika, Springer;The Psychometric Society, vol. 56(1), pages 7-27, March.
    15. Luís Francisco Aguiar & Pedro C. Magalhães & Maria Joana Soares, 2010. "Synchronism in Electoral Cycles: How United are the United States?," NIPE Working Papers 17/2010, NIPE - Universidade do Minho.
    16. Janghyeok Yoon & Kwangsoo Kim, 2012. "Detecting signals of new technological opportunities using semantic patent analysis and outlier detection," Scientometrics, Springer;Akadémiai Kiadó, vol. 90(2), pages 445-461, February.
    17. Kennen, Jonathan G. & Kauffman, Leon J. & Ayers, Mark A. & Wolock, David M. & Colarullo, Susan J., 2008. "Use of an integrated flow model to estimate ecologically relevant hydrologic characteristics at stream biomonitoring sites," Ecological Modelling, Elsevier, vol. 211(1), pages 57-76.
    18. Sagarra, Marti & Mar-Molinero, Cecilio & Agasisti, Tommaso, 2017. "Exploring the efficiency of Mexican universities: Integrating Data Envelopment Analysis and Multidimensional Scaling," Omega, Elsevier, vol. 67(C), pages 123-133.
    19. José Luis Ortega Priego, 2003. "A Vector Space Model as a methodological approach to the Triple Helix dimensionality: A comparative study of Biology and Biomedicine Centres of two European National Research Councils from a Webometri," Scientometrics, Springer;Akadémiai Kiadó, vol. 58(2), pages 429-443, October.
    20. Jacques de Wet & Daniela Wetzelhütter & Johann Bacher, 2021. "Standardising the reproduction of Schwartz’s two-dimensional value space using multi-dimensional scaling and goodness-of-fit test procedures," Quality & Quantity: International Journal of Methodology, Springer, vol. 55(4), pages 1155-1179, August.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:spr:eurphb:v:94:y:2021:i:10:d:10.1140_epjb_s10051-021-00200-0. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.