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Molecular dynamics investigation of halogenated amyloidogenic peptides

  • Alfonso GautieriEmail author
  • Alberto Milani
  • Andrea Pizzi
  • Federica Rigoldi
  • Alberto Redaelli
  • Pierangelo MetrangoloEmail author
Original Paper
Part of the following topical collections:
  1. Tim Clark 70th Birthday Festschrift

Abstract

Besides their biomolecular relevance, amyloids, generated by the self-assembly of peptides and proteins, are highly organized structures useful for nanotechnology applications. The introduction of halogen atoms in these peptides, and thus the possible formation of halogen bonds, allows further possibilities to finely tune the amyloid nanostructure. In this work, we performed molecular dynamics simulations on different halogenated derivatives of the β-amyloid peptide core-sequence KLVFF, by using a modified AMBER force field in which the σ-hole located on the halogen atom is modeled with a positively charged extra particle. The analysis of equilibrated structures shows good agreement with crystallographic data and experimental results, in particular concerning the formation of halogen bonds and the stability of the supramolecular structures. The modified force field described here allows describing the atomistic details contributing to peptides aggregation, with particular focus on the role of halogen bonds. This framework can potentially help the design of novel halogenated peptides with desired aggregation propensity.

Graphical abstract

Molecular dynamics investigation of halogenated amyloidogenic peptides

Keywords

Amyloid Peptide Self-assembly Halogen bond Molecular dynamics 

Notes

Acknowledgments

The authors wish to thank Fondazione Cariplo (grant no. 2016-0481) and the H2020 EU Project AMMODIT (grant no. 645672) for funding. P.M. wishes to acknowledge the ERC for funding the project FOLDHALO (grant no. 307108) and MINIRES (grant no. 789815).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

894_2019_4012_MOESM1_ESM.docx (3.4 mb)
ESM 1 (DOCX 3492 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Biomolecular Engineering Laboratory, Dipartimento di Elettronica, Informazione e BioingegneriaPolitecnico di MilanoMilanItaly
  2. 2.Dipartimento di EnergiaPolitecnico di MilanoMilanItaly
  3. 3.Dipartimento di Chimica, Materiali ed Ingegneria Chimica “Giulio Natta”Politecnico di MilanoMilanItaly

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