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The dynamical interplay between a megadalton peptide nanocage and solutes probed by microsecond atomistic MD; Implications for design

Research output: Contribution to journalArticle

Original languageEnglish
Pages (from-to)137-147
Number of pages11
JournalPhysical Chemistry Chemical Physics
Volume21
Issue number1
Early online date28 Nov 2018
DOIs
DateAccepted/In press - 28 Nov 2018
DateE-pub ahead of print - 28 Nov 2018
DatePublished (current) - Jan 2019

Abstract

Understanding the assembly and dynamics of protein-based supramolecular capsids and cages is of fundamental importance and could lead to applications in synthetic biology and biotechnology. Here we present long and large atomistic molecular dynamics simulations of de novo designed self-assembling protein nanocages (SAGEs) in aqueous media. Microsecond simulations, comprised of ≈42 million atoms for three pre-formed SAGEs of different charges, in the presence of solutes and solvent have been completed. Here, the dynamics, stability and porosity of the peptide networks are explored along with their interactions with ions, small molecules and macromolecular solutes. All assemblies are stable over the μs timescale, and the solutes show a mixture of transport behaviour across or adherence to the fabric of the SAGE particles. Solute proteins largely retained native-like conformation on contact with SAGE. Certain residues of the SAGE peptides are identified as "repeat offenders" for contacting many different solutes, which suggest modifications to reduce non-specific binding. These studies highlight how molecular dynamics can aid the design process of SAGE and similar assemblies for potential applications as diverse as platforms for drug and vaccine delivery and nanoreactors to encapsulate enzyme pathways.

    Research areas

  • SYNTHETIC BIOLOGY

    Structured keywords

  • BrisSynBio
  • Bristol BioDesign Institute

Documents

Documents

  • Full-text PDF (accepted author manuscript)

    Rights statement: This is the author accepted manuscript (AAM). The final published version (version of record) is available online via RSC at https://pubs.rsc.org/en/Content/ArticleLanding/2019/CP/C8CP06282J#!divAbstract . Please refer to any applicable terms of use of the publisher.

    Accepted author manuscript, 2 MB, PDF document

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  • Supplementary information PDF

    Rights statement: This is the author accepted manuscript (AAM). The final published version (version of record) is available online via RSC at https://pubs.rsc.org/en/Content/ArticleLanding/2019/CP/C8CP06282J#!divAbstract . Please refer to any applicable terms of use of the publisher.

    Accepted author manuscript, 9 MB, PDF document

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  • Supplementary information AVI 1

    Accepted author manuscript, 4 MB, application/x-troff-msvideo

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  • Supplementary information AVI 2

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  • Supplementary information AVI 3

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  • Supplementary information AVI 4

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