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Study · Not a test of the peptide alone · 2023

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SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories.

de Bruyn E, Dorn AE, Zimmermann O, Rossetti G

Biology10 Apr 2023Cited by 2 (Europe PMC)

PMID37106781 (opens in a new tab)PMCIDPMC10135740 (opens in a new tab)DOI10.3390/biology12040581 (opens in a new tab)PepBankPUB-37106781
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Summary

The disordered nature of Intrinsically Disordered Proteins (IDPs) makes their structural ensembles particularly susceptible to changes in chemical environmental conditions, often leading to an alteration of their normal functions. A Radial Distribution Function (RDF) is considered a standard method for characterizing the chemical environment surrounding particles during atomistic simulations, commonly averaged over an entire or part of a trajectory. Given their high structural variability, such averaged information might not be reliable for IDPs. We introduce the Time-Resolved Radial Distribution Function (TRRDF), implemented in our open-source Python package SPEADI, which is able to characterize dynamic environments around IDPs. We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion-residue interactions play an important role in the structures and behaviors of IDPs.
CC BYText from Europe PMC. Highlighted sentences are the source of results.

Results from this study1

No result from this study comes from a test of the peptide.

Studies that did not test the peptide alone1

In this study, Humanin was a lab tool or a carrier, part of a mix, or the subject of a lab method. These results are not evidence about taking Humanin.

  1. 01Computer modelNot a test of Humanin aloneIn silicoMechanism

    In molecular dynamics simulations of Alpha-Synuclein and Humanin, local ion-residue interactions played an important role in the structures and behaviors of the proteins.

    In plain wordsIn computer simulations, ions near Humanin and Alpha-Synuclein played an important role in the structures and behaviors of these proteins.

    Peptide
    Humanin
    Outcome
    Not applicableIon-residue interactions in IDP structure (simulation)
    Study

    n: not reported in source

    Molecular dynamics simulations of Alpha-Synuclein and Humanin
    Outcome group
    Receptor activity and mechanism · Pharmacology

    Source sentences

    Summary
    We use SPEADI to characterize the dynamic distribution of ions around the IDPs Alpha-Synuclein (AS) and Humanin (HN) from Molecular Dynamics (MD) simulations, and some of their selected mutants, showing that local ion-residue interactions play an important role in the structures and behaviors of IDPs.

    In this study, Humanin was a lab tool or a carrier, part of a mix, or the subject of a lab method. This result is not evidence about taking Humanin.

AI wrote and checked these results. AI can make mistakes, so check important results against the source.

Version history

PepBank keeps every version of the data on this study. Status changes from Retraction Watch, Europe PMC and Crossref are listed with their source.

  1. Version 2Current

    13 Oct 2026, 21:44 UTC

    Study results updated

  2. Version 1

    13 Oct 2026, 16:31 UTC

    First added · source update from Europe PMC

Subjects

Terms as the source lists them.

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