Electronic Notebook: Charge Regulation During Amyloid Formation of α-synuclein

This repository contains electronic notebooks for reproducing the simulation results presented in the above manuscript, published in the Journal of the American Chemical Society, 2021 [doi:10.1021/jacs.1c01925].

Layout

Each directory listed below contains simulation output of α-synuclein as a monomer and as a decamer, together with Jupyter Notebooks (*.ipynb) for reproducing analysis and figures presented in the publication.

• wildtype-0mM/ - α-synuclein wildtype, no salt
• wildtype-15mM/ - α-synuclein wildtype, 15 mM salt
• mutant_5Q-0mM/ - α-synuclein 5Q mutant, no salt
• extract-nmr-data/ - Notebook for extracting data NMR data
• faunus-source/ - C++ source of the MC simulation software (Faunus 2.4.1, git patch 075bf8de)

Requirements

To run the Notebooks online, click on the Launch Binder logo above. Alternatively, if you want to run on your own computer, install python via e.g. Miniconda or Anaconda and make sure all required packages are loaded by issuing the following terminal commands

    conda env create -f environment.yml
    source activate asyntitr
    jupyter-notebook