Supporting Information for Jankowski et al. 2024
Creators: name: Jankowski, Meaghan S.
name: Griffith, Daniel
name: Holehouse, Alex S.
name: Hurley, Jennifer M.
Publisher: name: Zenodo
Year: 2024

description: Supporting Information for Jankowski et al. 2024

Version 2: Uploaded 2024-03-07

Overview:

This repository contains additional information for the in press manuscript:

Disordered clock protein interactions and charge blocks turn an hourglass into a persistent circadian oscillator

Jankowski, M. S., Griffith, D., Shastry, D. G., Pelham, J. F., Ginell, G. M., Thomas, J., Karande, P., Holehouse, A. S., & Hurley, J. M. In Press at Nature Communications

Comparison with GitHub version

A "live" version of this data is available at https://github.com/holehouse-lab/supportingdata/tree/master/2024/jankowski_2024. There are two main differences between this Zenodo record and our GitHub repository:



The GitHub repository may be further updated with additional data if anyone has questions; this would be reflected in a CHANGELOG section in the root readme

The Zenodo record has the FULL set of all-atom simulations reported/analyzed in this paper shared as .xtc trajectory files, whereas for space reasons the GitHub version has the analysis used for figure making and sub-trajectories with 1000 conformers for each simulation. Specifically, the file simulations/jankowski_et_al_2024.zip contains all of the simulation trajectories used in this paper (ensembles with 12K-14K conformers per protein).


Other than that they should be identical.

Contents:



Jupyter notebook containing code to recreate certain manuscript figures (jankowski_et_al_computational_analyses_and_figures.ipynb)

/data folder containing various data files used for bioinformatic analysis

/simulations folder containing data and analysis for simulations, including scripts to generate all simulation-associated figures.

NB: In the Zenodo repository (but not on GitHub) the FULL set of all simulations is provided in simulations/jankowski_et_al_2024.zip


For more information on the files in this directory, please contact Alex or Dan. For information on the remainder of the paper, please contact Jen!

Reproducing analyses & figures:

Bioinformatics

The sequence and bioinformatic analyses in this manuscript were carried out using Python (version 3.8). To reproduce these analyses and figures download this entire repository, and open the Jupyter Notebook jankowski_et_al_computational_analyses_and_figures.ipynb. Then, run through the code sequentially, one cell at a time. Depending on how the repository was downloaded, you may need to update some of the file paths in the notebook to point to the files contained in the /data directory.

Simulations

The simulation analysis was run by performing all-atom Monte Carlo simulations using CAMPARI with the ABSINTH implicit solvent model. For more information on input files, see the readme file in this directory

Software requirements:

OS requirements

The sequence analyses have been tested on the following systems:



macOS: Big Sur (11.2.3), Monterey (12.2.1), Ventura (13.5.1) and Sonoma (14.3.1)

Linux: Ubuntu 18.04, Ubuntu 20.04, Ubuntu 22.04


Python dependencies

Analyses use standard Python scientific computing packages (specific versions are named in the jankowski_et_al_computational_analyses_and_figures.ipynb notebook:



numpy - installation guidelines

scipy - installation guidelines

pandas - installation guidelines

seaborn - installation guidelines

matplotlib - installation guidelines


Additionally, you will also need the protfasta, localCIDER and metapredict (version 2.2) packages. These can be installed using pip:



pip install protfasta
pip install localcider
pip install metapredict==2.2