HydrTDependenceAmFibrils

Data and scripts to generate the figures in the manuscript on the hydrophobic temperature dependence of amyloid fibril formation.

Code for the simulation

Link to the source code of the model simulations: https://bitbucket.org/abeln/amyloid_hydrophobe/src/master/

Scripts and data for simulation analysis

The figures showing the analysis results of the simulations were generated with R scripts (version 3.5.2). If you run them, make sure to modify the directory names in 'setDataSources.R'. Also modify the location of the data files ('/path/dataframesEnthaly_....Rdata') in each of the scripts.

• Figure 3: ManuscriptFiguresSA_ac_b.R
• Figure 4: HeatMap_SA.R
• Figure S1: PaggrFiguresSA.R
• Figure S2 + S3: SuppFiguresSA.R

Scripts and data for experimental analysis

The figures showing the analysis results of the experiments were generated with Python scripts (version 2.7.15). Because for most figures multiple data files and/or scripts were used, these are organized per folder.

• Figure 5a: gamma: calculate_ASA.py -> fit_stats_onefig.py
• Figure 5b: gamma: plot_gamma.py (takes output from fit_stats_onefig.py as input) + barplot_ASA.py
• Figure 6: ionic_strength: ions_urea.py
• Figure S4: ITC_asyn_mf_raw: plot_ITC_raw_data.py
• Figure S6: depolymerisation: plot_glu_alac_depol.py
• Figure S7: GNNQQNY: plot_gnnqqny.py
• Figure S8: fluorescence: plot_fluorescence_spectra.py
• Figure S9: equilibration: fitting_g_340_330.py