This repository contains code, analysis scripts, a pulse sequence, and input files to recreate all figures for the manuscript entitled "Extreme dynamics of a small molecule in its bound state with an intrinsically disordered protein" by Heller, Shukla, Figueiredo, and Hansen.
- Bruker pulse sequence for the pseudo-2D ligand-detected transverse (spin-spin, R2,eff) relaxation experiment in pulse_sequence/
- Jupyter Notebook and code to create plots of 1D ligand-detected chemical shift data (19F and 1H NMR) in 1H_1D/ and 19F_1D/
- Jupyter Notebook and code to create plots of pseudo-2D ligand-detected longitudinal (spin-lattice, R1,eff) relaxation (19F NMR) in 19F_R1eff/
- Jupyter Notebook and code to create plots of pseudo-2D ligand-detected transverse (spin-spin, R2,eff) relaxation (19F NMR) in 19F_R2eff/
- Jupyter Notebook and code to create plots of pseudo-2D Diffusion Ordered SpectroscopY (DOSY) (1H NMR) in 1H_DOSY/
- Jupyter Notebook to create plots of CD data in CD/
- Scripts for the simultaneous analysis of 19F chemical shifts, DOSY, R1,eff, and R2,eff data in the context of rotational correlation times (tau_c) in tau_c_fit/
Experimental data, including nuclear magnetic resonance (NMR) spectroscopy data files (.ft2 format) and circular dichroism (CD) data files (.txt format), should first be downloaded from Zenodo: https://zenodo.org/record/7892349#.ZFKIaezMIUp and placed in a directory called 'Data' in the same directory as this README.md file.
Jupyter Notebook directories 2-6 (above) are independent and self-contained. Executing all cells in 19F_1D/ 19F_R1eff/ 19F_R2eff/ will output dictionaries containing data to various json files in json/. Executing json/write_file.ipynb will combine these data into an input data file for the tau_c_fit here: tau_c_fit/data.inp.
The script has been written and tested with the above dependencies. Performance with other module versions has not been tested.