19F NMR Analysis of SARS-CoV-2 3CLpro Inhibitor Dynamics

This repository contains the data, scripts, and analysis workflows for characterizing the conformational dynamics of SARS-CoV-2 3CLpro (Main Protease) in complex with the inhibitors Nirmatrelvir and Ensitrelvir.

By employing 19F NMR line-shape analysis and EXSY spectroscopy, we quantify the thermodynamic and kinetic parameters governing the equilibrium between distinct conformational states of the enzyme-inhibitor complexes.

📂 Repository Structure

The analysis is organized into a chronological experimental workflow. Each experiment sub-directory follows a standardized layout to ensure script portability:

raw_bruker/: Contains original data and TopSpin ASCII exports (asci_*.txt) organized by instrument and date.
processed_ascii/: Stores standardized two-column .dat files (Hz_centered and intensity) generated by conversion scripts.
scripts/: Houses Python workflows for data conversion, global fitting, and figure generation.
figures/: Publication-quality plots exported directly from the analysis scripts.

💊 MPro + Nirmatrelvir

01_1D_19F_titration: Binding stoichiometry and equilibrium at 298 K.
02_1D_19F_VT: Variable-temperature line-shape analysis (283–318 K). Includes multi-field global fitting (600/800 MHz) to Eyring and van't Hoff models.
03_2D_EXSY: 2D Exchange Spectroscopy data confirming the exchange topology.
04_C145A_1D_19F_298K: Mutant validation of conformational equilibrium at 298 K using catalytically inactive C145A.

💊 MPro + Ensitrelvir

01_1D_19F_VT: Comparative VT-NMR analysis (600 MHz) including high-sensitivity "long" acquisition 1D experiments.

🛠️ Data Conversion Workflow

To maintain reproducibility across different spectrometers and field strengths, we use standardized conversion scripts (e.g., 01_bruker_ascii_to_dat.py):

Normalization: Reads Bruker ASCII headers to identify the spectral region (PPM) and point count (SIZE).
Trimming: Automatically handles Bruker export point-count quirks (e.g., trimming N+1 points to N).
Standardization: Converts the PPM axis to a centered frequency axis (Hz) using the specific spectrometer SFO1 frequency to facilitate multi-field global fitting.

🧪 Experimental Notes

Spectrometers: Bruker NEO 600 MHz (SFO1 ~564.588 MHz) and 800 MHz (SFO1 ~752.843 MHz).
Standard Sizes: Point counts are experiment-specific (e.g., 16,283 for Nirmatrelvir VT, 20,840 for C145A, and 172,881 for Ensitrelvir Long-1D).

License

RPIBioinformatics/3CLpro-inhibitor-dynamics-19F_analysis

About

Resources

License

Uh oh!

Stars

Watchers

Forks

Releases

Packages 0

Uh oh!

Contributors 1

Languages

Packages