Distinct roles of monosaccharides in the inhibition of the Carbohydrate-Binding Module and Catalytic Domain of Cel7A

Supplementary data files for the article Description This repository contains the underlying data and computational workflow for the paper: "Distinct roles of monosaccharides in the inhibition of the Carbohydrate-Binding Module and Catalytic Domain of Cel7A". The dataset provides molecular-level insights into how glucose, mannose, and xylose modulate the structural and solvation properties of the Trichoderma reesei Cel7A cellulase. Main Contents ff.zip: Force field parameters for the CBM and CD domains, and the sugars (glucose, mannose, and xylose). mdp_files.zip: GROMACS simulation parameters (Minimization, NVT, NPT, and Production MD). pdbs.zip: Initial PDB structures for all simulated components. scripts.zip: - packmolinputcreator_*.jl: Julia scripts to generate Packmol input files for various concentrations. - run_folder.sh: Bash script to automate directory creation containing files for MD simulations in GROMACS. - cm_*.jl: Scripts to calculate solvation properties using ComplexMixtures.jl. - plot*.jl: Julia scripts used to generate the figures presented in the paper. --- Solvation Analysis (ComplexMixtures.jl) Located in the CBM_ComplexMixtures_*.zip and CD_ComplexMixtures_*.zip files. Each output includes Minimum Distance Distribution Functions (MDDFs), Residue Contributions to the Distribution Functions, Coordination Numbers, and Kirkwood-Buff Integrals (KBI). Format: .json files. Loading: Data should be loaded in Julia via ComplexMixtures.load("file.json"). Naming Convention: Files with the Water identifier treat water as the solvent. Files without it consider the cosolute (glucose, mannose, or xylose) as the solvent. Structural Properties Analysis Located in the CD_structural_properties_*.zip files. All properties are pooled or averaged across 5 replicas per system. RMSD (B3 loop): Values in Ångströms (Å). Data includes 25,000 values extracted from the production trajectories. RMSF: Values in Ångströms (Å). - Column 1: Residue ID. - Column 2: RMSF value. Secondary Structure (average_ss*): - Column 1: Residue ID. - Column 2: $\beta$-sheet content (fraction). - Column 3: $\alpha$-helix content (fraction). Surface Area (average_wasa*): Water Accessible Surface Area (WASA, in Ų) for every atom of the CD domain. - Column 1: Atom Index (matches the provided PDB files). - Column 2: WASA value. Representative Structures: rep_cd_ensemble* files provide CD representative structures in C-$\alpha$ graining (see Figure 5B). --- Usage & Reproducibility To replicate the simulation setup and analysis environment: 1. System Setup: bash ./run_folder.sh <cosolvent> <concentration> <replica> <protein> 2. Environment: The scripts/ folder contains Project.toml and Manifest.toml. To instantiate the exact Julia environment used: julia using Pkg; Pkg.activate("scripts"); Pkg.instantiate() Version Control: Continual updates and source code maintenance are available at: https://github.com/ander-f/Cel7A_Inhibition_MD