Simulation data and scripts from: Catalytic triad-inspired nanozyme catalysts for ester hydrolysis in organic solvent mixtures
Data files
May 05, 2026 version files 192.14 GB
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Nanozymes.tar.gz
192.14 GB
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README.md
15.45 KB
Abstract
We synthesized a series of molecular nanozyme catalysts containing functional groups (imidazole, carboxylic acid, and hydroxyl groups) inspired by the catalytic triad found in natural serine hydrolases. Different structural features were incorporated using two distinct synthesis routes to investigate the influence of interactions beyond the active site on catalytic activity in designing molecular nanozymes. Molecular dynamics simulations suggest that nanozyme activity is affected by structural features that influence nanozyme hydrophilicity and the organization of the local solvent environment. The most active nanozyme showed activity comparable to the enzyme α-chymotrypsin for the hydrolysis of a model ester (4-nitrophenyl 4-hydroxybenzoate) in a 95:5 (v/v %) water/acetonitrile mixture at ambient temperature. Increasing the temperature and organic solvent content decreases the activity of α-chymotrypsin while enhancing the activity of the nanozymes. The nanozymes can be immobilized on supported metal nanoparticles using a dithiol self-assembled monolayer, which facilitates their removal from the post-reaction solution. These results demonstrate the potential in creating solvent-tolerant bio-inspired catalysts, thereby combining the advantages of biocatalysts and chemical catalysts as next-generation industrial catalysts.
Dataset DOI: 10.5061/dryad.r2280gbrg
Description of the data and file structure
This document includes processed data for the main simulation results in the paper "Catalytic Triad-Inspired Nanozyme Catalysts for Ester Hydrolysis in Organic Solvent Mixtures" as well as the input files and scripts required to reproduce the computational workflow and analyses.
Tarball includes README.sh with code to generate main text figures, perform data analysis, and run full independent replicates, and processed data files to reproduce main text figures.
Labels:
- NNZ01d: His-MAL-S-OH
- NNZ02d: His-MAL-SC6
- NNZ03d: FDM-His-MAL
- NNZ04d: FUR-His-MAL
- NNZ05: FDM-GA-MAL
- NNZ06d: His-MAL-S-PH
- NNZ08d: FDM-His-S-MAL
Files and variables
File: Nanozymes.tar.gz
Description: Contains data and scripts to reproduce figures from the main text. Contains files and scripts necessary to reproduce computational methods.
# Simulation data and scripts from: Catalytic Triad-Inspired Nanozyme Catalysts for Ester Hydrolysis in Organic Solvent Mixtures
#
# File type description:
# .gro (GRO): structure file used in GROMACS
# .itp (ITP): topology file used in GROMACS
# .prm (PRM): parameter file used in the CHARMM forcefield
# .dat (DAT): text file - here used to facilitate group selection in GROMACS
# .py (PY): Python file - here used to process simulation files, analyze data, and plot data
# .sh (SH): bash file - here used to run simulation workflows and analyses
#
# Nanozymes labels:
# NNZ01d: His-MAL-S-OH
# NNZ02d: His-MAL-S-C6
# NNZ03d: FDM-His-MAL
# NNZ04d: FUR-His-MAL
# NNZ05: FDM-GA-MAL
# NNZ06d: His-MAL-S-PH
# NNZ08d: FDM-His-S-MAL
#
# File structure:
# Nanozymes/
# |__ analysis_scripts/ : contains PY and SH scripts to analyze and plot data
# | |__ homogeneous_analyze_distances_imidazole-NHd_carboxylicAcid-O.py : python script to compute hydrogen bond distances for nanozymes
# | |__ homogeneous_analyze_distances_imidazole-NHd_carboxylicAcid-O.sh : bash script to run hydrogen bond distances analysis
# | |__ homogeneous_analyze_distances_imidazole-NHd_carboxylicAcid-O_PETase.py : python script to compute hydrogen bond distances for PETase
# | |__ homogeneous_analyze_gHyd.py : python script to compute preferential hydration
# | |__ homogeneous_analyze_sdf.sh : bash script to run spatial distribution function analysis
# | |__ homogeneous_plot_distances.py : python script to plot closed state probabilities (Figure 5A)
# | |__ homogeneous_plot_ghyd.py : python script to plot preferential hydration (Figure 6C)
# | |__ plot_distances_imidazole-NHd_carboxylicAcid-O_labeled.pdf : plot for closed state probabilities
# | |__ plot_distances_imidazole-NHd_carboxylicAcid-O_labeled.png : plot for closed state probabilities
# | |__ plot_gHyd_labeled_NNZ02d.pdf : plot for preferential hydration of NNZ02d nanozyme
# | |__ plot_gHyd_labeled_NNZ02d.png : plot for preferential hydration of NNZ02d nanozyme
# | |__ plot_gHyd_labeled_NNZ03d.pdf : plot for preferential hydration of NNZ03d nanozyme
# | |__ plot_gHyd_labeled_NNZ03d.png : plot for preferential hydration of NNZ03d nanozyme
# |__ inputs/ : contains input files for each simulation
# | |__ forcefields/ : contains forcefield files
# | |__ mdp/ : contains MDP parameter files to run simulations
# | |__ nanozymes/ : contains GRO, ITP, PRM, and DAT files for each nanozyme to run simulations
# | |__ python_scripts/ : contains PY files to make group selections and to extract specific timesteps for sequential simulations
# | |__ raw_files/ : contains raw files for each nanozyme and cosolvents: GRO, ITP, MOL2, PRM, STR, PDB
# | |__ solvents/ : contains GRO, ITP, PRM files for each cosolvent to run simulations - H2O uses forcfield parameters
# | |__ substrates/ : contains GRO, ITP, PRM, and DAT files for each substrate to run simulations
# |__ <Nanozyme label>/ : directory for each nanozyme
# | |__ 1-4NP4HB_<acetonitrile concentration>-ACN_0.125M-NaCl/ : directory for one molecule of 4NP4HB in % ACN and 0.125M NaCl
# | |__ <replicate number> : directory for the corresponding replicate
# | |__ input_files/ : contains input files required to run simulations
# | | |__ index.ndx : index file with groups for analysis
# | |__ ue/ : contains directories for each simulated window
# | |__ window_1/ : data for calculation of window trajectory
# | | |__ distances/ : data and rendered plot for computing data used in Figure 5A
# | | | |__ data_plot_imidazole-NHd_carboxylicAcid-O_probabilityClosed.pdf : distances histogram
# | | | |__ data_plot_imidazole-NHd_carboxylicAcid-O_probabilityClosed.png : distances histogram
# | | | |__ imidazole-NHd_carboxylicAcid-O_dist.xvg : distances data from GROMACS
# | | | |__ imidazole-NHd_carboxylicAcid-O_hist.xvg : histogram data from GROMACS
# | | | |__ pickle_data_imidazole-NHd_carboxylicAcid-O_probabilityClosed.p : data useed to compute state probabilities
# | | |__ sdf/ : VMD file and rendered simulation snapshots used in Figure 5C
# | | |__ prod.tpr : GROMACS run file
# | | |__ prod_centered.gro : GROMACS structure file
# | | |__ prod_centered.xtc : GROMACS trajectory file
# | |__ window_18/
# | |__ distances/ : data and rendered plot for computing data used in Figure 5A
# | | |__ data_plot_imidazole-NHd_carboxylicAcid-O_probabilityClosed.pdf : distances histogram
# | | |__ data_plot_imidazole-NHd_carboxylicAcid-O_probabilityClosed.png : distances histogram
# | | |__ imidazole-NHd_carboxylicAcid-O_dist.xvg : distances data from GROMACS
# | | |__ imidazole-NHd_carboxylicAcid-O_hist.xvg : histogram data from GROMACS
# | | |__ pickle_data_imidazole-NHd_carboxylicAcid-O_probabilityClosed.p : data useed to compute state probabilities
# | |__ sdf/ : VMD file and rendered simulation snapshots used in Figure 5C
# | |__ gHyd/ : contains pickle file with preferential hydration data - only for window_18/
# | |__ prod.tpr : GROMACS run file
# | |__ prod_centered.gro : GROMACS structure file
# | |__ prod_centered.xtc : GROMACS trajectory file
# |__ Validations/ : directory with PETase control simulations
# |__ PETase/ : directory for PETase simulation
# | |__ em/ : energy minimization
# | | |__ COLVAR.dat : COLVAR file with data from PLUMED
# | | |__ em.edr : GROMACS energy file
# | | |__ em.gro : GROMACS structure file
# | | |__ em.log : GROMACS log output file
# | | |__ em.tpr GROMACS run file
# | | |__ em.trr : GROMACS trajectory file
# | | |__ em_mdout.mdp : GROMACS parameter output file
# | |__ input_files/ : contains input files required to run simulations
# | | |__ em.mdp : GROMACS parameters for energy minimization
# | | |__ init.gro : GROMACS structure file (initial configuration)
# | | |__ npt.mdp : GROMACS parameters for NPT simulation
# | | |__ nvt.mdp : GROMACS parameters for NVT simulation
# | | |__ plumed.dat : PLUMED file for production simulation
# | | |__ plumed_em.dat : PLUMED file for energy minimization
# | | |__ template_em.mdp : GROMACS parameters for energy minimization (template)
# | | |__ template_npt.mdp : GROMACS parameters for NPT simulation ( template)
# | | |__ template_nvt.mdp : GROMACS parameters for NVT simulation (template)
# | | |__ template_prod.mdp : GROMACS parameters for production simulation (template)
# | | |__ topology.top : GROMACS topology file
# | |__ npt/ : NPT simulation
# | | |__ COLVAR.dat : COLVAR file with data from PLUMED
# | | |__ data_plot_imidazole-NHd_carboxylicAcid-O_probabilityClosed.pdf : distances histogram
# | | |__ data_plot_imidazole-NHd_carboxylicAcid-O_probabilityClosed.png : distances histogram
# | | |__ npt.cpt : GROMACS checkpoint file
# | | |__ npt.edr : GROMACS energy file
# | | |__ npt.gro : GROMACS structure file
# | | |__ npt.log : GROMACS log output file
# | | |__ npt.tpr : GROMACS run file
# | | |__ npt.xtc : GROMACS trajectory file
# | | |__ npt_mdout.mdp : GROMACS parameter output file
# | | |__ npt_prev.cpt : GROMACS checkpoint file (for previous simulation step)
# | | |__ pickle_data_imidazole-NHd_carboxylicAcid-O_probabilityClosed.p
# | |__ nvt/ : NVT simulation
# | |__ COLVAR.dat : COLVAR file with data from PLUMED
# | |__ nvt.cpt : GROMACS checkpoint file
# | |__ nvt.edr : GROMACS energy file
# | |__ nvt.gro : GROMACS structure file
# | |__ nvt.log : GROMACS log output file
# | |__ nvt.tpr : GROMACS run file
# | |__ nvt.xtc : GROMACS trajectory file
# | |__ nvt_mdout.mdp : GROMACS parameter output file
# |__ PETase_substrate/ : directory for PETase simulation
# |__ em/ : energy minimization
# | |__ COLVAR.dat : COLVAR file with data from PLUMED
# | |__ em.edr : GROMACS energy file
# | |__ em.gro : GROMACS structure file
# | |__ em.log : GROMACS log output file
# | |__ em.tpr GROMACS run file
# | |__ em.trr : GROMACS trajectory file
# | |__ em_mdout.mdp : GROMACS parameter output file
# |__ input_files/ : contains input files required to run simulations
# | |__ em.mdp : GROMACS parameters for energy minimization
# | |__ init.gro : GROMACS structure file (initial configuration)
# | |__ npt.mdp : GROMACS parameters for NPT simulation
# | |__ nvt.mdp : GROMACS parameters for NVT simulation
# | |__ plumed.dat : PLUMED file for production simulation
# | |__ plumed_em.dat : PLUMED file for energy minimization
# | |__ template_em.mdp : GROMACS parameters for energy minimization (template)
# | |__ template_npt.mdp : GROMACS parameters for NPT simulation ( template)
# | |__ template_nvt.mdp : GROMACS parameters for NVT simulation (template)
# | |__ template_prod.mdp : GROMACS parameters for production simulation (template)
# | |__ topology.top : GROMACS topology file
# |__ npt/ : NPT simulation
# | |__ COLVAR.dat : COLVAR file with data from PLUMED
# | |__ data_plot_imidazole-NHd_carboxylicAcid-O_probabilityClosed.pdf : distances histogram
# | |__ data_plot_imidazole-NHd_carboxylicAcid-O_probabilityClosed.png : distances histogram
# | |__ npt.cpt : GROMACS checkpoint file
# | |__ npt.edr : GROMACS energy file
# | |__ npt.gro : GROMACS structure file
# | |__ npt.log : GROMACS log output file
# | |__ npt.tpr : GROMACS run file
# | |__ npt.xtc : GROMACS trajectory file
# | |__ npt_mdout.mdp : GROMACS parameter output file
# | |__ npt_prev.cpt : GROMACS checkpoint file (for previous simulation step)
# | |__ pickle_data_imidazole-NHd_carboxylicAcid-O_probabilityClosed.p
# | |__ state_npt_2118.png : simulation snapshot
# | |__ state_npt_2118.vmd : simulation snapshot VMD state file
# |__ nvt/ : NVT simulation
# |__ COLVAR.dat : COLVAR file with data from PLUMED
# |__ nvt.cpt : GROMACS checkpoint file
# |__ nvt.edr : GROMACS energy file
# |__ nvt.gro : GROMACS structure file
# |__ nvt.log : GROMACS log output file
# |__ nvt.tpr : GROMACS run file
# |__ nvt.xtc : GROMACS trajectory file
# |__ nvt_mdout.mdp : GROMACS parameter output file
USAGE:
# Untar files
tar -xzvf Nanozymes.tar.gz
#############################
##### SECTION I #####
##### REPRODUCE FIGURES #####
#############################
cd Nanozymes/analysis_scripts
# Figure 5A
python3.10 homogeneous_plot_distances.py 4NP4HB 1 NaCl 125 ACN 50 2.0 0.3 NNZ04d NNZ02d NNZ03d NNZ08d NNZ01d NNZ06d
# Figure 6C
for NNZ in NNZ02d NNZ03d; do
python3.10 homogeneous_plot_ghyd.py $NNZ 4NP4HB 1 NaCl 125 0.3 ACN 50 25
done
#########################
##### SECTION II #####
##### DATA ANALYSIS #####
#########################
# Note: bash scripts overwrite existing analysis folders
cd Nanozymes/analysis_scripts
# GROMACS analysis of NHd-O P_closed/distances for nanozyme simulations
# Note: for data management purposes, only relevant windows are included: 2.0 nm and 0.3 nm (windows 1 and 18, respectively)
for NNZ in NNZ01d NNZ02d NNZ3d NNZ04d NNZ06d NNZ08d; do
for ACN in 50; do
for REP in rep_0 rep_1 rep_2 rep_3 rep_4 rep_5 ; do
for WINDOW in 1 18; do
bash homogeneous_analyze_distances_imidazole-NHd_carboxylicAcid-O.sh $NNZ 4NP4HB 1 ACN $ACN NaCl 125 $REP window_$WINDOW
done
done
done
done
# Python analysis of NHd-O P_closed/distances for nanozyme simulations
for NNZ in NNZ01d NNZ02d NNZ3d NNZ04d NNZ06d NNZ08d; do
for ACN in 50; do
for REP in rep_0 rep_1 rep_2 rep_3 rep_4 rep_5; do
for DIST in 2.0 0.3; do
python3.10 homogeneous_analyze_distances_imidazole-NHd_carboxylicAcid-O.py $NNZ 4NP4HB 1 ACN $ACN NaCl 125 $DIST $REP
done
done
done
done
# Python analysis of NHd-O P_closed/distances for PETase simulations
for SYS in PETase PETase_substrate; do
python3.10 homogeneous_analyze_distances_imidazole-NHd_carboxylicAcid-O_PETase.py $SYS
done
# Repeat SECTION I - Figure 3B
# GROMACS analysis of spatial distribution functions for nanozymes
for NNZ in NNZ01d NNZ02d NNZ03d NNZ04d NNZ05 NNZ06d NNZ08d; do
for ACN in 50; do
for REP in rep_0 rep_1 rep_2 rep_3 rep_4 rep_5; do
for WINDOW in 18; do
bash homogeneous_analyze_sdf.sh $NNZ 4NP4HB 1 ACN $ACN NaCl 125 $REP window_$WINDOW
done
done
done
done
# Python analysis of gHyd for nanozymes
for NNZ in NNZ02d NNZ03d; do
for ACN in 50 25; do
for REP in rep_0 rep_1 rep_2 rep_3 rep_4 rep_5; do
python3.10 homogeneous_analyze_gHyd.py $NNZ 4NP4HB 1 ACN $ACN NaCl 125 0.3 $REP
done
done
done
# Repeat SECTION I - Figure 4C
# At this point, all simulation figures from the main text should have been generated.
##############################
##### SECTION III #####
##### REPRODUCE WORKFLOW #####
##############################
# Prepare simulation files
cd Nanozymes/scripts/
bash homogeneous_prep_files.sh NNZ02d 4NP4HB 1 ACN 50 NaCl 125 rep_6
cd ../NNZ02d/1-4NP4HB_0.500-ACN_0.125M-NaCl/rep_6
# Run NVT, NPT, and PROD
bash homogeneous_run_nvt.sh
bash homogeneous_run_npt.sh
bash homogeneous_run_prod.sh
# Run umbrella evolution simulations
cd ../../../scripts/
bash homogeneous_run_ue.sh NNZ02d 4NP4HB 1 ACN 50 NaCl 125 rep_6
# Repeat SECTION II for analyses