DOI: 10.5281/zenodo.13767740
title: Impact of water models on structure and dynamics of enzyme tunnels

description: 1-initial_topologies_coordinates.tar.gz



primary input coordinates and parameter-topology files of all initial systems (LinBwt, LinB32, and Linb86 variants of haloalkane dehalogenase) in OPC and TIP3P water models

prepared with the tleap module of AMBER18 package

parm7 and crd formatted



2-cap_domain_gate_distances.tar.gz



datasets with minimum distance calculation between Asp146 and Leu176

calculated by CPPTRAJ module of AMBER 18 for each performed simulation

plain text formatted



3-protein_trajectories-linbwt.tar.gz



three replicated 400 ns (20,000 frames, i.e., every second frame) dry production phase trajectories of LinBwt in OPC and Tip3P water models with corresponding parameter-topology files

produced by pmemd.cuda module of AMBER 18

netcdf and parm7 formatted



3-protein_trajectories-linb32-closed.tar.gz



two replicated 400 ns (20,000 frames, i.e., every second frame) dry production phase trajectories of closed state LinB32 in OPC and Tip3P water models with corresponding parameter-topology files

produced by pmemd.cuda module of AMBER 18

netcdf and parm7 formatted



3-protein_trajectories-linb32-open.tar.gz



two replicated 400 ns (20,000 frames, i.e., every second frame) dry production phase trajectories of open state LinB32 in OPC and Tip3P water models with corresponding parameter-topology files

produced by pmemd.cuda module of AMBER 18

netcdf and parm7 formatted



3-protein_trajectories-linb86-closed.tar.gz



 two replicated 400 ns (20,000 frames, i.e., every second frame) dry production phase trajectories of closed state LinB86 in OPC and Tip3P water models with corresponding parameter-topology files

produced by pmemd.cuda module of AMBER 18

netcdf and parm7 formatted



3-protein_trajectories-linb86-open.tar.gz



two replicated 400 ns (20,000 frames, i.e., every second frame) dry production phase trajectories of open state LinB86 in OPC and Tip3P water models with corresponding parameter-topology files

produced by pmemd.cuda module of AMBER 18

netcdf and parm7 formatted



4-basic_analyses.tar.gz



datasets on RMSF, RMSD, RoG, and RDF from the CPPTRAJ module of AMBER 18

for selected replicas 3x LinBwt, 2x LinB32-closed, 2x LinB32-open, 2x LinB86-closed and 2x LinB86-open

plain text and PDB formatted



5-caver_analyses.tar.gz



results of tunnel analyses for two replicas of open & closed state each for LinB32 & LinB86 in OPC and TIP3P, and three replicas of LinBWT in OPC and TIP3P

generated by CAVER 3.0 using "Divide-and-conquer approach" (MethodsX, 10, 2023, 101968)

comprising csv and pdb formatted: tunnel_profiles.csv and bottlenecks.csv, stripped_system.10001.pdb, v_origins.pdb

For this and following analyses, the names of the trajectories were modified as follows:



linbwt_opc1_2 = md1_opc_linbwt; linbwt_opc2_2 = md2_opc_linbwt; linbwt_opc3_2 = md3_opc_linbwt;

linbwt_tip3p1_2 = md1_tip3p_linbwt; linbwt_tip3p2_2 = md2_tip3p_linbwt; linbwt_tip3p3_2 = md3_tip3p_linbwt;

linb32-closed_opc1_2 = md1_closed_opc_linb32; linb32-closed_opc2_2 = md2_closed_opc_linb32;

linb32-open_opc1_2 = md1_open_opc_linb32; linb32-open_opc2_2 = md2_open_opc_linb32;

linb32-closed_tip3p1_2 = md1_closed_tip3p_linb32; linb32-closed_tip3p2_2 = md2_closed_tip3p_linb32;

linb32-open_tip3p1_2 = md1_open_tip3p_linb32; linb32-open_tip3p2_2 = md2_open_tip3p_linb32;

linb86-closed_opc1_2 = md1_closed_opc_linb86; linb86-closed_opc2_2 = md2_closed_opc_linb86;

linb86-open_opc1_2 = md1_open_opc_linb86; linb86-open_opc2_2 = md2_open_opc_linb86;

linb86-closed_tip3p1_2 = md1_closed_tip3p_linb86; linb86-closed_tip3p2_2 = md2_closed_tip3p_linb86;

linb86-open_tip3p1_2 = md1_open_tip3p_linb86; linb86-open_tip3p2_2 = md2_open_tip3p_linb86.





6-transport_tools_analyses.tar.gz



results of comparative analyses for all simulations generated in 5-caver_analyses.tar.gz

generated by TransportTools 0.9.3

comprising csv, pdb, plain text and py formatted: configuration file (config_TT.ini), tunnel_profiles (data folder) for all filtered tunnels and bottlenecks (data folder) for all filtered tunnels, statistics (statistics folder) and visualization (visualization folder)        




 

 

 

 

 
description: This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548) and ANM postdoc grant (no. ANM_OSI_PG_65). The computations were performed at the Poznan Supercomputing and Networking Center.