DOI: 10.5281/zenodo.7929606
title: Impact of water models on structure and dynamics of ligand-transport tunnels in enzymes derived from molecular dynamics simulations

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 representative structures from TTCLust for selected replicas 3x LinBwt, 2x LinB32-closed, 2x LinB32-open, 2x LinB86-closed and 2x LinB86-open plain text and PDB formatted 5-tunnel_networks-linbwt.tar.gz results of tunnel analyses for three replicas of LinBwt in OPC and TIP3P generated by CAVER 3.0 comprising tunnel profiles (tunnel_profiles.csv) and bottlenecks residues (bottlenecks.csv) for each tunnel cluster, as well as an overall summary of cluster characteristics (summary.txt) plain text formatted 5-tunnel_networks-linb32-closed.tar.gz results of tunnel analyses for two replicas of closed state LinB32 in OPC and TIP3P generated by CAVER 3.0 comprising tunnel profiles (tunnel_profiles.csv) and bottlenecks residues (bottlenecks.csv) for each tunnel cluster, as well as an overall summary of cluster characteristics (summary.txt) plain text formatted 5-tunnel_networks-linb32-open.tar.gz results of tunnel analyses for two replicas of open state LinB32 in OPC and TIP3P generated by CAVER 3.0 comprising tunnel profiles (tunnel_profiles.csv) and bottlenecks residues (bottlenecks.csv) for each tunnel cluster, as well as an overall summary of cluster characteristics (summary.txt) plain text formatted 5-tunnel_networks-linb86-closed.tar.gz results of tunnel analyses for two replicas of closed state LinB86 in OPC and TIP3P generated by CAVER 3.0 comprising tunnel profiles (tunnel_profiles.csv) and bottlenecks residues (bottlenecks.csv) for each tunnel cluster, as well as an overall summary of cluster characteristics (summary.txt) plain text formatted 5-tunnel_networks-linb86-open.tar.gz results of tunnel analyses for two replicas of open state LinB86 in OPC and TIP3P generated by CAVER 3.0 comprising tunnel profiles (tunnel_profiles.csv) and bottlenecks residues (bottlenecks.csv) for each tunnel cluster, as well as an overall summary of cluster characteristics (summary.txt) plain text formatted 6-representative_tunnels.tar.gz data for visualization of representative tunnels named as p1b, p1a, p2a, p2b, p2c, p3 generated by TransportTools library 0.9.5 for selected replicas 3x LinBwt, 2x LinB32-closed, 2x LinB32-open, 2x LinB86-closed and 2x LinB86-open PDB formatted data with Pymol-based visualization scripts in Python 3.8 or higher
description: This work was supported by the National Science Centre, Poland (grant no. 2017/26/E/NZ1/00548) and ERDF postdoc grant (no.1.1.1.2/VIAA/4/20/757). The computations were performed at the Poznan Supercomputing and Networking Center.