Supporting Data: Exploring the Molecular Mechanisms of Nanoplastic Interactions with Blood Proteins by Molecular Dynamics and Docking Simulations

This dataset provides the structure and interface data supporting the study of nanoplastic particle (PE, PP, PS, PET, PVC, PEG) interactions with Human Serum Albumin (HSA), Transthyretin (TTR), Aβ1−40 , and α-Synuclein (α-Syn) as described in the associated manuscript.

Methods Summary:

Simulations were performed using GROMACS 2024.2 and the CHARMM36m force field. Polymer particles were generated using the CHARMM-GUI Polymer Builder.  Molecular Docking simulations were perfromed using the HDOCK webserver with Binding Free Energies calculated by gmx_MMPBSA.

Contents include:

01_Relaxed_Proteins: Average structures of proteins retrieved from 100 ns relaxation simulations and RMSD-based clustering.

02_Polymer_Topologies: Initial all-atom coordinates for multi-chain polymer particles (PE, PP, PS, PET, PVC, PEG), including CHARMM-GUI-derived parameter and topology files.

03_Docking_Results: Top 100 binding poses in PDB format for each protein-polymer complex and their corresponding contact interface residue lists.

04_Binding_Energetics_MMPBSA: Raw MM/PBSA energy decomposition data (.dat) for all protein-polymer complexes and technical replicates (n=3).

05_Interfacial_Dynamics: GROMACS .xvg files containing hydrogen bond counts and lifetime statistics.

06_Equilibrated_Complex_Conformations: Atomic coordinates (PDB format) for all protein-polymer complexes following equilibration.