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Supporting Data: Exploring the Molecular Mechanisms of Nanoplastic Interactions with Blood Proteins by Molecular Dynamics and Docking Simulations
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This supporting dataset accompanies a study on nanoplastic interactions with blood proteins using molecular dynamics and docking simulations. Researchers modeled how particles from six common plastic types bind to human serum albumin, transthyretin, and proteins linked to neurodegenerative processes. The data includes relaxed protein structures, polymer topologies, docking results, and binding energy calculations that help characterize how nanoplastics may interact with biological molecules.
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.
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