Molecular Docking Analysis of Heavy Metal Interactions with OuterMembrane Porins of Pseudomonas aeruginosa: Implications for Environmental Adaptation and Bioremediation

Abstract

Background: Heavy metal contamination poses a persistent threat to environmental ecosystems, exerting selective pressure on microbial communities and promoting adaptive resistance mechanisms. In Gram-negative bacteria, outer membrane porin protein OprF of Pseudomonas aeruginosa play a crucial role in regulating membrane permeability and mediating interactions with environmental stressors.

Objectives: This study investigates the molecular interactions between selected heavy metals (Pb, Hg, Cr, Cu, Zn, and Cd) and outer membrane proteins of Pseudomonas aeruginosa using molecular docking analysis.

Methods: Three-dimensional protein structures were prepared from the Protein Data Bank, and ligand structures were obtained from PubChem. Docking simulations were performed using PyRx software, and interaction patterns were visualized using Discovery Studio.

Results: Binding affinity values revealed differential metal–protein interactions, with copper demonstrating the highest binding affinity (−8.3 kcal/mol), followed by zinc (−7.8 kcal/mol), while mercury exhibited the lowest interaction energy (−3.1 kcal/mol). The interactions were stabilized through van der Waals forces and π-related bonding patterns, suggesting potential coordination within porin-associated amino acid residues.

Conclusion: The stronger affinity observed for essential trace metals such as copper and zinc may reflect structural compatibility with membrane transport systems, whereas weaker mercury interaction may indicate alternative detoxification pathways. These findings suggest that outer membrane porin protein OprF could contribute to bacterial adaptation in metal-contaminated environments by modulating permeability and influencing metal transport dynamics. This study provides molecular-level insight into heavy metal–porin interactions and highlights the potential relevance of membrane-associated mechanisms in environmental resistance and bioremediation strategies. Experimental validation is recommended to confirm the biological implications of the predicted interactions.