Molecular and Computational Studies Reveal That Per- and Polyfluoroalkyl Substances Can Impair Protamine–DNA Interaction, Potentially Inducing DNA Damage
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethical Statement
2.2. Recruitment
2.3. Inclusion, Exclusion and Confounding Criteria
2.4. PFAS’s Determination
2.5. Extraction of Sperm Nuclear Basic Proteins (SNBP) from Spermatozoa
2.6. Electrophoresis of SNBP in AU-PAGE
2.7. Plasmid DNA Extraction
2.8. DNA Protection Assay
2.9. Computational Approach for Biomolecular Modeling
- Rigid-body docking, involving randomization of ligand orientations and energy minimization (1000 structures generated);
- Semi-flexible refinement, in which the interface regions are treated as flexible and refined using simulated annealing in torsion angle space (200 structures generated);
- Final refinement, consisting of energy minimization in an explicit solvent model (200 structures generated).
3. Results
3.1. Analysis of the SNBP
3.2. Analysis of the Potential Involvment of SNBP in DNA Oxidative Damage
3.3. Molecular Docking Analyses
4. Discussion
5. Conclusions
6. Limitation and Future Perspectives
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Musella, F.; Guarnieri, M.G.; Amore, S.; Montano, L.; Bertola, F.; Micali, S.; Busardò, F.P.; Di Giovanni, C.; Lettieri, G.; Piscopo, M. Molecular and Computational Studies Reveal That Per- and Polyfluoroalkyl Substances Can Impair Protamine–DNA Interaction, Potentially Inducing DNA Damage. Biomolecules 2025, 15, 1279. https://doi.org/10.3390/biom15091279
Musella F, Guarnieri MG, Amore S, Montano L, Bertola F, Micali S, Busardò FP, Di Giovanni C, Lettieri G, Piscopo M. Molecular and Computational Studies Reveal That Per- and Polyfluoroalkyl Substances Can Impair Protamine–DNA Interaction, Potentially Inducing DNA Damage. Biomolecules. 2025; 15(9):1279. https://doi.org/10.3390/biom15091279
Chicago/Turabian StyleMusella, Federica, Maria Grazia Guarnieri, Simona Amore, Luigi Montano, Francesco Bertola, Salvatore Micali, Francesco Paolo Busardò, Carmen Di Giovanni, Gennaro Lettieri, and Marina Piscopo. 2025. "Molecular and Computational Studies Reveal That Per- and Polyfluoroalkyl Substances Can Impair Protamine–DNA Interaction, Potentially Inducing DNA Damage" Biomolecules 15, no. 9: 1279. https://doi.org/10.3390/biom15091279
APA StyleMusella, F., Guarnieri, M. G., Amore, S., Montano, L., Bertola, F., Micali, S., Busardò, F. P., Di Giovanni, C., Lettieri, G., & Piscopo, M. (2025). Molecular and Computational Studies Reveal That Per- and Polyfluoroalkyl Substances Can Impair Protamine–DNA Interaction, Potentially Inducing DNA Damage. Biomolecules, 15(9), 1279. https://doi.org/10.3390/biom15091279