In a paper published in the journal Scientific Reports, researchers used molecular dynamics (MD) simulations to investigate the interactions between graphene quantum dots (GQDs), graphene oxide QDs (GOQDs), and the human intestinal fatty acid binding protein (HIFABP).
Study: Potential toxicity of Graphene (Oxide) quantum dots to the human intestinal fatty acid binding protein (HIFABP) via obstructing the protein’s openings. Image Credit: vectorfusionart/Shutterstock.com
The study found that both graphene quantum dots (GQDs) and graphene oxide quantum dots (GOQDs) can block the opening of the HIFABP protein, potentially causing toxicity by hindering its normal biological function. The binding of GQDs to HIFABP was driven by van der Waals (vdW), pi (π)-π stacking, cation-π, and hydrophobic interactions, while GOQDs used similar interactions, including vdW and Coulomb forces. These results highlight the potentially toxic effects of GQDs on HIFABP.
Related Work
Previous studies have demonstrated the unique properties of GQDs, which hold promise for applications in electronics, optics, and medicine. However, concerns have emerged over their toxicity, with conflicting reports on their environmental and biological safety.
Some studies indicate minimal toxicity, while others emphasize that factors such as size, concentration, and surface chemistry play significant roles. Despite ongoing research, challenges remain in fully understanding the molecular interactions and long-term safety of these nanomaterials.
Simulation Methodology Overview
This study used molecular dynamics (MD) simulations with the GROMACS software and the CHARMM27 force field to examine interactions between GQDs, GOQDs, and HIFABP.
Systems were dissolved in water with 0.15 M NaCl, with an additional system containing 10 GQDs to assess concentration effects. Simulations were run at 300 K with long-range electrostatic interactions calculated using the particle mesh Ewald (PME) method and vdW interactions cut off at 1.2 nm. Data were collected every 10 ps over 100-ns trajectories.
Interactions Between GQDs/GOQDs and HIFABP
HIFABP has an internal cavity surrounded by β-strands that facilitates fatty acid transport, with two openings allowing fatty acids to enter. Through 20 parallel simulations, researchers observed that GQD consistently positioned itself near one of HIFABP’s openings, often partially or fully entering the cavity and potentially obstructing fatty acid transport.
Contact probability analysis showed that GQD was highly likely to bind to the top portal of HIFABP, suggesting preferential obstruction at this site. Additional contacts with residues near the bottom portal were observed, though only one simulation showed GQD obstructing this region. These interactions indicate that GQD may interfere with both portals of HIFABP, affecting its function.
Analysis of specific residues involved in GQD binding revealed that several hydrophobic and aromatic residues contributed to GQD’s affinity for HIFABP, with hydrophobic forces and π-π stacking playing a significant role. Time-evolution analysis of vdW interaction energy indicated dynamic binding, with GQD establishing stable contact as it approached the cavity interior.
GOQD showed similar binding behavior, obstructing the HIFABP portal consistently across multiple simulations. Contact probability analysis confirmed this pattern, suggesting that GOQD likely disrupts HIFABP function via mechanisms similar to those of GQD.
Conclusion
This study constructed two simulation systems—GQD/HIFABP and GOQD/HIFABP—to examine the potential impact of these nanostructures on HIFABP. Results showed that GQDs bound to HIFABP’s portal, blocking fatty acid entry and inhibiting normal function. Binding was mediated by vdW, π-π stacking, cation-π, and hydrophobic interactions. GOQD also obstructed the same portal, suggesting a comparable mechanism of toxicity. Overall, these findings highlight how GQDs and GOQDs may disrupt HIFABP’s carrier function, emphasizing potential risks in future applications. Further biophysical studies are needed to validate these results in complex biological environments.
Journal Reference
Luo, Y., et al. (2024). Potential toxicity of Graphene (Oxide) quantum dots to the human intestinal fatty acid binding protein (HIFABP) via obstructing the protein’s openings. Scientific Reports, 14:1, 1-12. DOI: 10.1038/s41598-024-73037-z, https://www.nature.com/articles/s41598-024-73037-z
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