Molecular dynamics simulations reveal concentration-dependent blockage of graphene quantum dots to water channel protein openings

Abstract

Graphene quantum dots (GQDs) have attracted significant attention across various scientific research areas due to their exceptional properties. However, studies on the potential toxicity of GQDs have yielded conflicting results. Therefore, a comprehensive evaluation of the toxicity profile of GQDs is essential for a thorough understanding of their biosafety. In this work, employing a molecular dynamics (MD) simulation approach, we investigate the interactions between GQDs and graphene oxide quantum dots (GOQDs) with the AQP1 water channel protein, aiming to explore the potential biological influence of GQDs/GOQDs. Our MD simulation results reveal that GQDs can adsorb to the loop region around the openings of AQP1 water channels, resulting in the blockage of these channels and potential toxicity. Interestingly, this blockage is concentration-dependent, with higher GQD concentrations leading to a greater likelihood of blockage. Additionally, GOQDs show a lower probability of blocking the openings of AQP1 water channels compared to GQDs, due to the hydrophobicity of the loop regions around the openings, which ultimately leads to lower interaction energy. Therefore, these findings provide new insights into the potential adverse impact of GQDs on AQP1 water channels through the blockage of their openings, offering valuable molecular insights into the toxicity profile of GQD nanomaterials.

Fig. 1

(a-j) Final conformations of ten parallel simulations of 5GQD/AQP1 system. The GQDs are showed by gray spheres and the AQP1 tetramer is displayed by cyan ribbons.

Fig. 2

(a-j) Final conformations of ten parallel simulations of 10GQD/AQP1 system. The GQDs are showed by gray spheres and the AQP1 tetramer is displayed by cyan ribbons.

Fig. 3

The contact probability surface of AQP1 protein in 5GQD/AQP1 (a) and 10GQD/AQP1 (c) systems. The contact probability secondary structure of AQP1 protein in 5GQD/AQP1 (b) and 10GQD/AQP1 (b) systems. The contact probability of each residue is averaged from all ten parallel simulations.

Fig. 4

Interaction energy between GQDs and AQP1 protein in two selected trajectories of 5GQD/AQP1 (a) and 10GQD/AQP1 systems. Some snapshots are plotted to show the binding conformations.

Fig. 5

(a-j) Final conformations of ten parallel simulations of 5GOQD/AQP1 system. The GOQDs are showed by gray (carbon), red (oxygen) and white (hydrogen) spheres and the AQP1 tetramer is displayed by cyan ribbons.

Fig. 6

(a-j) Final conformations of ten parallel simulations of 10GOQD/AQP1 system. The GOQDs are showed by gray (carbon), red (oxygen) and white (hydrogen) spheres and the AQP1 tetramer is displayed by cyan ribbons.

Fig. 7

The contact probability surface of AQP1 protein in 5GOQD/AQP1 (a) and 10GOQD/AQP1 (c) systems. The contact probability secondary structure of AQP1 protein in 5GOQD/AQP1 (b) and 10GOQD/AQP1 (b) systems. The contact probability of each residue is averaged from all ten parallel simulations.

Fig. 8

Interaction energy between GOQDs and AQP1 protein in two selected trajectories of 5GOQD/AQP1 (a) and 10GOQD/AQP1 systems. Some snapshots are plotted to show the binding conformations.