Anti-biofilm Activity of Graphene Quantum Dots via Self-Assembly with Bacterial Amyloid Proteins

Yichun Wang; Usha Kadiyala; Zhibei Qu; Paolo Elvati; Christopher Altheim; Nicholas A. Kotov; Angela Violi; J. Scott VanEpps

The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/550285 doi: bioRxiv preprint MD simulations were also used to elucidate the impact of GQDs on the assembly of PSMα1 monomers. Specifically, the statistics of the inter-peptide distance (center of mass) were collected and analyzed (Figure 5f) . The results show that the average distance increased from 0.76 ± 0.062 nm to 1.03 ± 0.055 nm when a GQD is in close proximity. Moreover, the distribution changes from a relatively symmetric monomodal bell-shaped curve centered at 0.9 nm to a distribution with three peaks (at 0.57, 0.97 and 1.2 nm) with a wide shoulder at 0.8 nm. While each peak is composed by a variety of configurations (representative complexes are shown in correspondence of each peak in Figure 5f ), the analysis of the trajectories suggests that the inter-peptide Nterminal/C-terminal interaction, responsible for the dimer stability is disrupted by the presence of the GQD. Additionally, as the GQD interacts with N-terminal of a peptide, it alters the contact angle of the peptide backbones and causes the groups close to the N-terminal to stretch. Overall, the interaction between GQD and PSM peptides strongly suggests a frustration of the amyloid fibrillation, as observed experimentally (Figure 6a) , caused by the GQDs docking near the Nterminus of the peptides and by changes in the secondary structure (Figure 6b, c) .