## 3 Results and Discussion
### Analysis of Salt Bridges in bR Protein to Determine the Stability of the bR-Graphene Complex  
Salt bridges are an important form of electrostatic interactions that involve non-binding interactions between an oxygen atom of an acidic residue and the nitrogen atom of a basic residue. These not only determine the stability of but also contribute to the structure and function of a protein. Salt bridges were analyzed for both bR control (Table 1) and bR-graphene (Table 2), and the individual plots are as shown in Figure S2A,B. More salt bridges were formed in the case of bR control compared to the bR-graphene complex, whereas more salt bridges were broken for the bR-graphene complex compared to the bR control. This is because the protein undergoes large conformational changes exposing the internal hydrophobic residues to adsorb onto the graphene surface with greater energy and stability. Tables 1 and 2 also highlight the common salt bridges and their status during the control and experimental simulations. Although GLU166-ARG227 and ASP212-ARG82 salt bridges are sustained in both the control and experimental simulations, it is found that LYS216, which broke its interaction with ASP212 and formed one with ASP85 in the case of bR control, did the opposite in the presence of graphene. Here, LYS216 sustained its salt bridge with ASP212 and broke it with ASP85. It is important to highlight that the salt bridge ASP85-ARG82 in the case of the bR control is directly responsible for releasing the proton via ARG82 to trigger the conformational changes in the bR protein from photon absorption. As can be seen from Table 1, this salt bridge is formed and stays intact through the simulation (Figure S2A). In contrast to this, in the presence of graphene, it is found that the salt bridge between ASP85 and ARG82 breaks down (Table 2 and Figure S2B),  
Figure 3: Role of hydrogen bonds in bR–graphene interactions: (**a**) Hydrogen bonds within bR in the absence of graphene; (**b**) Hydrogen bonds within bR in the presence of graphene; (**c**) Hydrogen bonds within 5 Å of the retinal in the absence of graphene; (**d**) Hydrogen bonds within 5 Å of the retinal in the presence of graphene. indicating that adsorption of bR onto graphene is capable of triggering conformational changes, similar to those of bR's photocycle. This, in turn, is hypothesized to create a favorable environment to increase the yield of the Q state and, hence, the binary bit '1' relevant to optical memory devices. ASP96, which is responsible for reprotonating the retinal during the final stages of the photocycle, can also be seen in Tables 1 and 2 (Figure S1A,B). In both the absence and presence of graphene, it is found that ASP96 loses its salt bridge with LYS41. Similarly, GLU194, which is also an important residue for proton transport, shows up forming a salt bridge with LYS129 in the case of bR control, whereas in the presence of graphene, it loses this bridge with LYS129. Finally, the residue GLU204 that is important for transporting \begin{table}
\begin{tabular}{c c c c} \hline \hline
**Salt Bridges * & **Broken** & **Formed** & **Sustained** \\ \hline
**ASP96-LYS41** & \(\surd\) & & \\ \hline GLU194-ARG134 & \(\surd\) & & \\ \hline
**ASP85-ARG82** & \(\surd\) & & \\ \hline
**GLU166-ARG227** & & & \(\surd\) \\ \hline GLU9-ARG7 & & \(\surd\) & \\ \hline
**ASP212-ARG82** & & & \(\surd\) \\ \hline
**ASP21-LYS216** & \(\surd\) & & \\ \hline
**GLU194-LYS129** & \(\surd\) & & \\ \hline
**ASP104-LYS159** & \(\surd\) & & \\ \hline
**GLU166-ARG164** & \(\surd\) & & \\ \hline \hline \end{tabular}  
* Data in bold represent the common salt bridges between control and experimental simulations.  
\end{table}