# Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead?
## 4 Protein/Surface Interactions
### Adsorption on Low Dimensional Materials
The process behind the adsorption mechanism is nowadays fully described and supported by robust demonstrations [199], yet it is based on short peptide sequences and not on proteins. On the other hand, the protein/surface interaction is specific for each protein/substrate pair, and depends on both the nature of the protein and the specific surface composition. Moreover, the relationship between the structure of the adsorbed protein and its function (i.e., is the function retained after adsorption? Is there a relation between the adsorbed state and the ET?) is still not clear. In a recent study, [PERSON] et al. focused on the adsorption mechanism of cyt c on CNT by mean of MD simulations [200], and in particular on the dynamic of the process when water is present. The authors considered a double layer of water molecules in between CNT and the protein and characterize the dynamic of adsorption of cyt considering 64 initial orientations over CNT. They found that water molecules strongly affect long-range electrostatic interactions which in turn, affects the adsorption of cyt. In this process, once the protein is anchored to the surface, a lockdown phase in which water is repelled from CNT takes place, in order to obtain stable conformations. Once more, this study shows that water molecules should not be neglected in simulations, either when ET or adsorption dynamic process are considered. Moreover, they described the relationship between the adsorption conformation and the ET by considering the distance and tilting of the heme group from the CNT surface. They consider the ET through bond mechanism, in which electrons flow form the iron of heme to CNT is maximized when the heme is perpendicular to the surface [201] and is strongly dependent on the relative distance between Fe and CNT. Graphene and its soluble derivative graphene oxide (GO) hold great promises also for the creation of biological interfaces and can be considered as materials of choice for the regulation of ET of adsorbed proteins [202; 203; 204], not only due to their peculiar electronic properties, but also to the high surface area. It has been reported that these materials can accommodate a vast range of redox proteins and facilitate a rapid ET through the layered materials [205]. Moreover, adsorption of cyt c over GO/reduced GO (rGO) resulted in a modulation of the protein activity due to the changes in the heme micro environment caused by the different interactions between the protein and the materials [206]. [PERSON] et al. [207] reported the study of cyt c adsorption over graphene and GO by mean of parallel tempered Monte Carlo (PTMC) algorithm coupled with MD simulations to assess the orientation of protein on the surface, the nature of the interactions, the subsequent conformational changes and the ET pathway. With the PTCM method, cyt c is considered in a united-residue model in which each amino acid is reduced to a site centered interaction at the carbon alpha, and the structure of the whole protein is kept rigid. The graphene/GO surface is regarded structureless and the interactions with the protein described with both vdW and electrostatic interactions. At the end of this process, optimal orientations are obtained and the most favorable were chosen as input structures for MD simulations. This protocol replaces the traditional docking procedure which is commonly performed when protein-protein interactions are present, but fails for heterogeneous interfaces as the one reported here. From MD simulations the authors obtained that hydrophobic interactions determine the cyt-surface adsorption, with the heme group parallel to the graphene surface and almost perpendicular when adsorbed over GO (which in this study was negatively charged). The authors concluded that ET for the cyt/graphene interface is thus inhibited, while it is enhanced for the cyt/GO interface.