# The Role of Metal Ions in the Electron Transport through Azurin-Based Junctions
## 3 Results and Discussion
The difference is quantified by the RMSD between both averaged configurations. The protein representation used in all figures is the same as in Figure 2. A comparison between the averaged Cu-azurin obtained in this work (black) with the one obtained in previous MD simulations where a different force-field for the cooper coordination sphere was used [3] is included on (**d**). (**e**) Percentage of \(\beta\)-sheet content for the three azurin variants considered. It is calculated using the DSSP algorithm [66] included on the CPPTRAJ ambertools [67]. Note that the \(\beta\)-sheet content of the azurin averaged structures is also included as the protein is represented with its secondary structure (\(\beta\)-sheets represented as planar arrows). Figure 3: (**a**) Transmission as a function of energy for the four metalloprotein studied at the four different tip-protein distance values considered; and (**b**) projected density of states on the metal ion in each protein for the shortest tip-ion distance (1.40 nm). For each row, the corresponding metal ion is indicated on the left-hand side. Figure 2: Initial (**a**) and final (**b**) geometries obtained during the simulations of the lateral STM-tip indentation carried out for the Cu-azurin. The arrow indicates the central copper ion which has been replaced with three different metals to reproduce the other junctions under study. The azurin is represented with its secondary structure: \(\beta\)-sheet (red arrows), \(\alpha\)-helix (purple helix), 310-helix (dark-blue helix), turns (cyan) and random-coils (white). The ion is shown using its van der Waals representation in an opaque green color, and its coordination residues are represented with a ball-stick model. The disulfide bridge and the main chain of the two cysteines which formed it are colored in light orange. The sulfur atoms of these two cysteines are highlight in pink. The variation of the protein structure on the junction is quantified by computing its root-mean-square-deviation from the Cu-azurin free solved in water structure (RMSD\({}_{f\rm{s}}\)) [3]. In the right column of the same figure, we report the projected density of states (PDOS) on the metal ion for the shortest tip-protein distance. The curve for Zn clearly differs from the other three in that the \(d\)-level peaks lie at lower energies with respect to the Fermi level as compared to the other metal ions (this, in turn, derives from the closed-shell electronic Zn configuration). This difference is reflected in the corresponding transmission curve, in which no peaks appear in a broad range immediately below the Fermi level as opposed to the other three proteins. Indeed, the lower density currents measured for the Zn-protein junctions and reported by [PERSON] et al. [15] were ascribed to the different energy alignment of the metal-derived levels. A common feature to the transmission curves of all proteins is the energetic position of the lowest occupied orbital (localized on HIS35), which shows minimal changes from one curve to another. This is not surprising because, in our simulations, the position of the amino acids (including HIS35) within the protein is the same for all cases. Consequently, they contribute to the transmission with similar features. Note that, although the lack of re-optimization might in principle lead to some artifacts, the MD simulations discussed above revealed minimal changes upon ion replacement. This suggests that they would result into energy shifts of individual orbitals the effect of which would most likely be hidden by the rest of the contributions of the whole electronic structure of the protein (given the extreme sharpness of all peaks in the transmission curves of Figure 3, it is hard to believe that any shift of one of these peaks would affect the transmission at the Fermi level). The same applies to possible shifts of individual peaks arising from the spin polarization of the metallic ion which could not be described in our closed-shell calculations.