π-π and π-cation interactions play an important role in maintaining the structural stability of PrP. In this short article, we consider all the PrP structures listed in the PDB Bank: first we use the Swiss-PdbViewer 4.1.0 (spdbv.vital-it.ch) to relax (i.e. do Energy Minimisation in the use of Steepest Descent - Conjugate Gradients -Steepest Descent optimization methods) all the PrP structures, and then we use Maestro 10.1 2015–1 (Academic use only) (www.schrodinger.com) to find the π interactions see Table 1, where the code in the ( ) bracket is the PBD ID for each PrP species).

Let us denote some notations for a PrP structure: L0 is the N-terminal structured region before the β-strand 1, B1 is β-strand 1, L1 is the loop between B1 and α- helix 1, H1 is the α-helix 1, L2 is the loop between H1 and β-strand 2, B2 is β- strand 2, L3 is the loop between B2 and α-helix 2, H2 is the α-helix 2, L4 is the loop between H2 and α-helix 3, and H3 is the α-helix 3. From Table 1, we may see that there are π-π stackings (Figure 1): Y218–F175–Y169 (linking H3–H2–L3), H187–F198 (linking H2–L4), F141–Y150–Y157 (in H1), Y225–Y226 (in H3), Y162–Y128 (linking B2–B1), etc. From Table 1, we also see the following π-cations (Figure 1): F141– R208.(N) NH2 (linking L1–H3), Y162–L125.(N)N–Y128–R164.(N)NH2–Y169 (linking B2–L0–B1–L3), F198–R156.(N)NH2 (linking L4–L2), H155– R136.(N)NH2 (linking L2– L1), Y127–L125.(N)N (in L0), etc. The above bioinformatics might be acted as a “quick reference card” for PrP protein structure π-interaction studies [1,2].

Figure 1: Some selected π-interactions of PrPs, where the green dashedlines denote the π-π stackings and the orange colored dashed-lines denote the π-cations

Table 1: π-π-stackings and π-cations for each (optimized) PrP.

This research was supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant numbered VR0063 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian Government (Australia).