A Survey on π-π Stackings and π-Cations in Prion Protein Structures

Jiapu Zhang

Abstract

π-π stackings and π-cations clearly do some contributions to maintain the structural stability of a normal cellular prion protein (PrP). This short article is to do a survey on the π-π stackings and π-cations in all the PrP structures listed in the PDB (www.rcsb.org) Bank. We find the following important π-π stackings: Y218–F175– Y169 (around the β2-α2 loop), Y162–Y128 (linking the two β-strands), F141–Y150– Y157 (in α-helix 1), H187–F198 (linking α-helix 2 and the α2-α3 loop); and we also find the following important π-cations: F141–R208.(N)NH2 (linking the β1-α1 loop and α- helix 3), Y128–R164.(N)NH2–Y169 (linking β-strand 1 and the β2-α2 loop). Thus, for PrPs, there exists a long “π-chain” Y218– F175–Y169–R164–Y128–Y162 covering the β2-α2 loop, and there exists another long “π-chain” R208–Y141–Y150– Y157–F198– H187 covering the α-helix 1. This short article can be acted as a “quick reference card” for PrP protein structure π-interaction studies in laboratories or in theories.