Modeling the interplay of glycine protonation and multiple histidine binding of copper in the prion protein octarepeat subdomains

• Published in: Journal of biological inorganic chemistry Vol. 14; no. 3; pp. 361 - 374
• Main Authors: Guerrieri, Francesco, Minicozzi, Velia, Morante, Silvia, Rossi, Giancarlo, Furlan, Sara, La Penna, Giovanni
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Berlin/Heidelberg : Springer-Verlag 01.03.2009; Springer-Verlag
• Subjects: Binding Sites; Biochemistry; Biomedical and Life Sciences; Computational chemistry; Computer Simulation; copper; Copper - chemistry; Density functional theory; Glycine - chemistry; Histidine - chemistry; Life Sciences; Microbiology; Models, Chemical; molecular dynamics; Original Paper; Prion; Prions - chemistry; Protons; Repetitive Sequences, Amino Acid; Time Factors; Molecular dynamics; Computational chemistry; Density functional theory; Prion; Copper
• ISSN: 0949-8257; 1432-1327
• DOI: 10.1007/s00775-008-0454-8

The octarepeat region of the prion protein can bind Cu²⁺ ions up to full occupancy (one ion per octarepeat) at neutral pH. While crystallographic data show that the HGGG octarepeat subdomain is the basic binding unit, multiple histidine coordination at lower Cu occupancy has been reported by X-ray absorption spectroscopy, EPR, and potentiometric experiments. In this paper we investigate, with first principles Car-Parrinello simulations, the first step for the formation of the Cu low-level binding mode, where four histidine side chains are coordinated to the same Cu²⁺ ion. This step involves the further binding of a second histidine to an already HGGG domain bonded Cu²⁺ ion. The influence of the pH on the ability of Cu to bind two histidine side chains was taken into account by simulating different protonation states of the amide N atoms of the two glycines lying nearest to the first histidine. Multiple histidine coordination is also seen to occur when glycine deprotonation occurs and the presence of the extra histidine stabilizes the Cu-peptide complex. Though the stabilization effect slightly decreases with the number of deprotonated glycines (reaching a minimum when both N atoms of the two nearest glycines are available as Cu ligands), the system is still capable of binding the second histidine in a 4N tetrahedral (though slightly distorted) coordination, whose energy is very near to that of the crystallographic square-planar 3N1O coordination. This result suggests that at low metal concentration the reorganization energy associated with Cu(II)/Cu(I) reduction is small also at pH ~ 7, when glycines are deprotonated.