Deciphering Copper Coordination in the Mammalian Prion Protein Amyloidogenic Domain

Abstract

Prions are pathological isoforms of the cellular prion protein that is responsible for transmissible spongiform encephalopathies (TSE). Cellular prion protein interacts with copper, Cu(II), through octarepeat and nonoctarepeat (non-OR) binding sites. The molecular details of Cu(II) coordination within the non-OR region are not well characterized yet. By the means of small angle x-ray scattering and x-ray absorption spectroscopic methods, we have investigated the effect of Cu(II) on prion protein folding and its coordination geometries when bound to the non-OR region of recombinant prion proteins (recPrP) from mammalian species considered resistant or susceptible to TSE. As the prion resistant model, we used ovine recPrP (OvPrP) carrying the protective polymorphism at residues A136, R154, and R171, whereas as TSE-susceptible models, we employed OvPrP with V136, R154, and Q171 polymorphism and bank vole recPrP. Our analysis reveals that Cu(II) affects the structural plasticity of the non-OR region, leading to a more compacted conformation. We then identified two Cu(II) coordination geometries: in the type 1 coordination observed in OvPrP at residues A136, R154, and R171, the metal is coordinated by four residues; conversely, the type 2 coordination is present in OvPrP with V136, R154, and Q171 and bank vole recPrP, where Cu(II) is coordinated by three residues and by one water molecule, making the non-OR region more exposed to the solvent. These changes in copper coordination affect the recPrP amyloid aggregation. This study may provide new insights into the molecular mechanisms governing the resistance or susceptibility of certain species to TSE.

Direct Mechanistic Evidence for a Nonheme Complex Reaction through a Multivariate XAS Analysis

“…It is well-known that systematic errors are present in the XANES analysis performed with MXAN and that they arise mostly because of the poor approximation used for the phenomenological broadening function Γ­( E ) that mimics the electronic damping. In all cases studied until now such systematic errors did not appreciably affect the structural results, confirming how this spectroscopy is dominated by the geometry of the atomic cluster rather than by its electronic structure. − The full list of nonstructural parameters is reported in Table .…”

Structural and Electronic Analysis of the Octarepeat Region of Prion Protein with Four Cu(II) by Polarizable MD and QM/MM Simulations

“…These results are consistent with experimental results showing that copper promotes the formation of compact structures in the non-octarepeat region, with reported inter-Cu 2+ distances of 3-6Å from EPR measurements. [67] The analysis of the distances of each copper ion with the first coordination shell atoms provides a) b) Figure 6: a) Labeling of the closest atoms to each copper ion. N1 and N2 are the nitrogen atoms of the first and second deprotonated glycine, respectively.…”

Structural and Electronic Analysis of the Octarepeat Region of Prion Protein with Four Cu(II) by Polarizable MD and QM/MM Simulations

“…These results are consistent with experimental results showing that copper promotes the formation of compact structures in the non-octarepeat region, with reported inter-Cu 2+ distances of 3-6 Å from EPR measurements. [67] The analysis of the distances of each copper ion with the first coordination shell atoms provides further structural insights (see Figure 6a for atom labels). As expected, the distances of the atoms including bonded contributions change very little compared with the distances where the interaction is modeled only using non-bonded contributions in the parametrization.…”