Combined EXAFS and DFT Structure Calculations Provide Structural Insights into the 1:1 Multi‐Histidine Complexes of Cu^II, Cu^I, and Zn^II with the Tandem Octarepeats of the Mammalian Prion Protein

Abstract

The metal coordinating properties of the prion protein (PrP) have been the subject of intense focus and debate since the first reports of copper interaction with PrP just before the turn of the century. The picture of metal coordination to PrP has been improved and refined over the past decade, and yet the structural details of the various metal coordination modes have not been fully elucidated in some cases. Herein we employ X-ray absorption near edge spectroscopy as well as extended X-ray absorption fine structure (EXAFS) spectroscopy to structurally characterize the dominant 1:1 coordination modes for CuII, CuI and ZnII with an N-terminal fragment of PrP. The PrP fragment constitutes four tandem repeats representative of the mammalian octarepeat domain, designated OR4, which is also the most studied PrP fragment for metal interactions, making our findings applicable to a large body of previous work. Density functional theory (DFT) calculations provide additional structural and thermodynamic data, and candidate structures are used to inform EXAFS data analysis. The optimized geometries from DFT calculations are used to identify potential coordination complexes for multi-histidine coordination of CuII, CuI and ZnII in an aqueous medium, modeled using 4-methylimidazole to represent the histidine side chain. Through a combination of in silico coordination chemistry as well as rigorous EXAFS curve fitting, using full multiple scattering on candidate structures from DFT calculations, we have characterized the predominant coordination modes for the 1:1 complexes of CuII, CuI and ZnII with the OR4 peptide at pH 7.4 at atomic resolution, which are best represented as a square planar [CuII(His)4]2+, digonal [CuI(His)2]+ and tetrahedral [ZnII(His)3(OH2)]2+, respectively.

Cellular prion protein is present in mitochondria of healthy mice

“…Our finding that the PrP C N-terminus appears to be facing the inter membrane space is consistent with the possibility that mitochondrial PrP C may play a role in transmitting specific cellular signals across the IMM. The N-terminus of PrP C has been shown to bind many different molecules and contains an octapeptide repeat region that can bind metals, in particular copper 5 51 52 53 54 55 56 . Copper is a crucial cofactor for several mitochondrial proteins of the electron transport chain embedded within the IMM and Cu 2+ is transported and kept ligand-bound within the mitochondrial matrix 57 58 59 .…”

Interaction between Prion Protein's Copper-Bound Octarepeat Domain and a Charged C-Terminal Pocket Suggests a Mechanism for N-Terminal Regulation

“…The initial model was constructed from the MoPrP globular domain NMR structure (residues 120–230, pdb 1xyx) extended to include the Cu 2+ -bound OR and the intervening linker (residues 59–119). Additional refinements to the component 3 coordination structure were included from recent EXAFS and DFT calculations (Pushie et al, 2014). The initial structure was subjected to steepest-decent energy minimization with interdomain arrangement restrained by the experimental distances obtained with DEER EPR.…”

The part of a long beta hairpin from the scrapie form of the human prion protein is reconstructed in the synthetic CC36 protein

“…The structure of the N‐terminal part of the prion protein cannot be determined by X‐ray and NMR methods . There are numerous imperfect tandem repeats in this part of the protein and they were shown to bind different metal cations .…”

“…The structure of the N‐terminal part of the prion protein cannot be determined by X‐ray and NMR methods . There are numerous imperfect tandem repeats in this part of the protein and they were shown to bind different metal cations . Peptides corresponding to those repeats are able to form beta sheet in the presence of metal cations in certain concentrations …”