New Insights into Metal Interactions with the Prion Protein: EXAFS Analysis and Structure Calculations of Copper Binding to a Single Octarepeat from the Prion Protein

Abstract

Copper coordination to the prion protein (PrP) has garnered considerable interest for almost 20 years, due in part to the possibility that this interaction may be part of the normal function of PrP. The most characterized form of copper binding to PrP has been Cu2+ interaction with the conserved tandem repeats in the N-terminal domain of PrP, termed the octarepeats, with many studies focusing on single and multiple repeats of PHGGGWGQ. Extended X-ray absorption fine structure (EXAFS) spectroscopy has been used in several previous instances to characterize the solution structure of Cu2+ binding into the peptide backbone in the HGGG portion of the octarepeats. All previous EXAFS studies, however, have benefitted from crystallographic structure information for [CuII (Ac-HGGGW-NH2)–2H], but have not conclusively demonstrated that the complex EXAFS spectrum represents the same coordination environment for Cu2+ bound to the peptide backbone. Density functional structure calculations as well as full multiple scattering EXAFS curve fitting analysis are brought to bear on the predominant coordination mode for Cu2+ with the Ac-PHGGGWGQ-NH2 peptide at physiological pH, under high Cu2+ occupancy conditions. In addition to the structure calculations, which provide a thermodynamic link to structural information, methods are also presented for extensive deconvolution of the EXAFS spectrum. We demonstrate how the EXAFS data can be analyzed to extract the maximum structural information and arrive at a structural model that is significantly improved over previous EXAFS characterizations. The EXAFS spectrum for the chemically reduced form of copper binding to the Ac-PHGGGWGQ-NH2 peptide is presented, which is best modeled as a linear 2-coordinate species with a single His imidazole ligand and a water molecule. The extent of in situ photoreduction of the copper center during standard data collection is also presented and EXAFS curve fitting of the photoreduced species reveals an intermediate structure that is similar to the Cu2+ form with reduced coordination number.

The Opposite Effect of Metal Ions on Short-/Long-Range Water Structure: A Multiple Characterization Study

“…Besides anions, cations dissolved in aqueous solution have proved to be the key to the changes in water properties [ 1 , 2 ]. In addition, metal ions can also interact with a variety of biomolecules, such as protein [ 3 ] and DNA [ 4 ], and further lead to their structural changes to different extents. In this process, metal ions may bind directly with the functional groups on biomolecules [ 3 , 5 ] but may also indirectly force biomolecules to degenerate by alternating the water structure surrounding the biomolecules [ 6 ].…”

The non-octarepeat copper binding site of the prion protein is a key regulator of prion conversion

“…EXAFS spectroscopy is a powerful technique for obtaining structural and chemical information about metal binding to a protein of interest, providing accurate bond length measurements within 5 Å or less. Several groups have analyzed by EXAFS copper coordination bound to recombinant PrP in the OR 29 and non-OR regions 30 31 . In a previous EXAFS study we found that at pH 5.5 Cu(II) and Cu(I) bound to wild-type (WT) are specifically coordinated by the N δ -atom in the imidazole ring of two His residues (H96 and H111), by deprotonated amide nitrogens from adjacent residues ( e.g.…”

Metal complexes of amino acids and peptides

“…253 The role of metal ions in these conformational changes and in the onset of prion disease is still a matter of debate but more and more experimental evidence support the role of Cu(II) ions in these processes. 257 The results of theoretical calculations combined with experimental UV-visible studies on the Cu(II) complexes of a similar prion fragment were also reported. One of them describes the solution equilibria and structures of the Cu(II) complexes of the N-terminal peptide fragments of prion protein.…”