**3. Copper Binding**

Copper ions bind to the N-term of HuPrPC in vivo [24]. Since the protein is anchored to the neuronal membrane, facing the extracellular space, it is exposed to fluctuations in Cu2+ ion concentrations, that can reach 100 μM during synaptic transmission [68]. This represents orders of magnitude larger than the experimentally measured range of binding affinities for Cu(II) ions at the N-term (nM to μM) [69]. Thus, it is plausible that the protein responds to Cu(II) ion concentration changes at the synapse. On the other hand, upon endocytosis, HuPrP<sup>C</sup> is exposed to the intracellular reducing environment, where the interaction of its N-term with Cu<sup>+</sup> ions would also be relevant. Two main functions of copper binding to the N-term have been proposed so far: (i) stimulation of HuPrPC endocytosis [70–73] and (ii) copper sensing associated to cell signaling. Copper-induced endocytosis of HuPrP<sup>C</sup> requires its N-term terminus, specifically the octarepeat region, and it might involve conformational alterations of the N-term with the subsequent delivery of copper ions to endosomes. This has led to a proposed role for HuPrPC in copper transport. However, it is unlikely that HuPrP<sup>C</sup> delivers copper efficiently into the cytosol, since high concentrations are needed for copper-induced endocytosis (150–300 μM) [71,73]. On the other hand, HuPrPC can interact with the human N-methyl-D-aspartate receptors (HuNMDAR) and alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (HuAMPAR) involved in synaptic transmission, while both receptors are regulated by Cu ions [74–76]. In the case of HuNMDAR activity, copper binding to HuPrPC is necessary to regulate the activity of this receptor [75]. Indeed, HuPrP<sup>C</sup> and Cu2+ are required to inhibit HuNMDAR activity through a mechanism that involves post-translational S-nitrosylation of cysteine residues in HuNMDAR [77]. Overall, these important findings underscore a role for Cu-HuPrPC interactions in neuroprotective mechanisms, which could be disrupted by other Cu-binding proteins or peptides at the synapse. For instance, human amyloid-β (Aβ) neurotoxicity has recently been linked to its ability to compete for Cu2+ ions with HuPrPC, thereby interfering with the modulation of HuNMDAR activity [75].

The N-term region of HuPrPC contains six His residues that may serve as anchoring sites for Cu2+ ions [78]. The ion binds to different sites within the protein [79–82], which are conserved in mammalian species [83], a fact that underscores its physiological relevance. Four of them are located in the OR region, spanning residues 60-91 with four repeats of the highly conserved octapeptide PHGGGWGQ (Figure 3). Beyond the OR region, two additional His residues, 96 and 111, also act as copper-binding sites in the 92-115 region. Studies on synthetic peptide fragments have suggested that metal coordination modes depend on copper concentration [69], as well as the relative copper:protein ratio and proton concentration [79,80]. At physiological pH, three distinct Cu2+ coordination modes have been identified by electron paramagnetic resonance (EPR) [84]. At low Cu:protein ratios, three or four His residues can chelate one metal ion, leading to a multiple histidine Cu-binding mode, named Component 3 (Figure 3). At higher Cu:protein ratios, a species with two His ligands forming a 2N2O equatorial coordination mode is observed (Component 2 in Figure 3). When enough Cu2+ is provided to reach a 1:1 ratio for each octapeptide fragment, a species with a 3N1O equatorial coordination mode is formed, named Component 1, where the coordinating residues are as follows: one His imidazole ligand, two deprotonated backbone amide groups, and a carbonyl group from the glycine residues that follow the anchoring His in the sequence (Figure 3) [78,85]. X-ray crystallographic studies of the Cu2+ complex with one octapeptide PHGGGWGQ fragment also revealed the participation of a water molecule as an axial ligand, stabilized by hydrogen bonding to the Trp residue [86]. This is the only Cu-binding site fragment that has been characterized so far by X-ray crystallography.

**Figure 3.** Cu coordination properties of the N-terminal region of human HuPrPC. The six His residues that act as anchoring sites for Cu ions are highlighted: His61, His69, His77, and His85 in the OR region, and His96 and His111 in the non-OR region. The models for the different Cu2+ coordination modes identified at each site at physiological pH are drawn. The impact of α-cleavage processing on the His111 binding site is also shown.

The Kd for the low occupancy multiple-His coordination mode (Component 3) is 0.12 nM, whereas it ranges from 7 to 10 μM for the high-occupancy 3N1O mode (Component 1) [69]. Hence, Cu binding to the OR region displays a negative cooperativity. This is consistent with the formation of intermediate species such as Component 2. Electrochemical studies have determined that the high-occupancy Component 1 species is capable of reducing dioxygen to produce low levels of hydrogen peroxide that may be relevant for cell signaling, whereas the low-occupancy multiple-His mode cannot activate dioxygen at all [87,88].

Outside the OR region, His 96 and 111 act as anchoring sites for Cu2+ ions, constituting the closest Cu-binding sites to the amyloidogenic region of HuPrPC [81,89,90]. An X-ray absorption spectroscopy (XAS) study of a HuPrP (90–231) construct of the protein showed that at low pH Cu ions can coordinate to both His residues in the non-OR region, while at physiological pH only the His111 site is populated [91]. The peptide fragments mostly used to characterize the individual non-OR Cu-binding sites are HuPrP (92-96) and HuPrP (106-115) with sequences GGGTH and KTNMKHMAGA, respectively [85,92]. EPR and other spectroscopic studies have determined that Cu2+ coordination is highly pH-dependent in these sites, yielding two different equatorial coordination modes at physiological pH, 3N1O and 4N, related by a pKa value near 7.5 (7.8 for the His 96 site and 7.5 for the His 111 site) [93–96]. In both sites, Cu2+ coordination in the 3N1O mode involves the His imidazole group, two deprotonated amide nitrogens, and a carbonyl group from the backbone amide bonds that precede the His residue in the sequence, while a third deprotonated amide group replaces the carbonyl moiety in the 4N equatorial mode (Figure 3). Although the equatorial coordination modes of Cu2+ bound to these sites are identical, the presence of two Met residues in the His 111 site provides it with distinct properties, particularly in terms of relative binding affinity, and redox properties. The thioether groups of Met 109 and Met 112 can participate in Cu1+ coordination to the PrP(106-115) fragment, as demonstrated by XAS studies, yielding coordination modes where the His111 imidazole ring, the two Met residues, and a backbone carbonyl group stabilize a tetra-coordinated Cu1+ species at physiological pH, where Met109 plays a more important role in metal coordination, as compared to Met112 [97]. Anchoring of Cu1+ ions by Met residues persists even at low pH values (<5), as those found in endosomes. Thus, the MKHM motif and Cu coordination features of the His111 site assure that the metal ion would still be bound to the protein, even under decreased pH and reducing conditions, such as those encountered upon endocytosis. Additionally, the capability of the His111 site to stabilize both Cu2+ and Cu1+ makes it a unique site in the N-term region of HuPrPC that may support redox activity to activate dioxygen.

The relative binding affinity of Cu2+ for the non-OR sites has also been studied [98–102]. While a slight preference for Cu2+ binding to His111 over His96 has been observed spectroscopically and ascribed to the Met residues nearby, the two sites get loaded simultaneously with Kd values in the range of 0.4 to 0.7 μM at physiological pH [102]. Given the Cu-binding affinity features of the OR region, this implies that upon increasing Cu2+ levels, the multiple His species (Component 3) would first form, followed by the population of the non-octarepeat His96/His111 sites, before the OR region is fully loaded to yield the high occupancy mode (Component 1). Overall, the Cu(II) coordination and binding features of the N-term region provide HuPrP<sup>C</sup> with the ability to respond to a wide range of Cu concentrations, adopting different metal coordination modes, which in turn may impose different conformations to this unstructured region of the protein.

The conformational flexibility of the N-term\_HuPrP<sup>C</sup> and the presence of several His residues as Cu anchoring sites provide a platform to accommodate different Cu2+ coordination modes as a function of relative metal:protein concentrations. Unlike the static (entatic) Cu active sites of cuproenzymes, where the protein structure imposes restrictions on the metal coordination and geometry, the preferred coordination modes at each Cu-binding site in the flexible N-term domain of HuPrP<sup>C</sup> are dictated by the geometric and electronic preferences of the metal ion, which can actually impose metal-induced conformations with potentially different functional implications or a propensity to aggregate. For example, the participation of deprotonated backbone amides in Cu2+ coordination, as in the high-occupancy (Component 1) mode of the OR region, inevitably imposes a certain turn in the backbone chain, which is known to yield more compact conformations [81]. Indeed, full loading of Cu2+ ions into the OR region yields a conformation where the average Cu–Cu distance is 4 to 7 Å, as determined by EPR [84]. Given the relatively high Cu concentrations needed for endocytosis of HuPrPC and the Cu-binding affinity features of the OR region, this high-occupancy conformation of the OR region is likely involved in the mechanism of endocytosis.

Recent studies have revealed metal-induced interactions between the N-term and C-term regions of MoPrPC [103–105]. An NMR study suggested interactions of the region 90-120, containing His96 and His111 Cu-binding sites, with residues in the vicinity of helix-1 (specifically 144-147), while the Cu-loaded OR region may also interact with helix-2, involving residues 174-185 [105]. The latter was confirmed by an elegant NMR and site-directed spin labeling EPR study that provided detailed structural information on how Cu binding at the low occupancy multiple His site (Component 3) in the OR region promotes electrostatic interactions with a highly conserved negatively charged region at helices 2 and 3 of the globular protein [103]. The C-term region of the protein engaged in the interaction with Cu-loaded OR overlaps with the region where neurotoxic PrP antibodies bind, and it also involves acidic residues associated with disease-related mutations, such as E200K. These observations underscore the important role of Cu2+ loading into the low-occupancy multiple-His coordination mode in promoting electrostatic interactions between the Cu-bound N-terminal region and the helical C-terminal domain, a stabilizing interaction that is considered to be regulatory for prion conversion [103,105].

On the other hand, in the non-OR region, the two His coordination modes identified at low pH for the PrP(90-231) construct were also found to induce stabilizing interactions with the globular C-terminal domain, whereas Cu2+ binding solely to the His111 site induced local beta-sheet structure [91]. Consistently, copper binding to the non-OR sites in the amyloidogenic fragment 90-126 induces a β-sheet-like transition [106]. These observations underscore the important role that Cu binding to the non-OR region may play in amyloid aggregation and prion conversion.

Cu2+-PrPC interactions and their perturbation by disease-related mutations have been suggested to play a role for Hu/Mo PrPC aggregation and prion disease progression [107]. Specifically, the GSS-linked Q211P PM [60] (Q212P in Hu numbering) in the HuPrPC GD can influence the Cu2+ binding coordination at H96 and H111 [108], implicating a role of abnormal Cu2+ binding in the pathology of PMs in HuPrPC. As discussed above, the multiple His Cu-binding modes induce stabilizing interactions of the N-term\_HuPrPC with the globular C-terminal domain, whereas Cu2+ binding solely to the His111 site induces local beta-sheet structure [91,103,105]. Thus, any perturbation of the local conformation around the Cu-binding sites may have an impact on the stability of the protein. Consistently, structural analysis by molecular simulations of the N-term\_HuPrPC indicates that some disease-linked mutations may affect the local conformation and intramolecular interactions around the Cu2+ binding sites, including His111 [31,32], providing a molecular basis to understand their impact on disease progression. Although further studies are needed to understand how Cu binding impacts the folding and conformation of the flexible N-term\_HuPrPC, it is clear that the different Cu2+ coordination modes formed at the His anchoring sites can favor distinct metal-induced conformations, while disease-related mutations may also impact the conformation of the N-term region, its Cu-binding properties, and its interactions with the C-terminal globular region of HuPrPC.

Copper binding may also be affected by a specific post-translational modification, namely the proteolytic processing at specific sites of the N-term region [109]. This includes the following: (i) the β-cleavage of the OR region, leading to the N2 (23-89) and C2 (90-231) fragments [109]. This is induced by reactive oxygen species (ROS) produced in the presence of Cu2+ ions [110,111] (It can be also catalyzed by calpain and ADAM8—a member of the A Disintegrin And Metalloproteinase (ADAM) family of enzymes [112,113]). While the N2 fragment may be released, maintaining the Cu2+ binding properties of the OR sites as described above, the C2 fragment may remain anchored to the membrane, conserving the His96 and His111 sites, but with a free N-term group at residue 90 [109]. The free NH2 moiety is expected to change significantly the Cu2+ coordination features of these non-OR sites. (ii) The α-cleavage occurs at several sites in the region encompassing residues 109-120, and it is a common feature in a wide range of cell lines [114]. The process, performed by members of the ADAM enzymes [112], increases in the presence of Cu2+ ions [115]. This metal also may modulate the relative amount of α-cleavage at each site, possibly by inducing local conformational changes that impact how the protein docks into the protease active site [112,113]. The most described α-cleavage site is located between Lys110 and His111 in the human sequence, producing two fragments N1 (23-110) and C1 (111-231) [109]. The released N1 fragment may still contain the OR region and the His96 site; however, the His111 site may be significantly disturbed, as the cleavage occurs between residues that participate in Cu2+ coordination, leaving a His111 with a free NH2 terminal group at the membrane bound C1

fragment. A recent spectroscopic study determined the impact of α-cleavage processing on Cu2+ binding to His111, using a model peptide for the C1 fragment [116]. Indeed, in this fragment His111 and the free NH2 terminal group act as the main anchoring sites for Cu2+, resulting in coordination modes that are highly dependent on proton and copper concentrations, and are quite different from those characterized for the intact His111 site in the full protein (Figure 3). The Cu-binding affinity features and redox activity of this perturbed His111 site remain to be investigated. It is interesting to note that, while Cu ions can modulate the relative amount of α-cleavage at different sites of the 109-120 region of HuPrP<sup>C</sup> [112], the resulting membrane-bound C1 fragments and their Cu-binding properties could in turn determine the metal-induced conformation of the N-term region and its ability to interact with important receptors, such as the HuNMDAR and HuAMPAR [113,117].
