Ab initio simulations of Cu binding sites on the N-terminal region of prion protein

The human prion protein binds Cu²⁺ ions in the octarepeat domain of the N-terminal tail up to full occupancy at pH 7.4. Recent experiments have shown that the HGGG octarepeat subdomain is responsible for holding the metal bound in a square-planar configuration. By using first principle ab initio molecular dynamics simulations of the Car–Parrinello type, the coordination of copper to the binding sites of the prion protein octarepeat region is investigated. Simulations are carried out for a number of structured binding sites. Results for the complexes Cu(HGGGW)(wat), Cu(HGGG), and [Cu(HGGG)]₂ are presented. While the presence of a Trp residue and a water molecule does not seem to affect the nature of the copper coordination, high stability of the bond between copper and the amide nitrogen of deprotonated Gly residues is confirmed in all cases. For the more interesting [Cu(HGGG)]₂ complex, a dynamically entangled arrangement of the two domains with exchange of amide nitrogen bonds between the two copper centers emerges, which is consistent with the short Cu–Cu distance observed in experiments at full copper occupancy.     

Computational studies of Cu(II)[peptide] binding motifs: Cu[HGGG] and Cu[HG] as models for Cu(II) binding to the prion protein octarepeat region

The binding of Cu(II) to the prion protein is investigated by computations at the B3LYP level of theory on models of the octarepeat domain of the prion protein. The models incorporate the functionality of the glycine (G) and histidine (H) residues which occur in the octarepeat domain, PHGGGWGQ. The copper complexes are designated Cu[HG] and Cu[HGGG]. Coordination to the metal via the imidazole ring of the histidine, the amide carbonyl groups, and the backbone nitrogen atom of the amide groups were examined, as well as several protonation/deprotonation states of each structure. EPR and CD titration experiments suggest that the octarepeat segments of the unstructured N-terminal domain of prion protein can bind Cu(II) in a 1:1 Cu-to-octarepeat ratio. The results identify the extent to which the Cu(II) facilitates peptide backbone deprotonation, and the propensity of binding in the forward (toward the C-terminus) direction from the anchoring histidine residue. A plausible mechanism is suggested for changing from amide O-atom to deprotonated amide N-atom coordination, and for assembly of the observed species in solutions of Cu[PrP] and truncated models of it. A structure is proposed which has the N2O2 coordination pattern for the minor component observed experimentally by EPR spectroscopy for the Cu[HGGG] model. The most stable neutral Cu[HGGG] structure found, with coordination environment N3O1, corresponds to that observed for Cu[HGGGW] and Cu[HGGG] both in the solid state and as the major component in solution at neutral pH.     

Can copper binding to the prion protein generate a misfolded form of the protein?

The native prion protein (PrP) has a two domain structure, with a globular folded α-helical C-terminal domain and a flexible extended N-terminal region. The latter can selectively bind Cu²⁺ via four His residues in the octarepeat (OR) region, as well as two sites (His96 and His111) outside this region. In the disease state, the folded C-terminal domain of PrP undergoes a conformational change, forming amorphous aggregates high in β-sheet content. Cu²⁺ bound to the ORs can be redox active and has been shown to induce cleavage within the OR region, a process requiring conserved Trp residues. Using computational modeling, we have observed that electron transfer from Trp residues to copper can be favorable. These models also reveal that an indole-based radical cation or Cu⁺ can initiate reactions leading to protein backbone cleavage. We have also demonstrated, by molecular dynamics simulations, that Cu²⁺ binding to the His96 and His111 residues in the remaining PrP N-terminal fragment can induce localized β-sheet structure, allowing us to suggest a potential mechanism for the initiation of β-sheet misfolding in the C-terminal domain by Cu²⁺.

Characterization of the copper(II) binding site in the pink copper binding protein CusF by electron paramagnetic resonance spectroscopy

Electron paramagnetic resonance (EPR) spectroscopy has been used to structurally characterize the copper-binding site in CusF protein from Escherichia coli. The EPR spectra indicate a single type II copper center with parameters typical for nitrogen and oxygen ligands (A~200 G, g~2.186, g~2.051). The pulsed EPR data show that one of the ligands to Cu²⁺ is an imidazole ring of a histidine residue. The remote amino nitrogen of this imidazole ring is readily observed by electron spin-echo envelope modulation spectroscopy, while the imino nitrogen that is directly coordinated to the Cu²⁺ ion is observed by pulsed electron–nuclear double resonance (ENDOR). In addition, the ENDOR spectra reveal the presence of one more nitrogen ligand that was assigned to be a deprotonated peptide nitrogen. Apart from the two nitrogen ligands, it has been established that there are two nearby hydroxyl protons, although whether these belong to a single equatorial water ligand or two equatorial hydroxide ligands is not known.

Interplay between glutathione, Atx1 and copper: X-ray absorption spectroscopy determination of Cu(I) environment in an Atx1 dimer

X-ray absorption techniques have been used to characterise the primary coordination sphere of Cu(I) bound to glutathionate (GS⁻), to Atx1 and in Cu₂^I(GS⁻)₂(Atx1)₂, a complex recently proposed as the major form of Atx1 in the cytosol. In each complex, Cu(I) was shown to be triply coordinated. When only glutathione is provided, each Cu(I) is triply coordinated by sulphur atoms in the binuclear complex Cu^I ₂(GS⁻)₅, involving bridging and terminal thiolates. In the presence of Atx1 and excess of glutathione, under conditions where Cu^I ₂(GS⁻)₂(Atx1)₂ is formed, each Cu(I) is triply coordinated by sulphur atoms. Given these constraints, there are two different ways for Cu(I) to bridge the Atx1 dimer: either both Cu(I) ions contribute to bridging the dimer, or only one Cu(I) ion is responsible for bridging, the other one being coordinated to two glutathione molecules. These two models are discussed as regards Cu(I) transfer to Ccc2a.

The configuration of the Cu2+ binding region in full-length human prion protein

The cellular prion protein (PrP^C) is a Cu²⁺ binding protein connected to the outer cell membrane. The molecular features of the Cu²⁺ binding sites have been investigated and characterized by spectroscopic experiments on PrP^C-derived peptides and the recombinant human full-length PrP^C (hPrP-[23-231]). The hPrP-[23-231] was loaded with ⁶³Cu under slightly acidic (pH 6.0) or neutral conditions. The PrP^C/Cu²⁺-complexes were investigated by extended X-ray absorption fine structure (EXAFS), electron paramagnetic resonance (EPR), and electron nuclear double resonance (ENDOR). For comparison, peptides from the copper-binding octarepeat domain were investigated in different environments. Molecular mechanics computations were used to select sterically possible peptide/Cu²⁺ structures. The simulated EPR, ENDOR, and EXAFS spectra of these structures were compared with our experimental data. For a stoichiometry of two octarepeats per copper the resulting model has a square planar four nitrogen Cu²⁺ coordination. Two nitrogens belong to imidazole rings of histidine residues. Further ligands are two deprotonated backbone amide nitrogens of the adjacent glycine residues and an axial oxygen of a water molecule. Our complex model differs significantly from those previously obtained for shorter peptides. Sequence context, buffer conditions and stoichiometry of copper show marked influence on the configuration of copper binding to PrP^C. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Imidazolate-bridged dicopper(II) and copper(II)–zinc(II) complexes of macrocyclic ligand with methylimidazol pendants: Model study of copper(II)–zinc(II) superoxide dismutase

Two new homo- and hetero-dinuclear complexes, [Cu₂L(im)](ClO₄)₃4H₂O (1) and [CuZnL(im)](ClO₄)₃4H₂O (2) (where Im=1H-1midazole and L = 3, 6, 9, 16, 19, 22-hexaaza-6, 19-bis(1H-imidazol-4-ylmethyl)tricycle[22, 2, 2, 2^11,14]triaconta-1, 11, 13, 24, 27, 29-hexaene) were synthesized and characterized as model compounds for the active site of copper(II)–zinc(II) superoxide dismutase (Cu₂Zn₂–SOD). X-ray crystal structure analysis revealed that the metal centers in both complexes exhibit distorted trigonal-bipyramid coordination geometry and the CuCu and CuZn distances are both 6.02 Å. Magnetic and ESR spectral measurements of 1 showed antiferromagnetic exchange interactions between the imidazolate-bridged Cu(II) ions. The ESR spectrum of 2 displays typical signals of mononuclear Cu(II) complex, demonstrating the formation of heterodinuclear complex 2 rather than a mixture of homodinuclear Cu(II)/Zn(II) complexes. pH-dependent ESR and UV–visible spectral measurements manifest that the imidazolate exists as a bridging ligand from pH 6 to 11 for both complexes. The IC₅₀ values of 1.96 and 1.57 μM [per Cu(II) ion] for 1 and 2 suggest that they are good models for the Cu₂Zn₂–SOD.     

The affinity of copper binding to the prion protein octarepeat domain: evidence for negative cooperativity

The prion protein (PrP) binds Cu(2+) in its N-terminal octarepeat domain, composed of four or more tandem PHGGGWGQ segments. Previous work from our laboratory demonstrates that copper interacts with the octarepeat domain through three distinct coordination modes at pH 7.4, depending upon the precise ratio of Cu(2+) to protein. Here, we apply both electron paramagnetic resonance (EPR) and fluorescence quenching to determine the copper affinity for each of these modes. At low copper occupancy, which favors multiple His coordination, the octarepeat domain binds Cu(2+) with a dissociation constant of 0.10 (+/-0.08) nM. In contrast, high copper occupancy, involving coordination through deprotonated amide nitrogens, exhibits a weaker affinity characterized by dissociation constants in the range of 7.0-12.0 microM. Decomposition of the EPR spectra reveals the proportions of all coordination species throughout the copper concentration range and identifies significant populations of intermediates, consistent with negative cooperativity. At most copper concentrations, the Hill coefficient is less than 1.0 and approximately 0.7 at half copper occupancy. These findings demonstrate that the octarepeat domain is responsive to a remarkably wide copper concentration range covering approximately 5 orders of magnitude. Consideration of these findings, along with the demonstrated ability of the protein to quench copper redox activity at high occupancy, suggests that PrP may function to protect cells by scavenging excess copper.     

Synthesis, characterization and copper chemistry of a non-symmetric phenanthroline ligand: 2-Methyl-9-(3,5-dimethyl-N-pyrazolylmethyl)-1,10-phenanthroline

The synthesis of an unsymmetrical phenanthroline-based ligand, 2-methyl-9-(3,5-dimethylpyrazolylmethyl)-1,10-phenanthroline (L), and its cupric [Cu(II)] (1) and cuprous [Cu(I)] (2) complexes, are reported. The X-ray structures of each of these Cu complexes show distinct changes in coordination environments consistent with the geometrical preferences of the two oxidation states. In the solid-state, the Cu(II) complex (1) adopts a geometry best described as trigonal bipyramidal, while the Cu(I) complex (2) consists of a single dicationic dimer in which the ligand bridges between two copper ions, separated by 4.26 Å. The two Cu(I) coordination sites differ in 2 with one copper center complexed in a trigonal planar geometry and the other copper in a distorted tetrahedral environment; the latter coordination results from an additional CH₃CN ligand. Complex 1 exhibits a reversible redox process at −0.34 V versus Fc/Fc⁺ in CH₃CN, attributable to the Cu²⁺/Cu⁺ couple, while the dimeric Cu(I) complex (2) does not display this redox couple on the CV timescale. Over minutes however, complex 1 does oxidize in the presence of dioxygen to 2 in CH₃CN.     

Dinuclear Ni(II) and Cu(II) complexes with indolecarboxamide ligand: Synthesis, structure and properties

A potential tetradentate indolecarboxamide ligand, H₄L³ is synthesized and investigated for its coordination abilities towards Ni(II) and Cu(II) ions. Two H₄L³ ligands in their tetra-deprotonated form [L³]⁴⁻, were found to coordinate two metal centers resulting in the formation of [Ni₂(L³)₂]⁴⁻ (5) and [Cu₂(L³)₂]⁴⁻ (6) complexes. The crystal structure of 6 displays the formation of a dinuclear structure where two fully deprotonated ligands, [L³]⁴⁻ hold two copper(II) ions together. Even more interesting is the fact that both deprotonated ligands, [L³]⁴⁻ coordinate the copper ions in an identical and symmetrical fashion. The Na⁺ cations present in the complex 6 stitch together the dinuclear units resulting in the formation of a coordination chain polymer. Four sodium ions connect two dinuclear units via interacting with the O_amide groups. Further, Na⁺ cations were found to coordinate several DMF molecules; some of them are terminal and a few are bridging in nature. The solution state structure (determined by the NMR spectral analysis) of the diamagnetic complex 5 also supported the fact that two deprotonated ligands, coordinate two nickel ions in an identical and symmetrical fashion. Absorption spectral studies reveal that the solid-state square-planar geometry is retained in solution and both complexes do not show any tendency to coordinate potential axial ligands. The variable-temperature magnetic measurements and EPR spectra indicate spin-spin exchange between two copper centers in complex 6. The electrochemical results for both complexes show three irreversible oxidative responses that correspond to the oxidation of first and second metal ion followed by the ligand oxidation, respectively.     

Synthesis, magnetic properties and MCD spectra of a four coordinate copper(II) complex with two chelated phenolate-substituted imino nitroxides

A reaction of Cu(II) nitrate and 4,4,5,5-tetramethyl-2-(2-hydroxophenyl)imidazolin-1-oxyl (IM2PhOH) with potassium methoxide in methanol gave a homoleptic bis(imino nitroxide) complex of [Cu(IM2PhO)₂] (1). The single-crystal X-ray analysis of 1 showed that the imino nitroxide anion, IM2PhO⁻, chelated to a Cu^II ion via an imino-N and a phenoxide-O atoms to form a six-membered chelate ring. The coordination geometry around the Cu(II) ion was a distorted square-planar polygon; the dihedral angle between the two coordination planes, each of which was defined by Cu and two ligating atoms of IM2PhO⁻, was 40.81°. The temperature dependences of the magnetic susceptibility and the EPR spectra of 1 indicate that the magnetic interaction between Cu(II) and the imino nitroxide is ferromagnetic, while there is a moderate antiferromagnetic interaction between two coordinated imino nitroxides. A balance between these opposite interactions attains the lowest molecular doublet spin-state in 1. The variable temperature magnetic circular dichroism (MCD) spectrum of the complex 1 also showed two negative components with a large C term, which may be due to the charge-transfer (CT) transition originated from the d orbital to the SOMO π^* orbital in the spin-coupled IM2PhO⁻ radicals; resulting in the largely split doublet excited states with the spin singlet and triplet d⁸ configurations.     

Steric Effects in Release of Amides from Linkers in Solid-Phase Synthesis. Molecular Mechanics Modeling of Key Step in Peptide and Combinatorial Chemistry

   Acidolytic release of an amide from a solid support by C–N bond cleavage is an ubiquitous and crucial step in many solid-phase syntheses. We have used molecular modeling of a pseudo-equilibrium to explore substituent and steric effects in the release of peptides. The high acid-lability of the backbone amide linkage (BAL), which releases sec. amides, compared to C-terminal amide anchoring, which releases primary amides, was rationalized by steric relief upon cleavage. Thus, the relative stability of the carbenium ion formed from the linker in the acidolytic release is an insufficient measure of the lability of a linkage. In addition, predictions indicated that steric effects from the C^α-substituent in a BAL anchored amino acid residue should accelerate the acidolytic release. The finding that steric crowding leads to increased acid-lability will be important for further development and use of handles.

A new method to determine the structure of the metal environment in metalloproteins: investigation of the prion protein octapeptide repeat Cu2+ complex

Since high-intensity synchrotron radiation is available, extended X-ray absorption fine structure spectroscopy (EXAFS) is used for detailed structural analysis of metal ion environments in proteins. However, the information acquired is often insufficient to obtain an unambiguous picture. ENDOR spectroscopy allows the determination of hydrogen positions around a metal ion. However, again the structural information is limited. In the present study, a method is proposed which combines computations with spectroscopic data from EXAFS, EPR, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). From EXAFS a first picture of the nearest coordination shell is derived which has to be compatible with EPR data. Computations are used to select sterically possible structures, from which in turn structures with correct H and N positions are selected by ENDOR and ESEEM measurements. Finally, EXAFS spectra are re-calculated and compared with the experimental data. This procedure was successfully applied for structure determination of the Cu²⁺ complex of the octapeptide repeat of the human prion protein. The structure of this octarepeat complex is rather similar to a pentapeptide complex which was determined by X-ray structure analysis. However, the tryptophan residue has a different orientation: the axial water is on the other side of the Cu.     

The syntheses, characterizations, X-ray crystal structures and properties of Cu(I) complexes of a bis-bidentate schiff base ligand

Bis-bidentate Schiff base ligand L and its two mononuclear complexes [CuL(CH₃CN)₂]ClO₄ (1) and [CuL(PPh₃)₂]ClO₄ (2) have been prepared and thoroughly characterized by elemental analyses, IR, UV-Vis, NMR spectroscopy and X-ray diffraction analysis. In both the complexes the metal ion auxiliaries adopt tetrahedral coordination environment. Their reactivity, electrochemical and photophysical behavior have been studied. Complex 1 shows reversible Cu^II/I couple with potential 0.74 V versus Ag/AgCl in CH₂Cl₂. At room temperature L is weakly fluorescent in CH₂Cl₂, however in Cu(I) complexes 1 and 2 the emission in quenched.     

Copper(II) complexes of 3-amino-1,2,4-triazine and 2-aminopyrazine: Strategies for designing crystalline materials using coordination polymers

Reaction of 3-amino-1,2,4-triazine (3-atz) or 2-aminopyrazine (2-apz) with Cu(hfac)₂·xH₂O led to the formation of the monometallic and trimetallic complexes Cu(hfac)₂(3-atz)₂ (1), Cu₃(hfac)₆(3-atz)₂ (2), Cu(hfac)₂(2-apz)₂ (3) and Cu₃(hfac)₆(2-apz)₂ (4). The azine molecules behave as both monodentate and bridging bidentate ligands. The Cu(II) ions exhibit a range of coordination geometries. In 1 and 3, the complex is distorted octahedral with the Jahn-Teller axis lying along one of the O-Cu-O axes. In 2 and 4, the central Cu(II) ion is also distorted octahedral with the Jahn-Teller axis lying along the N-Cu-N axis, while the terminal Cu(II) ions are five-coordinate. Structure analysis reveals that addition of the amino-substituent makes the ligands more coordinating, leading to shorter CuN bonds. In the case of 4, this results in a stronger magnetic superexchange pathway and the complex exhibits antiferromagnetic behavior at low temperatures.     

Modeling by assembly and molecular dynamics simulations of the low Cu2+ occupancy form of the mammalian prion protein octarepeat region: gaining insight into Cu2+-mediated beta-cleavage

The prion protein has garnered considerable interest because of its involvement in prion disease as well as its unresolved cellular function. The octarepeat region in the flexible N-domain is capable of binding copper through multiple coordination modes. Under conditions of low pH and low Cu²⁺ concentration, the four octarepeats (ORs) cooperatively coordinate a single copper ion. Based on the average structure of the PHGG and GWGQ portions of a copper-free OR₂ model from molecular dynamics simulations, the starting structures of the OR₄ complex could be constructed by assembling the repeating structure of PHGG and GWGQ fragments. The resulting model contains a preformed site suitable for Cu²⁺ coordination. Molecular dynamics simulations of Cu²⁺ bound to the assembled OR₄ model (Cu:OR₄) reveal a close association of specific Trp and Gly residues with the Cu²⁺ center. This low Cu²⁺-occupancy form of prion protein is redox-active and can readily initiate cleavage of the OR region, mediated by reactive oxygen species generated by Cu⁺. The OR region is known to be required for β-cleavage, as are the Trp residues within the OR region. The β-cleaved form of the prion protein accumulates in amyloid fibrils. Hence, the close approach of Trp and Gly residues to the Cu²⁺ coordination site in the low Cu²⁺-occupancy form of the OR region may signal an important interaction for the initiation of prion disease.     

Molecular dynamics simulations of two tandem octarepeats from the mammalian prion protein: fully Cu2+-bound and metal-free forms

Molecular dynamics simulations have been conducted on a model fragment (Ac-PHGGGWGQPHGGGW-NH₂) of the prion protein octarepeat domain, both in the Cu²⁺-bound and metal-free forms. The copper-bound models are based on the consensus structure of the core Cu²⁺-binding site of an individual octarepeat, relevant to the fully Cu²⁺-occupied prion protein octarepeat region. The model peptides contain Cu²⁺ bound through a His imidazole ring and two deprotonated amide N-atoms in the peptide backbone supplied by the following two Gly residues. Both the copper-bound and metal-free models have been simulated with the OPLS all-atom force field with the GROMACS molecular dynamics package. These simulations, with two tandem copper-binding sites, represent the minimum model necessary to observe potential structuring between the copper-binding sites in the octarepeat region. The GWGQ residues constitute a flexible linker region that predominantly adopts a turn, serving to bring adjacent His residues into close proximity. The consequent formation of stable structures demonstrates that the copper-bound octarepeat region allows the copper-coordinating sites to come into van der Waals contact, packing into particular orientations to further stabilize the bend in the GWGQ linker region.     

Dinuclear triply-bridged copper(II) compounds containing carboxylato bridges and di-2-pyridylamine as a ligand: synthesis, crystal structure, spectroscopic and magnetic properties

Three new triply-bridged dinuclear copper(II) compounds with carboxylato bridges, [Cu₂(μ-O₂CH)(μ-OH)(μ-Cl)(dpyam)₂](PF₆) (1), [Cu₂(μ-O₂CH)₂(μ-OH)(dpyam)₂](PF₆) (2) and [Cu₂(μ-O₂CCH₂CH₃)₂(μ-OH)(dpyam)₂](ClO₄) (3) (dpyam = di-2-pyridylamine) have been synthesized and characterized crystallographically and spectroscopically. Compound 1 consists of a dinuclear unit in which both copper(II) ions are bridged by three different ligands, i.e., formate, chloride and hydroxide anions, providing a distorted trigonal bipyramidal geometry with a CuN₂O₂Cl chromophore. Compounds 2 and 3 have two bridging formato ligands and two bridging propionato ligands, respectively, together with a hydroxo bridge. The carboxylato ligands in both compounds 2 and 3 exhibit different coordination modes. One is in a syn, syn η¹:η¹:μ₂ bridging mode and the other is in a monoatomic bridging mode. The structure of compound 2 involves a dinuclear unit, with a distorted trigonal bipyramidal geometry around each Cu(II) ion with a CuN₂O₃ chromophore. Compound 3 contains a non-centrosymmetric unit; the coordination environment around Cu(1) is a distorted square-pyramidal geometry and an intermediate geometry of sp and tbp around the Cu(II) ion. The Cu?Cu separations are 3.061, 3.113 and 3.006 Å for compounds 1, 2 and 3, respectively. The EPR spectra of all three compounds show a broad isotropic signal with a g value around 2.10.The magnetic susceptibility measurements, measured from 5 to 280 K, revealed a moderate ferromagnetic interaction between the Cu(II) ions with a singlet-triplet energy gap (J) of 79.7, 47.8 and 24.1 cm⁻¹, for compounds 1, 2 and 3, respectively. Also a very weak intermolecular antiferromagnetic interaction was observed between the dinuclear units.     

Double salts of copper(I) chloride incorporated hydroxylpyrimidine and tetrazole ligands

Hydrothermal reaction of copper(II) chloride with 2-hydroxypyrimidine generated double salt of [Cu₂Cl(μ₄-pymo)] (1) (Hpymo = hydroxylpyrimidine) while hydrothermal treatment of CuCl₂, NaN₃ and acetonitrile resulted in double salt of [Cu₂(mtta)Cl] (2) (Hmtta = 5-methyltetrazole) in which in situ [2 + 3] cycloaddition reactions of acetonitrile with azide formed mtta ligand. X-ray single crystal structural analyses revealed that 1 shows a two-dimensional layer formed by fusion of one-dimensional structural motifs. The two-dimensional layers in 1 are held together by C-H?Cl hydrogen bonds to form three-dimensional supramolecular array. Compound 2 has a three-dimensional framework constructed from ribbons and [Cu₈Cl₄]⁴⁺ units. Uncommon coordination modes of μ₄-1,2κO:3κN:4κN′ pymo and μ₄-Cl (Cl at the apex of a Cu₄Cl square pyramid) in 1 and μ₄-η¹:η¹:η¹:η¹ mtta in 2 were also observed. The short Cu(I)?Cu(I) distances were found in 1 and 2, indicating the existence of Cu(I)?Cu(I) interactions.