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

Prion Protein Octarepeat Domain Forms Transient β-Sheet Structures upon Residue-Specific Binding to Cu(II) and Zn(II) Ions

Misfolding of the cellular prion protein (PrP^C) is associated with the development of fatal neurodegenerative diseases called transmissible spongiform encephalopathies (TSEs). Metal ions appear to play a crucial role in PrP^C misfolding. PrP^C is a combined Cu(II) and Zn(II) metal-binding protein, where the main metal-binding site is located in the octarepeat (OR) region. Thus, the biological function of PrP^C may involve the transport of divalent metal ions across membranes or buffering concentrations of divalent metal ions in the synaptic cleft. Recent studies have shown that an excess of Cu(II) ions can result in PrP^C instability, oligomerization, and/or neuroinflammation. Here, we have used biophysical methods to characterize Cu(II) and Zn(II) binding to the isolated OR region of PrP^C. Circular dichroism (CD) spectroscopy data suggest that the OR domain binds up to four Cu(II) ions or two Zn(II) ions. Binding of the first metal ion results in a structural transition from the polyproline II helix to the β-turn structure, while the binding of additional metal ions induces the formation of β-sheet structures. Fluorescence spectroscopy data indicate that the OR region can bind both Cu(II) and Zn(II) ions at neutral pH, but under acidic conditions, it binds only Cu(II) ions. Molecular dynamics simulations suggest that binding of either metal ion to the OR region results in the formation of β-hairpin structures. As the formation of β-sheet structures can be a first step toward amyloid formation, we propose that high concentrations of either Cu(II) or Zn(II) ions may have a pro-amyloid effect in TSE diseases.

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

The metal-coordinating properties of the prion protein (PrP) have been the subject of intense focus and debate since the first reports of its interaction with copper just before the turn of the century. The picture of metal coordination to PrP has been improved and refined over the past decade, but structural details of the various metal coordination modes have not been fully elucidated in some cases. In the present study, we have employed 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 Cu(II) , Cu(I) , and Zn(II) with an N-terminal fragment of PrP. The PrP fragment corresponds to four tandem repeats representative of the mammalian octarepeat domain, designated as 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 have provided additional structural and thermodynamic data, and candidate structures have been used to inform EXAFS data analysis. The optimized geometries from DFT calculations have been used to identify potential coordination complexes for multi-histidine coordination of Cu(II) , Cu(I) , and Zn(II) in an aqueous medium, modelled 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 derived from DFT calculations, we have characterized the predominant coordination modes for the 1:1 complexes of Cu(II) , Cu(I) , and Zn(II) with the OR4 peptide at pH 7.4 at atomic resolution, which are best represented as square-planar [Cu(II) (His)4 ](2+) , digonal [Cu(I) (His)2 ](+) , and tetrahedral [Zn(II) (His)3 (OH2 )](2+) , respectively.

Histidine-containing host-defence skin peptides of anurans bind Cu2+. An electrospray ionisation mass spectrometry and computational modelling study

Anuran peptides which contain His, including caerin 1.8 (GLFKVLGSVAKHLLPHVVPVIAEKL-NH(2)), caerin 1.2 (GLLGVLGSVAKHVLPHVVPVIAEHL-NH(2)), Ala(15) maculatin 1.1 (GLFGVLAKVAAHVVAIEHF-NH(2)), fallaxidin 4.1 (GLLSFLPKVIGHLIHPPS-OH), riparin 5.1 (IVSYPDDAGEHAHKMG-NH(2)) and signiferin 2.1 (IIGHLIKTALGMLGL-NH(2)), all form MMet(2+) and (M + Met(2+)-2H(+))(2+) cluster ions (where Met is Cu, Mg and Zn) following electrospray ionisation (ESI) in a Waters QTOF 2 mass spectrometer. Peaks due to Cu(II) complexes are always the most abundant relative to other metal complexes. Information concerning metal(2+) connectivity in a complex has been obtained (at least in part) using b and y fragmentation data from ESI collision-induced dissociation tandem mass spectrometry (CID MS/MS). Theoretical calculations, using AMBER version 10, show that MCu(2+) complexes with the membrane active caerin 1.8, Ala(15) maculatin 1.1 and fallaxidin 4.1 are four-coordinate and approximating square planar, with ligands including His and Lys, together with the carbonyl oxygens of particular backbone amide groups. When binding can occur through two His, or one His and one Lys, the His/Lys ligand structure is the more stable for the studied systems. The three-dimensional (3D) structures of the complexes are always different from the previously determined structures of the uncomplexed model peptides (using 2D nuclear magnetic resonance (NMR) spectroscopy in membrane-mimicking solvents like trifluoroethanol/water).

Active-site dynamics and large-scale domain motions of sulfite oxidase: a molecular dynamics study

The physiologically vital enzyme sulfite oxidase employs rapid intramolecular electron transfer between a molybdenum ion in the C-terminal domain (the site of sulfite oxidation) and a heme moeity in the N-terminal domain to complete its catalytic cycle. Crystal structures of the enzyme show C- and N-terminal domain orientations that are not consistent with rapid intramolecular electron transfer. Domain motion has been postulated to explain this discrepancy. In the present work we employ molecular dynamics simulations to understand the large-scale domain motions of the enzyme. We observe motion of the N-terminal domain into an orientation similar to that postulated for rapid electron transfer. Our simulations also probe the dynamics of the active site and surrounding residues, adding a further level of structural and thermodynamic detail in understanding sulfite oxidase function.

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 alpha-helical C-terminal domain and a flexible extended N-terminal region. The latter can selectively bind Cu(2+) 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 beta-sheet content. Cu(2+) 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 Cu(2+) binding to the His96 and His111 residues in the remaining PrP N-terminal fragment can induce localized beta-sheet structure, allowing us to suggest a potential mechanism for the initiation of beta-sheet misfolding in the C-terminal domain by Cu(2+).

A potential mechanism for Cu2+ reduction, beta-cleavage, and beta-sheet initiation within the N-terminal domain of the prion protein: insights from density functional theory and molecular dynamics calculations

The N-terminal region of the native human prion protein encompasses four highly conserved octarepeats that each contain a single His, Pro, Gln, and Trp residue as well as several Gly residues. At neutral pH these repeats are capable of individually binding copper (Cu(2+)) ions, involving the His side chain and the backbone amide of the Gly residues. In addition, the two His residues at positions 96 and 111 are also capable of binding Cu(2+). At low concentrations of the metal ion or at low pH, one Cu(2+) may be bound by multiple His residues of the four octarepeats. This complex is known to be redox active, while none of the other Cu(2+)-bound complexes are. Using density functional theory and molecular dynamics calculations data demonstrated how this form of the protein could reduce Cu(2+), through a process involving electron transfer from the Trp side chain. The reduced Cu gives rise to reactive oxygen species (ROS), which can lead to beta-cleavage of the prion protein chain at any of the Gly residues around position 90. Protein fragments of lengths similar to those arising from beta-cleavage are predominantly found in both healthy and Creutzfeldt-Jakob disease (CJD)-affected brains. Models of Cu binding to the His96 and His111 residues also indicate that different modes of Cu(2+) binding result in formation of stable beta-hairpin structures in this region of the protein. It is postulated that through interactions with the C-terminal part of the protein these hairpins may initiate misfolding and yield more stable beta-sheet structures that might associate in the same fashion with additional prion proteins.

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 Cu(2+) 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 OR(2) model from molecular dynamics simulations, the starting structures of the OR(4) complex could be constructed by assembling the repeating structure of PHGG and GWGQ fragments. The resulting model contains a preformed site suitable for Cu(2+) coordination. Molecular dynamics simulations of Cu(2+) bound to the assembled OR(4) model (Cu:OR(4)) reveal a close association of specific Trp and Gly residues with the Cu(2+) center. This low Cu(2+)-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 beta-cleavage, as are the Trp residues within the OR region. The beta-cleaved form of the prion protein accumulates in amyloid fibrils. Hence, the close approach of Trp and Gly residues to the Cu(2+) coordination site in the low Cu(2+)-occupancy form of the OR region may signal an important interaction for the initiation of prion disease.

Studies of nitric oxide interaction with mono- and dinuclear copper(II) complexes of prion protein bis-octarepeat fragments

The interaction of nitric oxide with copper(ii) complexes of two octarepeat sequences belonging to the prion protein was studied, considering both mononuclear and dinuclear systems, i.e. Cu-Ac-(PHGGGWGQ)(2)-NH(2) and Cu(2)-Ac-(PHGGGWGQ)(2)-NH(2), respectively. The NO interaction with both systems was followed in aqueous solutions at physiological pH value, by using UV-Vis and EPR spectroscopic techniques as well as cyclic voltammetry. The mechanism of NO interaction with the mononuclear copper complex can be considered similar to that previously observed for the analogous copper systems with Ac-HGGG-NH(2) and Ac-PHGGGWGQ-NH(2). A more complicated behaviour was found with the copper dinuclear system, in which the involvement of two different intermediate complex species was evidenced. A positive cooperativity between the two copper ions, in the reduction process was inferred. When working with a large excess of the Ac-(PHGGGWGQ)(2)-NH(2) ligand, the frozen-solution EPR parameters pertain to the well characterized [Cu(N(im))(4)](2+) unit, which did not exhibit any interaction with NO. The presence of a free coordination site is the necessary requirement for the NO interaction to occur, as found only in the square-pyramidal geometry of [Cu(L)H(-2)] or [Cu(2)(L)H(-4)] complex species, which form when copper and ligand concentrations are similar.

Expansion of the octarepeat domain alters the misfolding pathway but not the folding pathway of the prion protein

A misfolded conformation of the prion protein (PrP), PrP (Sc), is the essential component of prions, the infectious agents that cause transmissible neurodegenerative diseases. Insertional mutations that lead to an increase in the number of octarepeats (ORs) in PrP are linked to familial human prion disease. In this study, we investigated how expansion of the OR domain causes PrP to favor a prion-like conformation. Therefore, we compared the conformational and aggregation modulating properties of wild-type versus expanded OR domains, either as a fusion construct with the protein G B1 domain (GB1-OR) or as an integral part of full-length mouse PrP (MoPrP). Using circular dichroism spectroscopy, we first demonstrated that ORs are not unfolded but exist as an ensemble of three distinct conformers: polyproline helix-like, beta-turn, and "Trp-related". Domain expansion had little effect on the conformation of GB1-OR fusion proteins. When part of MoPrP however, OR domain expansion changed PrP's folding landscape, not by hampering the production of native alpha-helical monomers but by greatly reducing the propensity to form amyloid and by altering the assembly of misfolded, beta-rich aggregates. These features may relate to subtle pH-dependent conformational differences between wild-type and mutant monomers. In conclusion, we propose that PrP insertional mutations are pathogenic because they enhance specific misfolding pathways of PrP rather than by undermining native folding. This idea was supported by a trial bioassay in transgenic mice overexpressing wild-type MoPrP, where intracerebral injection of recombinant MoPrP with an expanded OR domain but not wild-type MoPrP caused prion disease.

Unveiling the role of histidine and tyrosine residues on the conformation of the avian prion hexarepeat domain

The prion protein (PrPC) is a glycoprotein that in mammals, differently from avians, can lead to prion diseases, by misfolding into a beta-sheet-rich pathogenic isoform (PrPSc). Mammal and avian proteins show different N-terminal tandem repeats: PHGGGWGQ and PHNPGY, both containing histidine, whereas tyrosine is included only in the primary sequence of the avian protein. Here, by means of potentiometric, circular dichroism (CD), and molecular dynamics (MD) studies at different pH values, we have investigated the conformation of the avian tetrahexarepeat (PHNPGY)4 (TetraHexaPY) with both N- and C-termini blocked by acetylation and amidation, respectively. We have found, also with the help of a recently proposed protein chirality indicator (Pietropaolo, A.; Muccioli, L.; Berardi, R.; Zannoni, C. Proteins 2008, 70, 667-677), a conformational dependence on the protonation states of histidine and tyrosine residues: the turn formation is pH driven, and at physiological pH a pivotal role is played by the tyrosine OH groups which give rise to a very compact bent structure of backbone upon forming a hydrogen-bond network.