Conformational Preferences of the Full Chicken Prion Protein in Solution and Its Differences with Respect to Mammals

Pietropaolo, Adriana; Muccioli, Luca; Zannoni, Claudio; Rizzarelli, Enrico

doi:10.1002/cphc.200900078

Cited by 9 publications

(12 citation statements)

References 66 publications

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“…Interestingly, the structural role played by water molecules was analyzed by a molecular dynamics approach [91], highlighting that the bound and buried water that stabilizes a β-bulge between one edge of the sheet and helix 3, could prevent the avian PrP C aggregation. This finding was also supported by a 130 ns long molecular dynamics simulation of the full avian prion protein chPrP1-267, which finds again the latter bulge and a water molecule tightly bound to the Valine 168 [92]. Moreover, a rigid domain in the hexarepeat region was found, revealing a hydrogen bond mainly between the imidazole nitrogen of histidine 72 and the phenolic hydrogen of tyrosine 64, found also in the tetra-hexarepeat fragment [84].…”

Section: The Avian Prion and Its Difference From Mammal Analoguesupporting

confidence: 61%

Prion Proteins Leading to Neurodegeneration

Mendola

Pietropaolo²,

Pappalardo³

et al. 2008

CAR

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Prion diseases are fatal neurodegenerative disorders related to the conformational alteration of the prion protein (PrP C ) into a pathogenic and protease-resistant isoform PrP Sc . PrP C is a cell surface glycoprotein expressed mainly in the central nervous system and despite numerous efforts to elucidate its physiological role, the exact biological function remains unknown. Many lines of evidences indicate that prion is a copper binding protein and thus involved in the copper metabolism. Prion protein is not expressed only in mammals but also in other species such as birds, reptiles and fishes. However, it is noteworthy to point out that prion diseases are only observed in mammals while they seem to be spared to other species. The chicken prion protein (chPrP C ) shares about 30% of identity in its primary sequence with mammal PrP C . Both types of proteins have an N-terminal domain endowed with tandem amino acid repeats (PHNPGY in the avian protein, PHGGGWQ in mammals), followed by a highly conserved hydrophobic core. Furthermore, NMR studies have highlighted a similar globular domain containing three α-helices, one short 3 10 -helix and a short antiparallel β-sheet. Despite this structural similarity, it should be noted that the normal isoform of mammalian PrP C is totally degraded by proteinase K, while avian PrP C is not, thereby producing N-terminal domain peptide fragments stable to further proteolysis. Notably, the hexarepeat domain is considered essential for protein endocytosis, and it is supposed to be the analogous copper-binding octarepeat region of mammalian prion proteins. The number of copper binding sites, the affinity and the coordination environment of metal ions are still matter of discussion for both mammal and avian proteins.In this review, we summarize the similarities and the differences between mammalian and avian prion proteins, as revealed by studies carried out on the entire protein and related peptide fragments, using a range of experimental and computational approaches. In addition, we report the metaldriven conformational alteration, copper binding modes and the superoxide dismutase-like (SODlike) activity of the related copper(II) complexes. necessary to obtain data on copper ions binding, complex species, affinity and coordination mode, in order to have valuable grounding to explain the so-called "metal paradox".As shown in the previous example of rat and human Aβ, a useful approach consists in making comparative studies on proteins and peptides of different organisms. This approach allows us also to obtain information on the possible biological role of the proteins. Currently another common aspect of several proteins or peptides involved in such diseases is that their biological function remains unknown.8 PrP C is a highly conserved protein in mammals, but genes encoding homologous prion proteins have been reported in different species such as avians/birds, turtles, amphibians and fish [53][54][55][56][57][58][59]. It is important to point out that prion diseases are ob...

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Section: The Avian Prion and Its Difference From Mammal Analoguesupporting

confidence: 61%

Prion Proteins Leading to Neurodegeneration

Mendola

Pietropaolo²,

Pappalardo³

et al. 2008

CAR

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“…Those involve the shortening of the β sheet involving L82–L120 and the transition from the α helix to the type I β turn involving residues P5–R9 (Figure S2). However, the structural transition from an α helix to a type I β turn occurs easily in proteins under standard conditions. , In line with the other states, the closed “D” state also deviates from the “A” state in the tertiary structure [C α RMSD from the X-ray structure of 10 Å (Figure S1a)]. A shortening of the TrkA β sheet is observed in the L82–L120 section, as well as the stabilization of a 3 10 helix involving residues I6–H8 of NGF chains (Figure S2).…”

Section: Resultsmentioning

confidence: 66%

Binding of Zn(II) to Tropomyosin Receptor Kinase A in Complex with Its Cognate Nerve Growth Factor: Insights from Molecular Simulation and in Vitro Essays

Pietropaolo

Magrı̀

Greco

et al. 2017

ACS Chem. Neurosci.

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The binding of the human nerve growth factor (NGF) protein to tropomyosin receptor kinase A (TrkA) is associated with Alzhemeir's development. Owing to the large presence of zinc(II) ions in the synaptic compartments, the zinc ions might be bound to the complex in vivo. Here, we have identified a putative zinc binding site using a combination of computations and experiments. First, we have predicted structural features of the NGF/TrkA complex in an aqueous solution by molecular simulation. Metadynamics free energy calculations suggest that these are very similar to those in the X-ray structure. Here, the "crab" structure of the NGF shape binds tightly to two TrkA "pincers". Transient conformations of the complex include both more extended and more closed conformations. Interestingly, the latter features facial histidines (His60 and His61) among the N-terminal D1-D3 domains, each of which is a potential binding region for biometals. This suggests the presence of a four-His Zn binding site connecting the two chains. To address this issue, we investigated the binding of a D1-D3 domains' peptide mimic by stability constant and nuclear magnetic resonance measurements, complemented by density functional theory-based calculations. Taken together, these establish unambiguously a four-His coordination of the metal ion in the model systems, supporting the presence of our postulated binding site in the NGF/TrkA complex.

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“…7,8 The globular fold of the mammalian PrP c is also maintained in the avian counterpart 9,10 and both N-terminal domains are featured by tandem amino-acid repeats (PHNPGY in avians, PHGGGWGQ in mammals). [11][12][13] Notably, prion diseases are only observed in mammals, appearing to be precluded from occurring in avian species. 14 The physiological function of PrP c is unknown, even if it is widely recognized that the prion protein binds copper in vivo, and this interaction is required for its biological role.…”

Section: Introductionmentioning

confidence: 99%

“…Prion diseases are associated with the accumulation of a misfolded pathogenic form (PrP sc ) of the endogenous prion protein (PrP c ), a membrane-bound glycoprotein normally expressed in the central nervous system (CNS) of all mammals. – Nuclear magnetic resonance (NMR) studies performed on recombinant human PrP c proteins demonstrated that the C-terminal region, starting approximately at residue 125, adopts a globular fold that is largely helical, along with a small two-stranded β-sheet. Conversely, the N-terminal region, containing approximately 120 residues, is unstructured and flexible in solution. – There are currently no high-resolution structures for PrP sc , but it is known that the β-sheet content is increased during pathogenic conversion. , The globular fold of the mammalian PrP c is also maintained in the avian counterpart , and both N-terminal domains are featured by tandem amino-acid repeats (PHNPGY in avians, PHGGGWGQ in mammals). – Notably, prion diseases are only observed in mammals, appearing to be precluded from occurring in avian species …”

Section: Introductionmentioning

confidence: 99%

Membrane Interactions and Conformational Preferences of Human and Avian Prion N-Terminal Tandem Repeats: The Role of Copper(II) Ions, pH, and Membrane Mimicking Environments

et al. 2010

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The flexible N-terminal domain of the prion protein (PrP(c)) is believed to play a pivotal role in both trafficking of the protein through the cell membrane and its pathogenic conversion into the β sheet-rich scrapie isoform (PrP(sc)). Unlike mammalian PrP(c), avian prion proteins are not known to undergo any pathogenic conformational conversions. Consequently, some critical advances in our understanding of the molecular mechanisms underlying prion pathogenesis are expected from comparative studies of the biophysical properties of the N-terminal domains of the two proteins. The present study addresses the role played by different environmental factors, i.e., copper(II), pH, and membrane-mimicking environments, in assisting the conformational preferences of huPrP60-91 and chPrP53-76, two soluble peptides encompassing the N-terminal copper(II) binding domains of the human and chicken prion proteins, respectively. Moreover, the membrane interactions of huPrP60-91, chPrP53-76, and their copper(II) complexes were evaluated by Trp fluorescence in conjunction with measurements of the variation in thermotropic properties of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) unilamellar vesicles. Circular dichroism experiments revealed that huPrP60-91 adopts a predominant polyproline II conformation in aqueous solution that is destabilized at basic pH or in the presence of trifluoroethanol (TFE). Unlike anionic sodium dodecyl sulfate (SDS), which seems to stabilize the polyproline II conformation further, zwitterionic dodecylphosphocholine (DPC) micelles do not affect the peptide structure. On the contrary, copper(II) promptly promotes an increase in β-turn-rich structures. Differential scanning calorimetry (DSC) and Trp fluorescence assays carried out on DPPC model membranes after incubation with huPrP60-91 showed a marked tendency of the peptide to slowly penetrate the lipid bilayer with a concomitant conformational transition toward an extended β-sheet-like structure. Such an event, which was ascribed to the hydrophobic Trp side chain residues, was shown to also depend on the level of copper(II) occupancy along the peptide. Conversely, the CD spectra of chPrP53-76 aqueous solutions indicated the presence of a mixture of random-coil/β-turn-like structures whose resulting equilibrium was influenced by SDS and copper(II) addition. Furthermore, chPrP53-76 did not exhibit any tendency to interact with model membranes in either the presence or absence of copper(II). The results reported here provide evidence of the different roles played by environmental factors in affecting the conformation and membrane activity of human and avian prion N-terminal domains.

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Conformational Preferences of the Full Chicken Prion Protein in Solution and Its Differences with Respect to Mammals

Cited by 9 publications

References 66 publications

Prion Proteins Leading to Neurodegeneration

Prion Proteins Leading to Neurodegeneration

Binding of Zn(II) to Tropomyosin Receptor Kinase A in Complex with Its Cognate Nerve Growth Factor: Insights from Molecular Simulation and in Vitro Essays

Membrane Interactions and Conformational Preferences of Human and Avian Prion N-Terminal Tandem Repeats: The Role of Copper(II) Ions, pH, and Membrane Mimicking Environments

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