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Structural transitions in full-length human prion protein detected by xenon as probe and spin labeling of the N-terminal domain.

Narayanan SP, Nair DG, Schaal D, Barbosa de Aguiar M, Wenzel S, Kremer W, Schwarzinger S, Kalbitzer HR - Sci Rep (2016)

Bottom Line: Xenon bound PrP was modelled by restraint molecular dynamics.As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain.This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn(2+)-binding to the octarepeat motif.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (CMRCB), University of Regensburg, 93040 Regensburg, Germany.

ABSTRACT
Fatal neurodegenerative disorders termed transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of fibrils of misfolded prion protein PrP. The noble gas xenon accommodates into four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23-230) as detected by [(1)H, (15)N]-HSQC spectroscopy. In thermal equilibrium a fifth xenon binding site is formed transiently by amino acids A120 to L125 of the presumably disordered N-terminal domain and by amino acids K185 to T193 of the well-folded domain. Xenon bound PrP was modelled by restraint molecular dynamics. The individual microscopic and macroscopic dissociation constants could be derived by fitting the data to a model including a dynamic opening and closing of the cavities. As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain. This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn(2+)-binding to the octarepeat motif.

No MeSH data available.


Related in: MedlinePlus

NMR-Structure of huPrP with bound xenon.The NMR structure of huPrP with xenon bound was calculated from the NMR data starting with the 20th structure of 2KUN. (a) Overlay of the structure in the presence (red) and absence of xenon (green). (b) Lowest energy structure with residues showing significant effects induced by binding of xenon and/or by applying high pressure1522. Residues showing only xenon effects > σ0 (red) and in addition high pressure effects > 2σ0 (orange). Residues showing high pressure effects > σ0 only are depicted in blue, residues not detectable (e.g. prolines) or with smaller effects are depicted in grey.
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f5: NMR-Structure of huPrP with bound xenon.The NMR structure of huPrP with xenon bound was calculated from the NMR data starting with the 20th structure of 2KUN. (a) Overlay of the structure in the presence (red) and absence of xenon (green). (b) Lowest energy structure with residues showing significant effects induced by binding of xenon and/or by applying high pressure1522. Residues showing only xenon effects > σ0 (red) and in addition high pressure effects > 2σ0 (orange). Residues showing high pressure effects > σ0 only are depicted in blue, residues not detectable (e.g. prolines) or with smaller effects are depicted in grey.

Mentions: The structural model of the prion protein with xenon bound at the four cavities was calculated by placing xenon atoms in the four cavities, optimizing the structure by a simulated annealing approach on the basis of pseudo restraints obtained from the chemical shift and cross peak volume changes after binding of xenon. The obtained structures were refined in explicit water (for details see Materials and Methods). The lowest energy structure is shown in Fig. 5 together with the residues showing significant effects after binding of xenon. The structure with five xenon atoms bound is compared with the initial structure where some of the cavities are too small to accept a xenon atom. Xenon binding induces some structural rearrangements in the xenon binding cavities but only small global changes are required for accommodating the xenon atoms. The xenon atoms mainly interact with hydrophobic amino acid side chains and aromatic rings, in cavity A1 with V161 and F175, in cavity B with F141 and Y150, in cavity C with Y157 and F198, and in cavity D with L125, Y128, and Y162. Only cavity A2 does not show an interaction with such typical hydrophobic residues. Here the methylene groups of E168, S170, and N174 constitute the main interaction partners (see supplementary Table S1). Note that the positions of the first N-terminal residues in this figure and especially the location of G93 is quite arbitrary, since it is the result of the molecular dynamics refinement but is not supported by sufficient experimental restraints.


Structural transitions in full-length human prion protein detected by xenon as probe and spin labeling of the N-terminal domain.

Narayanan SP, Nair DG, Schaal D, Barbosa de Aguiar M, Wenzel S, Kremer W, Schwarzinger S, Kalbitzer HR - Sci Rep (2016)

NMR-Structure of huPrP with bound xenon.The NMR structure of huPrP with xenon bound was calculated from the NMR data starting with the 20th structure of 2KUN. (a) Overlay of the structure in the presence (red) and absence of xenon (green). (b) Lowest energy structure with residues showing significant effects induced by binding of xenon and/or by applying high pressure1522. Residues showing only xenon effects > σ0 (red) and in addition high pressure effects > 2σ0 (orange). Residues showing high pressure effects > σ0 only are depicted in blue, residues not detectable (e.g. prolines) or with smaller effects are depicted in grey.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4920026&req=5

f5: NMR-Structure of huPrP with bound xenon.The NMR structure of huPrP with xenon bound was calculated from the NMR data starting with the 20th structure of 2KUN. (a) Overlay of the structure in the presence (red) and absence of xenon (green). (b) Lowest energy structure with residues showing significant effects induced by binding of xenon and/or by applying high pressure1522. Residues showing only xenon effects > σ0 (red) and in addition high pressure effects > 2σ0 (orange). Residues showing high pressure effects > σ0 only are depicted in blue, residues not detectable (e.g. prolines) or with smaller effects are depicted in grey.
Mentions: The structural model of the prion protein with xenon bound at the four cavities was calculated by placing xenon atoms in the four cavities, optimizing the structure by a simulated annealing approach on the basis of pseudo restraints obtained from the chemical shift and cross peak volume changes after binding of xenon. The obtained structures were refined in explicit water (for details see Materials and Methods). The lowest energy structure is shown in Fig. 5 together with the residues showing significant effects after binding of xenon. The structure with five xenon atoms bound is compared with the initial structure where some of the cavities are too small to accept a xenon atom. Xenon binding induces some structural rearrangements in the xenon binding cavities but only small global changes are required for accommodating the xenon atoms. The xenon atoms mainly interact with hydrophobic amino acid side chains and aromatic rings, in cavity A1 with V161 and F175, in cavity B with F141 and Y150, in cavity C with Y157 and F198, and in cavity D with L125, Y128, and Y162. Only cavity A2 does not show an interaction with such typical hydrophobic residues. Here the methylene groups of E168, S170, and N174 constitute the main interaction partners (see supplementary Table S1). Note that the positions of the first N-terminal residues in this figure and especially the location of G93 is quite arbitrary, since it is the result of the molecular dynamics refinement but is not supported by sufficient experimental restraints.

Bottom Line: Xenon bound PrP was modelled by restraint molecular dynamics.As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain.This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn(2+)-binding to the octarepeat motif.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (CMRCB), University of Regensburg, 93040 Regensburg, Germany.

ABSTRACT
Fatal neurodegenerative disorders termed transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of fibrils of misfolded prion protein PrP. The noble gas xenon accommodates into four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23-230) as detected by [(1)H, (15)N]-HSQC spectroscopy. In thermal equilibrium a fifth xenon binding site is formed transiently by amino acids A120 to L125 of the presumably disordered N-terminal domain and by amino acids K185 to T193 of the well-folded domain. Xenon bound PrP was modelled by restraint molecular dynamics. The individual microscopic and macroscopic dissociation constants could be derived by fitting the data to a model including a dynamic opening and closing of the cavities. As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain. This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn(2+)-binding to the octarepeat motif.

No MeSH data available.


Related in: MedlinePlus