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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

Cavities and pockets in human prion protein structures.Cavities were calculated with a probe radius of 0.12 nm in the huPrP structure deposited as (a) 2KUN (20th structure of the bundle) and (b) 1QM2 in the protein data base, respectively. The surface of the cavities is represented in violet. For more details see Table 2.
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f2: Cavities and pockets in human prion protein structures.Cavities were calculated with a probe radius of 0.12 nm in the huPrP structure deposited as (a) 2KUN (20th structure of the bundle) and (b) 1QM2 in the protein data base, respectively. The surface of the cavities is represented in violet. For more details see Table 2.

Mentions: NMR structures published of the human prion protein exhibit a number of hydrophobic cavities in the well-folded core (amino acids 125 to 231) but the full length prion protein may also transiently form new cavities when the presumably disordered N-terminus gets in contact with the compactly folded part of the protein. The cavities were analysed with the program CASTp in two sets of 20 NMR structures each published by Zahn et al.8 (pdb accession code 1QM1) and Ilc et al.42 (pdb accession code 2KUN), respectively. The size and shape of the cavities calculated by the program depends on the size of the probe that should fit into the cavity. We used two different probes, one with the size of a water molecule (radius 0.12 nm) and one with the size of a xenon atom (radius 0.22 nm). While the first NMR data set only contains coordinates of the folded core part of the structure (amino acid 125 to 228), the second data set provides additional information about the N-terminal amino acids (amino acid 90 to 227). It also has a point mutation at position 212 (Q to P), a mutation that is not expected to change the number or the properties of the cavities compared to the wild type. Using a water molecule as probe, it was found that cavities are not conserved among and within structural bundles as evidenced by cavity B shown in Fig. 2. An exception is cavity C that is present in all cases. Using a xenon atom as a probe the number of cavities that can accept a xenon atom without steric clashes is significantly reduced in the structural bundles. Cavity B is not large enough to host a xenon atom in any of the structures of the two data sets. Nevertheless, our experimental data support its (transient) existence in solution, since strong local effects induced by xenon binding are observable. A fifth cavity D is formed by the N-terminal part of the protein in some structures deposited in the data set 2KUN. This part of the structure is not included in data set 1QM1 and can therefore not be analyzed (Fig. 2). However, as a rule, the total volumes of most of the cavities found to fit a water molecule are larger than the corresponding volume of a sphere with the radius of a xenon atom with a volume of 0.045 nm3 (Table 2), indicating that these cavities could adopt xenon after a suitable change of their shapes.


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)

Cavities and pockets in human prion protein structures.Cavities were calculated with a probe radius of 0.12 nm in the huPrP structure deposited as (a) 2KUN (20th structure of the bundle) and (b) 1QM2 in the protein data base, respectively. The surface of the cavities is represented in violet. For more details see Table 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Cavities and pockets in human prion protein structures.Cavities were calculated with a probe radius of 0.12 nm in the huPrP structure deposited as (a) 2KUN (20th structure of the bundle) and (b) 1QM2 in the protein data base, respectively. The surface of the cavities is represented in violet. For more details see Table 2.
Mentions: NMR structures published of the human prion protein exhibit a number of hydrophobic cavities in the well-folded core (amino acids 125 to 231) but the full length prion protein may also transiently form new cavities when the presumably disordered N-terminus gets in contact with the compactly folded part of the protein. The cavities were analysed with the program CASTp in two sets of 20 NMR structures each published by Zahn et al.8 (pdb accession code 1QM1) and Ilc et al.42 (pdb accession code 2KUN), respectively. The size and shape of the cavities calculated by the program depends on the size of the probe that should fit into the cavity. We used two different probes, one with the size of a water molecule (radius 0.12 nm) and one with the size of a xenon atom (radius 0.22 nm). While the first NMR data set only contains coordinates of the folded core part of the structure (amino acid 125 to 228), the second data set provides additional information about the N-terminal amino acids (amino acid 90 to 227). It also has a point mutation at position 212 (Q to P), a mutation that is not expected to change the number or the properties of the cavities compared to the wild type. Using a water molecule as probe, it was found that cavities are not conserved among and within structural bundles as evidenced by cavity B shown in Fig. 2. An exception is cavity C that is present in all cases. Using a xenon atom as a probe the number of cavities that can accept a xenon atom without steric clashes is significantly reduced in the structural bundles. Cavity B is not large enough to host a xenon atom in any of the structures of the two data sets. Nevertheless, our experimental data support its (transient) existence in solution, since strong local effects induced by xenon binding are observable. A fifth cavity D is formed by the N-terminal part of the protein in some structures deposited in the data set 2KUN. This part of the structure is not included in data set 1QM1 and can therefore not be analyzed (Fig. 2). However, as a rule, the total volumes of most of the cavities found to fit a water molecule are larger than the corresponding volume of a sphere with the radius of a xenon atom with a volume of 0.045 nm3 (Table 2), indicating that these cavities could adopt xenon after a suitable change of their shapes.

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