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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

Xenon binding in a two state model.In state 1 the cavity is too small to accommodate a xenon atom, in state 2 it has opened up. The equilibrium constants ki are defined as k1 = [3]/([Xe][1]), k2 = [4]/([Xe][2]), k3 = [1]/[2], k4 = [3]/[4].
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f3: Xenon binding in a two state model.In state 1 the cavity is too small to accommodate a xenon atom, in state 2 it has opened up. The equilibrium constants ki are defined as k1 = [3]/([Xe][1]), k2 = [4]/([Xe][2]), k3 = [1]/[2], k4 = [3]/[4].

Mentions: Since we experimentally demonstrated xenon binding to all cavities, either (1) the NMR structures do not represent the cavities with sufficient reliability and all cavities are always large enough to accept a xenon atom, or (2) the cavities exist in a second transient state of the protein, where a xenon atom can be incorporated. A special case is cavity D that is only formed when the N-terminus is in contact with the main folded structure. This interaction has to be transient, since it is only found in a small number of the structures. A satisfactory fit of the experimental data was only possible assuming an equilibrium between an open and a closed state of the cavities. However, the quality of the data does not allow a stable fit including the equilibrium constant for the open and closed state as additional free parameter. In a first approximation for this equilibrium constant the statistical distribution of the states, where the cavities are large enough to accommodate a xenon atom in the solution NMR structural bundles obtained by restraint molecular dynamics, can be used as an estimate of the occupancy of the states where a xenon atom can be incorporated (open state 1) and where not (closed state 2). The minimum scheme for such a dynamical equilibrium is depicted in Fig. 3. Cavity D is only formed by the interaction of the core structure with the N-terminus (corresponding in the model of Fig. 3 to the open state) and disappears when the contact is lost (“closed” state). For reasons of simplicity the model assumes that xenon binding to different cavities is independent. When xenon cannot bind to the closed state since it does not fit into the corresponding cavity or the xenon binding state does not exist in one state, the xenon binding constant k1 can be set to zero.


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)

Xenon binding in a two state model.In state 1 the cavity is too small to accommodate a xenon atom, in state 2 it has opened up. The equilibrium constants ki are defined as k1 = [3]/([Xe][1]), k2 = [4]/([Xe][2]), k3 = [1]/[2], k4 = [3]/[4].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Xenon binding in a two state model.In state 1 the cavity is too small to accommodate a xenon atom, in state 2 it has opened up. The equilibrium constants ki are defined as k1 = [3]/([Xe][1]), k2 = [4]/([Xe][2]), k3 = [1]/[2], k4 = [3]/[4].
Mentions: Since we experimentally demonstrated xenon binding to all cavities, either (1) the NMR structures do not represent the cavities with sufficient reliability and all cavities are always large enough to accept a xenon atom, or (2) the cavities exist in a second transient state of the protein, where a xenon atom can be incorporated. A special case is cavity D that is only formed when the N-terminus is in contact with the main folded structure. This interaction has to be transient, since it is only found in a small number of the structures. A satisfactory fit of the experimental data was only possible assuming an equilibrium between an open and a closed state of the cavities. However, the quality of the data does not allow a stable fit including the equilibrium constant for the open and closed state as additional free parameter. In a first approximation for this equilibrium constant the statistical distribution of the states, where the cavities are large enough to accommodate a xenon atom in the solution NMR structural bundles obtained by restraint molecular dynamics, can be used as an estimate of the occupancy of the states where a xenon atom can be incorporated (open state 1) and where not (closed state 2). The minimum scheme for such a dynamical equilibrium is depicted in Fig. 3. Cavity D is only formed by the interaction of the core structure with the N-terminus (corresponding in the model of Fig. 3 to the open state) and disappears when the contact is lost (“closed” state). For reasons of simplicity the model assumes that xenon binding to different cavities is independent. When xenon cannot bind to the closed state since it does not fit into the corresponding cavity or the xenon binding state does not exist in one state, the xenon binding constant k1 can be set to zero.

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