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

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 [1H, 15N]-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 Zn2+-binding to the octarepeat motif.

Altered Domain Structure of the Prion Protein Caused by Cu2+ Binding and Functionally Relevant Mutations: Analysis by Cross-Linking, MS/MS, and NMR

“…However, these earlier experiments did not determine whether other regions of the N-terminal domain flanking the octapeptide repeats participated in the N-C interaction, and they did not address whether intramolecular docking occurred in the absence of metals. Several other previous studies, using biochemical or biophysical techniques, have also documented interactions between the N-and C-terminal domains of PrP C , although none have addressed the location of the extreme N-terminal residues (23-31) responsible for PrP toxicity, or the positioning of the segment between the octapeptide repeats and the globular domain (residues 91-127) (D'Angelo et al, 2012;Martinez et al, 2015;Narayanan et al, 2016;Thakur et al, 2011;Zahn et al, 2000).…”

Dissecting the Structural and Chemical Determinants of the “Open-to-Closed” Motion in the Mannosyltransferase PimA from Mycobacteria

“…Submicrosecond fluctuations arising from side chain rotations and small loop movements are commonly observed during substrate recognition and catalysis. In addition, enzyme function can involve slower and larger-amplitude collective motions, such as fold switches or domain motions, between a relatively small number of substates . Correlations between the conformational fluctuation time scale and the catalytic turnover have been empirically established for a variety of enzymes, e.g., CypA and HIV-1 protease .…”

Small Molecules with Anti-Prion Activity

“…The model was confirmed by its fairly good correlation with experimental data. The binding site is a cavity of PrP C known as pocket D [66]. In this model, interaction with compound 20b is dominated by hydrophobic contacts, involving the quinoline, thiazole and dimethoxyphenyl systems, but hydrogen bonds involving methoxyl groups play also a role.…”