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Localized and Collective Motions in HET-s(218-289) Fibrils from Combined NMR Relaxation and MD Simulation.

ABSTRACT: Nuclear magnetic resonance (NMR) relaxation data and molecular dynamics (MD) simulations are combined to characterize the dynamics of the fungal prion HET-s(218-289) in its amyloid form. NMR data is analyzed with the dynamics detector method, which yields timescale-specific information. An analogous analysis is performed on MD trajectories. Because specific MD predictions can be verified as agreeing with the NMR data, MD was used for further interpretation of NMR results: for the different timescales, cross-correlation coefficients were derived to quantify the correlation of the motion between different residues. Short timescales are the result of very local motions, while longer timescales are found for longer-range correlated motion. Similar trends on ns- and ?s-timescales suggest that ?s motion in fibrils is the result of motion correlated over many fibril layers.

SUBMITTER: Smith AA

PROVIDER: S-EPMC6618077 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Localized and Collective Motions in HET-s(218-289) Fibrils from Combined NMR Relaxation and MD Simulation.

Smith Albert A AA Ernst Matthias M Riniker Sereina S Meier Beat H BH

Angewandte Chemie (International ed. in English) 20190605 28

Nuclear magnetic resonance (NMR) relaxation data and molecular dynamics (MD) simulations are combined to characterize the dynamics of the fungal prion HET-s(218-289) in its amyloid form. NMR data is analyzed with the dynamics detector method, which yields timescale-specific information. An analogous analysis is performed on MD trajectories. Because specific MD predictions can be verified as agreeing with the NMR data, MD was used for further interpretation of NMR results: for the different times ...[more]

PMID: 31070275

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