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Conformational ensemble of native ?-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations.

ABSTRACT: Combining structural proteomics experimental data with computational methods is a powerful tool for protein structure prediction. Here, we apply a recently-developed approach for de novo protein structure determination based on the incorporation of short-distance crosslinking data as constraints in discrete molecular dynamics simulations (CL-DMD) for the determination of conformational ensemble of the intrinsically disordered protein ?-synuclein in the solution. The predicted structures were in agreement with hydrogen-deuterium exchange, circular dichroism, surface modification, and long-distance crosslinking data. We found that ?-synuclein is present in solution as an ensemble of rather compact globular conformations with distinct topology and inter-residue contacts, which is well-represented by movements of the large loops and formation of few transient secondary structure elements. Non-amyloid component and C-terminal regions were consistently found to contain ?-structure elements and hairpins.

SUBMITTER: Brodie NI

PROVIDER: S-EPMC6453469 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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