Protein functions result from local and collective atomic motions that span a wide range of time scales. An integrated analysis of experimental and simulation data can shed light on the detailed mechanism of these motions. Applying a high electric field to protein crystals enables conformational changes that can be captured by time-resolved X-ray crystallography. Such an experiment (referred to as EF-X) carried out on a human PDZ domain obtained a series of atomistic ''snapshots'' of ensemble averages protein dynamics at 50 to 100 ns time intervals. Here, we present a molecular dynamics (MD) study of the same system and provide a detailed picture of the protein dynamics in between the experimental ''snapshots''. We replicated the experimental conditions and system geometry in the presence and absence of an electric field. By constructing a model of the protein crystal as a 3x3x3 supercell with a total of 108 individual proteins, we achieved extensive sampling of the protein conformational ensemble at the sub-millisecond time scale. A number of techniques, including principal component analysis and strain analysis, were utilized to quantify the effects of the electric field on the protein structure and crystal symmetry. This study demonstrates how MD simulations can complement information obtained in EF-X experiments by providing the higher spatial and temporal resolution of underlying dynamical processes.
Abnormal (misfolded) form of human prion protein displays high propensity towards self-association which may result in formation of insoluble fibrillar
The misfolding and aggregation of the amyloid-b (Ab) peptide plays a central role in the pathogenesis of Alzheimer's disease (AD). Targeting the generation or structure of the highly cytotoxic oligomeric species that form during the deposition process represents a promising therapeutic strategy to reduce the toxicity associated with Ab aggregation. Through an integrative approach combining in vitro techniques, including chemical kinetics, atomic force microscopy, and other biophysical measurements, with in vivo methods, including neuroblastoma cells and a C. elegans model of neurodegenerative disease, we have investigated modes by which oligomeric aggregates can be targeted with small molecules. We thus report compounds that show that the cytotoxicity related to Ab aggregation can be reduced both by the promotion of fibril formation and by the direct modification of oligomer structure. Indeed, both approaches were revealed to generate aggregates with unique tinctorial properties and reduced cytotoxicity. These results provide insight into the role of oligomers in the induction of cellular toxicity, and suggest that novel mechanisms of modulating the aggregation process, in addition to inhibiting oligomer production, may provide a viable therapeutic route for the treatment of AD.
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