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1 TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

1 2014

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Comparative stability analysis of D23n mutated Aβ

Alred E. J., Scheele E. G., Berhanu W. M., Hansmann U. H. E.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2014

Vol. 18, No 4

365--371

Amyloid β (A β ) is the subject of numerous studies due to its link to the devastati ng Alzheimer’s disease and it exists in a parallel structure in fibril aggr egate. The Iowa mutant (D 23 N) A β posses a unique antiparallel fibril aggregate structure and can also form par allel structure. This structural difference, coupled with the fact that occurrence of the Iowa mutant is correlated with early onset Alzheimer’s, suggests to use these pep tides as candidates for computational studies of the structural determinants of the toxicity of Alzheimer’s disease. In order to compare the two observed A β structural motifs, we designed a computational study to probe the factors that affect the stability of parallel and antiparallel aggre gates. Since the structural changes may occur on a timescale beyond that sampled in traditi onal molecular dynamics ( MD ), we employed a techniques of scaling the mass to reduce the solution ’s viscosity and compared the results to regular molecular dynamics. The knowledge gaine d from this study could provide insight into the mechanism of selection for antiparallel and parallel two fold structures.