Differences in conformational behavior of amyloid beta in solvent with different ionic strength
Zdeněk Křı́ž, Zdena Krištofíková, Jaroslav Koča · 2009
NTRODUCTION Amyloid beta-peptide (Abeta) is the major component of plaques found in the brains of Alzheimers patients. Among its two predominate forms - Abeta(1-40) and Abeta(1-42), the latter possesses stronger aggregation and deposition propensity than the former. To explore the conformational preference of Abeta(1-42) in solvent with different ionic strength, molecular dynamics (MD) simulations were performed. METHODS The human Abeta(1-42) structure presented in PDB database (code 1Z0Q) was used as starting point for MD simulations. The rat structure was prepared from human by mutation of 3 residues using Modeller software. The input structures were solvated by program SOLVATE and sodium and chloride ions in different concentrations were added to the system. For each system, 50 ns long trajectory was run and stability of the secondary structures of the protein was investigated. strength.