title: Probing amyloid-beta fibril stability by increasing ionic strengths.
abstract: Previous experimental studies have demonstrated changing the ionic strength of the solvent to have a great impact on the mechanism of aggregation of amyloid-beta (Aβ) protein leading to distinct fibril morphology at high and low ionic strength. Here, we use molecular dynamics simulations to elucidate the ionic strength-dependent effects on the structure and dynamics of the model Aβ fibril. The change in ionic strength was brought forth by varying the NaCl concentration in the environment surrounding the Aβ fibril. Comparison of the calculated vibrational spectra of Aβ derived from 40 ns all-atom molecular dynamics simulations at different ionic strength reveals the fibril structure to be stiffer with increasing ionic strength. This finding is further corroborated by the calculation of the stretching force constants. Decomposition of binding and dynamical properties into contributions from different structural segments indicates the elongation of the fibril at low ionic strength is most likely promoted by hydrogen bonding between N-terminal parts of the fibril, whereas aggregation at higher ionic strength is suggested to be driven by the hydrophobic interaction.
authors.affiliation: National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
authors.forename: Jernej
authors.initials: J
authors.lastname: Zidar
authors.forename: Franci
authors.initials: F
authors.lastname: Merzel
mesh_terms: D016229:Amyloid beta-Peptides / Q000737:chemistry*; D019277:Entropy; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009994:Osmolar Concentration; D055503:Protein Multimerization; D055550:Protein Stability; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry; D014732:Vibration
chemical_list: D016229:Amyloid beta-Peptides; D012997:Solvents