Experimentally Consistent Simulation of Aβ Peptides with a Minimal NMR Bias

Misfolded amyloid peptides are neurotoxic molecules associated with Alzheimer's disease. The Aβ peptide fragment is a decapeptide fragment of the complete Aβ42 peptide which is a hypothesized cause of Alzheimer's disease via amyloid fibrillogenesis. Aβ is investigated here with a combination of NMR (nuclear magnetic resonance) spectroscopy experiments and molecular dynamics simulations with experiment directed simulation (EDS). EDS is a maximum entropy biasing method that augments a molecular dynamics simulation with experimental data (NMR chemical shifts) to improve agreement with experiments and thus accuracy. EDS molecular dynamics shows that the Aβ monomer has a β turn stabilized by the following interactions: S26-K28, D23-S26, and D23-K28. NMR, total correlation spectroscopy, and rotating frame Overhauser effect spectroscopy experiments provide independent agreement. Subsequent two- and four-monomer EDS simulations show aggregation. Diffusion coefficients calculated from molecular simulation also agreed with experimentally measured values only after using EDS, providing independent assessment of accuracy. This work demonstrates how accuracy can be improved by directly using experimental data in molecular dynamics of complex processes like self-assembly.