Flexible docking of an amyloid-forming peptide from β2-microglobulin

Using an all-atom, molecular dynamics-based, flexible docking method, the tertiary and quaternary structures of protofilaments of the “K3” fragment from β2-microglobulin (residues Ser20-Lys41) were predicted at low pH in a continuous mixture of water and 2,2,2-trifluoroethanol (TFE). Tetramers with energies very close to the global minimum were produced with Cα root-mean square deviation values under 4 Å over 88 residues compared to a recently solved SSNMR structure. The most accurate model distinguishes itself from other low-energy solutions in that it shows high structural similarity to another known fold, the parallel β-helix, in agreement with models proposed previously by several other groups. The method achieves efficiency without loss of generality or atomic detail by enforcing local symmetry on the individual peptides, rewarding intermolecular contacts, and iteratively building up the protofilaments by successively doubling the number of chains. Solvent effects were included in the model by treating the dielectric constant and surface tension as functions of the TFE concentration. In order to understand the physical basis for the stabilizing effects of TFE, the TFE concentration was varied from 0% to 50% (v/v) and a peak in stability was observed at 16%, where the polar and hydrophobic terms cancel out and close to the experimentally determined value of 20%.