Driving Forces of Amyloid Protofibril Stability

Amyloid protofibrils are highly ordered protein assemblies characterized by a high content of β-sheets and are implicated in a wide range of pathological conditions. Amyloid crystals represent a distinct polymorphic form of amyloid assemblies that arise from the progressive untwisting and lateral association of twisted ribbon fibrils and correspond to the ground state of the protein folding and aggregation energy landscape. However, the driving forces underlying these processes remain difficult to quantify at the molecular level and from a quantum-chemical perspective. Here, we present a computational framework that combines molecular dynamics simulations, the Jarzynski estimator, and symmetry-adapted perturbation theory (SAPT) to evaluate the potential of mean force associated with peptide transfer either from a soluble state to a crystalline protofibril or from the protofibril into the surrounding microenvironment. We apply this approach to the NNQQ peptide, which has been shown by X-ray microcrystallography to form amyloid fibrils composed of parallel β-strands in the presence of alkali halide salts (Nature 447, 453–457 (2007)). Structural stability increases from Na+ to K+, driven by enhanced ion-peptide electrostatic interactions as revealed by SAPT analysis. Furthermore, quantum-chemical analysis reveals a clear polarity-dependence in the dominant stabilizing forces of amyloid protofibrils. The highly polar NNQQ polymorphs are stabilized mainly by induction (charge transfer and polarization) and dispersion interactions, whereas the highly apolar MVGGVV polymorphs from the amyloid-β sequence are determined predominantly by electrostatic and dispersion contributions. Together, this multidimensional framework establishes a quantitative, molecular-level foundation for understanding amyloid stability and its modulation by environmental conditions and protein identity. More broadly, it provides a general and transferable strategy for assessing amyloid stability and for rationally designing inhibitors that disrupt amyloid assemblies.