MOLECULAR MECHANISMS OF AMYLOID AGGREGATION IN PHYSIOLOGICAL ENVIRONMENT

Abstract

Aggregation of proteins and peptides into fibrillar deposits is a hallmark of neurodegenerative disorders, including Alzheimer’s disease, Parkinson’s disease, and several systemic amyloidoses. Oligomeric intermediates populated during the early stages of aggregation, rather than mature fibrils, are recognized as the primary toxic species driving neurodegeneration. The toxicity of these oligomers is attributed to structural features, such as surface hydrophobicity, size, and conformational heterogeneity, rather than to peptide sequence. This allows mechanistic insights from one amyloidogenic peptide to inform our understanding of others. The structural features of oligomers, in turn, are shaped by the physiological environment in which aggregation occurs. Understanding how environmental components modulate the kinetics, thermodynamics, and structural features of oligomer formation is therefore essential for the rational design oftherapeutic strategies against amyloid disorders. Oligomers are transient and structurally heterogeneous, and are therefore difficult to characterize via experimental techniques, most of which provide only ensemble-averaged informationwith limited molecular detail. Molecular dynamics (MD) simulations complement experimental studies by capturing the molecular interactions in atomic detail. However, peptide aggregation occurs over long timescales and involves large, multi-component systems whose atomistic simulation is computationally intractable, both because of the computational cost of reaching relevant timescales and because the rugged free-energy landscape of peptide aggregation restricts sampling. Coarse-grained (CG) MD addresses these limitations by reducing the number of interaction centers and smoothing the underlying energy landscape, while retaining the chemical specificity needed to capture peptide self-assembly in physiological environments. In this thesis, we use CG-MD simulations to investigate how three components of thephysiological milieu—glucose, mixed anionic lipid membranes, and calcium ions at lipid membranes—modulate the aggregation of the A? model peptide, A?16−22. This work uses the Water-Explicit Polarizable PROtein (WEPPROM) and Polarizable MEMbrane (WEPMEM) models developed in the Matysiak lab and extends this CG suite by integrating coarse-grained representations of glucose and calcium ions within the polarizable framework. The first study examines A?16−22 aggregation across a range of glucose concentrationsspanning healthy to hyperglycemic levels and identifies a non-covalent thermodynamic pathway in which the loss of glucose’s rotational entropy at the aggregate interface accelerates A? aggregation. The second study investigates A?16−22 binding and aggregation on mixed POPC/POPS membranes across physiologically relevant molar ratios of anionic lipids, and shows how anionic lipids truncate large disordered peptide aggregates into small, ordered oligomers—an effect absent for pure zwitterionic membranes. The third study extends this to the coupled three-component system of A?16−22, mixed POPC/POPS membranes, and Ca2+ ions, and shows that Ca2+ prevents this truncation by bridging POPS phosphate headgroups together near the peptides, thereby restricting anionic lipid mobility. Together, these studies provide molecular insights into how the physiological environmentexerts mechanistic control over amyloid assembly through distinct molecular routes—cosolute partitioning, anionic lipid mobility, and ionic bridging. These insights enable future investigations of amyloid aggregation in increasingly complex environments and may inform therapeutic strategies against amyloid disorders.