Structural Hierarchy and Maturation of Amyloid Fibrils Revealed by Interface Descriptor Analysis

Here, we present a comprehensive, topology-driven analysis of 543 amyloid structures (all cryo-EM-determined parallel amyloid fibril structures available in the PDB and the Amyloid Atlas, covering multiple protein types, notably Tau and α-synuclein) utilizing a novel automated protocol, ACWF. By calculating per-residue interface descriptors─shape complementarity (Sc), buried surface area (Ab), and surface detail index (SDi)─via a sliding window approach, we quantify structural packing and interdigitation across ∼30,000 local interfaces. We introduce a sequence-overlap-modified RMSD (RMSDmod) metric for hierarchical clustering to robustly classify polymorphs and quantify structural diversity. Our results reveal that mature amyloid fibrils contain a mixture of tightly and loosely packed regions, with distinct interaction hot-spots characteristic to polymorph families. Clustering successfully distinguishes disease-specific topologies and tracks maturation pathways, demonstrating that ex vivo fibrils rearrange to more compact structures indicated by more buried side chains (larger Ab) and typically lowered Sc values compared to that seen in the case of in vitro produced fibrils formed over shorter time scales. This work establishes a topology- and interface-based framework that links residue-level interactions to polymorphic fibril evolution, exploring the most compacted as well as accessible and attackable regions.