Secondary nucleation drives polymorph diversity in hIAPP amyloids

Amyloid fibrils are implicated in a myriad of human diseases. A striking observation is that fibrils extracted from diseased tissues are characterized by a restricted set of folds unique to the specific pathology. In contrast, fibrils grown \textit{in vitro} exhibit extensive structural diversity, suggesting that specific environmental and biochemical mechanisms \textit{in vivo} enforce structural selectivity. Here, we combine two-dimensional infrared (2D IR) spectroscopy and cryo-electron microscopy (cryo-EM) to investigate the mechanisms governing polymorph formation in the human Islet Amyloid Polypeptide (hIAPP). We demonstrate that 2D IR can resolve populations of distinct polymorphs identified by cryo-EM, enabling rapid label-free screening of conditions prior to labor-intensive microscopy screening. We find that conditions favoring secondary nucleation, such as high protein concentration, increase polymorphic diversity. Crucially, cryo-EM reveals that formed by secondary nucleation do not structurally replicate the parent template. Finally, by selectively inhibiting secondary nucleation using the C-terminal domain of the DNAJB6 chaperone, we steer aggregation toward a monomorphic state. These findings highlight the critical role of molecular chaperones in fibril polymorph selection.