Histidine Tautomerism-Mediated Regulation of β-Hairpin Formation and Primary Nucleation in Amyloidogenic PrP(106–126) A117 V Peptides

Histidine tautomerism is increasingly recognized as a subtle yet powerful regulator of protein structural dynamics, yet its mechanistic role in amyloid nucleation remains poorly understood. In current study, we investigate how histidine protonation states govern the early stage aggregation and primary nucleation of PrP(106–126) A117 V, a prion-related peptide whose mutation markedly accelerates oligomer formation and cytotoxicity. Using molecular dynamics simulations, we systematically characterized the conformational ensembles of monomers through tetramers across distinct histidine tautomeric states (δ and ε). We find that tautomerism exerts minimal influence on β-sheet propensity in monomers and dimers, but becomes decisive at the trimer and tetramer level: the (δδε) trimer adopts a β-hairpin, while the (δεεε) tetramer harbors two β-hairpins that collectively define a nascent nucleation core. Based on these observations, we hypothesize a potential two-step nucleation mechanism within the primary nucleation stage, in which structurally heterogeneous intermediates first accumulate, and one β-hairpin then serves as a template to recruit and organize a second, culminating in a β-hairpin-enriched nucleus. Our results establish histidine tautomerism as a molecular switch that gates the transition from disordered oligomers to ordered nuclei, offering a physicochemical framework for understanding primary nucleation in prion and, more broadly, amyloidogenic systems.