Differences in the molecular structures of β2-microglobulin between the two morphologically different amyloid fibrils having a needlelike [long-straight (LS)] and flexible [wormlike (WL)] character were investigated by infrared, Raman, and vacuum-ultraviolet circular dichroism spectroscopy. It turned out that although the β-sheet content was comparable between the two kinds of fibrils (53 ± 6% for the LS fibril and 47 ± 6% for the WL fibril), the protonation states of the carboxyl side chains were distinctly different; the deprotonated (COO-) and protonated (COOH) forms were dominant in the LS and WL fibrils at pH 2.5, respectively,meaning that the pKa is specifically lowered in the LS fibril. Such a differencewas not observed for the fibrils of the core fragments. Since site-specific interactions generally cause variation in the pKa of carboxyl side chains in proteins, these results suggest that "hook"-like interactions generated by hydrogen bonding and the formation of a salt bridge are present in the LS fibril, providing enthalpic stabilization. Presumably, the carboxyl groups fix the spatial arrangement of β-strands and β-sheets, bringing about the needlelike morphology. The absence of this regulationwould result in the flexiblemorphology of the WL fibril, providing entropic stabilization.