Amyloid fibrils have been shown to have peculiar optical properties since they can exhibit fluorescence in the absence of aromatic residues. In a recent study, we have shown that proton transfer (PT) events along hydrogen bonds (HBs) are coupled to absorption in the near UV range. Here, we gain more insights into the different types of hydrogen bonding interactions that occur in our model systems and the molecular factors that control the susceptibility of the protons to undergo PT and how this couples to the optical properties. In the case of the strong N–C termini interactions, a nearby methionine residue stabilizes the non-zwitterionic NH$\mathrm{<mrow\; data-mjx-texclass="ORD">2</mrow>}$–COOH pair, while zwitterionic NH$\mathrm{<mrow\; data-mjx-texclass="ORD">3</mrow>}$+–COO– is stabilized by the proximity of nearby crystallographic water molecules. Proton motion along the hydrogen bonds in the fibril is intimately coupled to the compression of the heavier atoms, similar to what is observed in bulk water. Small changes in the compression of the hydrogen bonds in the protein can lead to significant changes in both the ground and excited state potential energy surfaces associated with PT. Finally, we also reinforce the importance of nuclear quantum fluctuations of protons in the HBs of the amyloid proteins.