Histidine (His) is a rare amino acid, comprising only ∼2% of proteins, yet it plays a critical biological role. Nearly half of all catalytic sites contain His, reflecting its unique ability to switch between neutral and positively charged states near physiological pH. This property allows His to mediate diverse interactions, including electrostatics, metal binding, cation-π, π-π, and hydrogen bonding, making it an ideal molecular switch in proteins. Despite its importance, most computational models treat His with a fixed or averaged charge. This overlooks how His protonation states impact protein structure, especially in intrinsically disordered proteins (IDPs), where local environments change rapidly. To address this limitation, we developed a coarse-grained framework (IDPH) that explicitly represents both neutral (His 0 ) and protonated (His + ) states. Rather than averaging charges, IDPH allows His to switch dynamically in response to pH and local interactions of His. Using IDPH, we reproduced experimental trends for His-containing IDPs and showed that His interactions with cationic and aromatic residues significantly alter the sampled conformations of IDPs. Our simulations reveal that His protonation is highly sensitive to its local contacts, demonstrating that even at fixed pH, shifts in the local chemical environment can trigger changes in His charge state. This switch, in turn, reshapes local contacts and ultimately IDP conformations. Together, these findings establish a mechanistic basis for histidine as a molecular switch in IDPs and highlight how chemical context, beyond pH, influences conformational sampling. This insight paves the way for the rational design of His-rich peptides with tailored environmental sensitivity, including applications in targeted drug delivery to acidic cancer cells.
Calinsky et al. (2026) studied this question.