Distinct Protochromic Mechanisms Driving Green/Red Absorption in Phycocyanobilin-Binding Proteins

RcaE, a phycocyanobilin (PCB)-binding protein, undergoes a reversible structural conversion, shifting light absorption between red (Pr-state) and green (Pg-state). Using a quantum mechanical/molecular mechanical approach combined with a linear Poisson–Boltzmann equation, we reveal the molecular mechanisms underlying this 130 nm blue shift. The experimentally measured Pg-RcaE absorption wavelength is reproduced only when ring B of PCB is deprotonated. While the low-dielectric chromophore environment remains unchanged during the Pr-to-Pg conversion, Lys261 deprotonation in Pg-RcaE is driven by the loss of key electrostatic interactions, specifically the loss of salt bridges with PCB propionic groups. Unlike Slr1393g3, where a 110 nm blue shift arises from PCB conformational changes, RcaE employs a distinct mechanism, leveraging proton-mediated electrostatic changes while maintaining a low-dielectric environment. This Pr-to-Pg conversion is triggered by ring B deprotonation via Glu217, facilitated by water molecules forming a Grotthuss-like proton transfer pathway. This unique strategy achieves efficient photochromic switching and a large spectral shift without PCB structural rearrangements.