Non-Equilibrium Dynamics of the Time-Dependent Excitonic Coupling in Fluorescent Protein Dimers

We quantify the excitonic coupling in the homodimer of the dimeric Venus fluorescent protein using a quantum-classical hybrid workflow. Because the anionic chromophore carries appreciable double-excitation character, we obtain its site energy from domain-based local-pair-natural-orbital similarity-transformed equation-of-motion coupled-cluster theory (DLPNO-STEOM-CCSD), which places the in-protein bright ππ* state at 523.90 nm, in good agreement with the experimental absorption maximum near 515 nm and validated against an explicit triples-corrected EOM-CCSD(fT) benchmark; single-excitation time-dependent density functional theory (TDDFT) blueshifts this state. Applying a transition-density coupling (TDC) formalism to the STEOM transition density and simulating the VenusA206 tandem-dimer construct (two β-barrels covalently joined by an inter-domain linker), the covalent tether holds the A206 interface docked throughout 1 ns of room-temperature dynamics. We obtain a thermally averaged coupling of J = 32.8 plus or minus 1.6 cm-1 across the 1000-frame trajectory (Davydov splitting 2J = 65.6 plus or minus 3.1 cm-1), representing a 19% near-field enhancement over the ensemble point-dipole estimate (J PDA = 27.6 plus or minus 1.3 cm-1) at the 24.69 plus or minus 0.32 Å chromophore centroid separation. Furthermore, we argue that a separation of timescales resolves the apparent theoretical tension between intermediate experimental excitonic couplings and the highly decoherent biological environment. While it has been hypothesised that the fluorescent protein β-barrel scaffold sustains coupling by shielding the chromophore from thermal fluctuations, we emphasise that the separation of timescales applies irrespective of the exact degree of environmental decoherence and dissipation.