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

Abstract: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 $\pi\pi^{*}$ state at $523.90~\mathrm{nm}$, in good agreement with the experimental absorption maximum near $515~\mathrm{nm}$ 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 $\beta$-barrels covalently joined by an inter-domain linker), the covalent tether holds the A206 interface docked throughout $1~\mathrm{ns}$ of room-temperature dynamics. We obtain a thermally averaged coupling of $J = 32.8 \pm 1.6~\mathrm{cm^{-1}}$ across the $1000$-frame trajectory (Davydov splitting $2|J| = 65.6 \pm 3.1~\mathrm{cm^{-1}}$), representing a $19\%$ near-field enhancement over the ensemble point-dipole estimate ($J_{\mathrm{PDA}} = 27.6 \pm 1.3~\mathrm{cm^{-1}}$) at the $24.69 \pm 0.32~\textÅ$ 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 $\beta$-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.

Chemical Physics (physics.chem-ph); Biological Physics (physics.bio-ph); Quantum Physics (quant-ph)

arXiv:2605.00027 [physics.chem-ph]

(or arXiv:2605.00027v2 [physics.chem-ph] for this version)

https://doi.org/10.48550/arXiv.2605.00027 Focus to learn more arXiv-issued DOI via DataCite

https://doi.org/10.1021/acs.jpcb.6c05048 Focus to learn more DOI(s) linking to related resources

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