The key to the yellow-to-cyan tuning in the green fluorescent protein family is polarisation

Abstract

Within a QM/MM approach, correctly predicting the tuning of the excitation energy of the chromophore in the GFP family requires to account for state-specific induction and for the coupling of the MM polarisation to the chromophore transition density.

Polarizable embedding QM/MM: the future gold standard for complex (bio)systems?

“…In more difficult cases where this strategy is not enough because of the intrinsic limits of the LR QM description in accurately describing the change in the state density, an integration of LR and SS QM methods (mostly CASSCF) has been proposed and successfully applied to various photoresponsive proteins. 90,91 To conclude the extension of polarizable QM/MM approaches to excitation processes, it is worth recalling a particular class of complex systems that have largely benefited from such a multiscale description, namely multichromophoric systems, in which an electronic excitation can be delocalized over several chromophoric units. A very important example of these systems are the pigment-protein complexes (also called antenna complexes) used in photosynthetic organisms to harvest light and transfer the excitation energy to the reaction centers for further transformation.…”

Two-Photon Absorption Cross-Sections in Fluorescent Proteins Containing Non-canonical Chromophores Using Polarizable QM/MM

“…In this work, the DsRed protein was chosen as the protein host for the set of non-canonical chromophores. Future work could involve the evaluation of 2PA properties of selected nCCs in other RFP hosts and/or a tailored environment, where amino acids surrounding the chromophore can be modified or substituted to tune its 1PA and 2PA properties (List et al, 2012b;Beerepoot et al, 2014b;Nifosì et al, 2019). Water molecules in the immediate surroundings of the chromophore can play a role in the absorption properties of fluorescent proteins (Zhang et al, 2011;Konold et al, 2014Konold et al, , 2016Faraji and Krylov, 2015;Şimşek and Brown, 2018).…”

Integrated structure-function dataset reveals key mechanisms underlying photochromic fluorescent proteins

“…Several studies, many involving QM/MM, have revealed that (de-)stabilization of the chromophore charge distribution, both in the ground and excited state, determines the absorption maximum. [35][36][37][38][39] The excited state of the FP chromophore displays charge transfer away from the hydroxybenzylidene moiety [34,[40][41][42]. Increased hydrogen bonding to the hydroxybenzylidene oxygen stabilizes the ground state and destabilizes the excited state, resulting in a blue-shift.…”

“…The W165 indole can also engage in electron-donating π-π interactions with the hydroxybenzylidene ring ( Figure S8B), which are assumed to stabilize the excited state charge transfer and lead to a red-shift. [34,39,[43][44][45] Instead, the observed blue-shift likely arises because the stacking perturbs the conjugation of the chromophore (tilt, twist and methylene bridge bond angles of -156°, -21°and 129°as compared to the average of -164°, -9°and 127°, respectively; see Figure S9 for angle definitions). This indicates that geometrical constraints on the chromophore can cancel the effects of hydrogen bonding and other chromophore interactions.…”

“…[37,44] However, the variation within the F145 mutants (zone 2 mutants) is only marginally captured by these two parameters. Whereas direct interactions, such as hydrogen bonding, with the chromophore can be expected to have the highest influence on the absorption maximum, indirect interactions can also play a role, such as a blue-shifting through the presence of polar residues [39,45]. However, the net effect of these polar residues appears to be minor: proteins with Y145 (rsEGFP and rsGreen07.b) are actually red-shifted compared to their non-polar residue-containing counterparts (rsGreen0.7 and rsGreenF) while the introduction of H/Q145 does not introduce the blue-shift that might be expected from these polar residues.…”