Computational and Spectroscopic Characterization of the Photocycle of an Artificial Rhodopsin

Abstract

The photocycle of a reversible photoisomerizing rhodopsin mimic (M2) is investigated. This system, based on the cellular retinoic acid binding protein, is structurally different from natural rhodopsin systems, but exhibits a similar isomerization upon light irradiation. More specifically, M2 displays a 15-cis to all-trans conversion of retinal protonated Schiff base (rPSB) and all-trans to 15-cis isomerization of unprotonated Schiff base (rUSB). Here we use hybrid quantum mechanics/molecular mechanics (QM/MM) tools coupled with transient absorption and cryokinetic UV–vis spectroscopies to investigate these isomerization processes. The results suggest that primary rPSB photoisomerization of M2 occurs around the C13C14 double bond within 2 ps following an aborted-bicycle pedal (ABP) isomerization mechanism similar to natural microbial rhodopsins. The rUSB isomerization is much slower and occurs within 48 ps around the C15N double bond. Our findings reveal the possibility to engineer naturally occurring mechanistic features into artificial rhodopsins and also constitute a step toward understanding the photoisomerization of UV pigments. We conclude by reinforcing the idea that the presence of the retinal chromophore inside a tight protein cavity is not mandatory to exhibit ABP mechanism.

Excited-state dynamics of the all-trans protonated retinal Schiff base in CRABPII-based rhodopsin mimics

“…We can not determine the structures of the two intermediate states through the spectra obtained from current experiments. However, according to the hypothesis proposed in literature (17), we infer that the intermediate state J should be the excited state of 13C-15T-PSB while the intermediate state K should be the excited state of 13C-15C-PSB.…”

“…The proposed photoreaction cycle according to the experimental observations. The states colored in orange are not directly observed in the experiment but inferred according to the hypothesis proposed in reference(17). …”

“…They also investigated the spectral characteristics and photoreaction dynamics of the RSB in several of the rhodopsin mimics. They tuned the light absorption in a wide spectral range from purple to red using point mutations around the RSB region in CRABPII-based mimic (10) and CRBPII-based mimic (14); They explored the dynamics of the AT-PRSB in CRBPII-based rhodopsin mimics from both TAS experiments and simulations (15; 16); They also revealed the conversion between 15C-PRSB and all-trans unprotonated RSB (AT-URSB) in a Hexa-mutant (M2-KFVQ:P39Y: R59Y) of the CRABPII-based rhodopsin mimics in the neutral solution (17). However, the dynamics of the AT-PRSB in the CRABPII-based rhodopsin mimics have not yet been investigated.…”

Xanthopsin‐Like Systems via Site‐Specific Click‐Functionalization of a Retinoic Acid Binding Protein

“…We have demonstrated the feasibility of a site-specific clickfunctionalization of a lysine residue buried into a lipophilic binding sites and leading to the production of three different xanthopsin-like structures. This result opens the path to the preparation of entire libraries of novel synthetic LRPs through the design of diverse MBHAs whose reactivity with M2 may be computationally screened via docking and -as done for rhodopsin mimics [44][45][46][47] -studied via quantum chemical calculations (see Ref. [46]) and X-ray crystallographic analysis.…”

“…This result opens the path to the preparation of entire libraries of novel synthetic LRPs through the design of diverse MBHAs whose reactivity with M2 may be computationally screened via docking and -as done for rhodopsin mimics [44][45][46][47] -studied via quantum chemical calculations (see Ref. [46]) and X-ray crystallographic analysis. For instance, such libraries can be prepared by: (i) designing MBHAs yielding sets of diversely substituted p-hydroxycinnamate (pcoumarate) derivatives that would then yield M2-based xanthopsin mimics with different spectroscopic and reactivity properties, (ii) engineering M2 variants to be conjugated with a specific MBHA derivative and useful for tuning/controlling, via the protein environment, the chromophore photochemistry and (iii) combining concepts i-ii to engineer systems where both the chromophore and protein are modified, yielding a plethora of M2-based xanthopsin-like LRPs to be used as a "labon-a-molecule": a tool that would allow the systematic modification of a reference LRP and, as a consequence, the discovery or verification of engineering principles (e. g. for the tuning of light absorption, emission and photochemical reactivity).…”