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Our understanding of the rules controlling the spectral tuning of light absorbing proteins is limited. When looking at rhodopsins as canonical examples, the fact that the cavity incorporates the chromophore counterion in different positions and polar residues with different orientations, leads to patterns of electrostatic potential whose effect is not obvious. In this work we use a model of the optogenetic reporter Arch-3 capable to describe the effect of the diffusion of its counterion charge on both excitation energies (lambda-max) ) and chromophore geometry. By optimizing such charge for a set of increasing lambda values, we show that progression towards redder values occurs along two distinct paths featuring a “compact” or an “extended” charge diffusion respectively. These results are validated by showing that both paths replicate the experimentally observed relationships between lambda-max and chromophore isomerization in different sets of Arch-3 variants, NeoR variants and other microbial rhodopsins from 16 different organisms. 

Abstract We use quantum-classical trajectories to investigate the origin of the different photoisomerization quantum efficiency observed in the dim-light visual pigment Rhodopsin and in the light-driven biomimetic molecular rotorpara-methoxy N-methyl indanylidene-pyrrolinium (MeO-NAIP) in methanol. Our results reveal that effective light-energy conversion requires, in general, an auxiliary molecular vibration (called promoter) that does not correspond to the rotary motion but synchronizes with it at specific times. They also reveal that Nature has designed Rhodopsin to exploit two mechanisms working in a vibrationally coherent regime. The first uses a wag promoter to ensure that ca. 75% of the absorbed photons lead to unidirectional rotations. The second mechanism ensures that the same process is fast enough to avoid directional randomization. It is found that MeO-NAIP in methanol is incapable of exploiting the above mechanisms resulting into a 50% quantum efficiency loss. However, when the solvent is removed, MeO-NAIP rotation is predicted to synchronize with a ring-inversion promoter leading to a 30% increase in quantum efficiency and, therefore, biomimetic behavior. 

Rhodopsins are light-responsive proteins forming two vast and evolutionary distinct superfamilies whose functions are invariably triggered by the photoisomerization of a single retinal chromophore. In 2018 a third widespread superfamily of rhodopsins called heliorhodopsins was discovered using functional metagenomics. Heliorhodopsins, with their markedly different structural features with respect to the animal and microbial superfamilies, offer an opportunity to study how evolution has manipulated the chromophore photoisomerization to achieve adaptation. One question is related to the mechanism of such a reaction and how it differs from that of animal and microbial rhodopsins. To address this question, we use hundreds of quantum-classical trajectories to simulate the spectroscopically documented picosecond light-induced dynamics of a heliorhodopsin from the archaea thermoplasmatales archaeon (TaHeR). We show that, consistently with the observations, the trajectories reveal two excited state decay channels. However, inconsistently with previous hypotheses, only one channel is associated with the –C13QC14– rotation of microbial rhodopsins while the second channel is characterized by the –C11QC12– rotation typical of animal rhodopsins. The fact that such –C11QC12– rotation is aborted upon decay and ground state relaxation, explains why illumination of TaHeR only produces the 13-cis isomer with a low quantum efficiency. We argue that the documented lack of regioselectivity in double-bond excited state twisting motion is the result of an ‘‘adaptation’’ that could be completely lost via specific residue substitutions modulating the steric hindrance experienced along the isomerization motion. 

Abstract This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.