Photoreaction Dynamics of Red-Shifting Retinal Analogues Reconstituted in Proteorhodopsin

A Set of Quantum-Mechanically Derived Force Fields for Natural and Synthetic Retinal Photoswitches

The diverse biological functions of rhodopsins are all triggered by the photoexcitation of retinal protonated Schiff base chromophores. This diversity can be traced back not only to variations in protein scaffolds in which the chromophore is embedded, but also to the different isomeric forms of the chromophore itself, whose role is crucial in several processes. Although most computational approaches for these systems often require classical molecular dynamics, efforts in providing a set of parameters able to accurately and consistently model several isomeric chromophores are lacking in the literature. The most recent efforts entail either refinements of general purpose force fields lacking in accuracy, or parametrization strategies that include environmental effects, which makes the resulting parameters not transferable to a different embedding. In this work, we provide accurate intramolecular force fields based on data purposely computed using Møller-Plesset second order perturbation theory, specifically tailored for varied natural retinal protonated Schiff bases and synthetic analogues often employed in retinal-based photoswitches. We demonstrate the quality of our quantum-mechanically derived force fields (QMD-FFs) through a wide set of validation tests. These consistently indicate that QMD-FFs outperform in all cases transferable, general-purpose FFs, delivering an excellent description of each chromophore in terms of equilibrium geometries, conformational landscapes, and optical properties in comparison to literature data, experimental measurements, and reference QM calculations. Our intramolecular QMD-FFs, distributed in electronic format, can be adopted to describe these chromophores in complex environments, exploiting intermolecular parameters compatible with those available in the literature for biological macromolecules.

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.

Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin

The green-light absorbing proteorhodopsin (GPR) is the archetype of bacterial light-driven proton pumps. Here, we present the 2.9 Å cryo-EM structure of pentameric GPR, resolving important residues of the proton translocation pathway and the oligomerization interface. Superposition with the structure of a close GPR homolog and molecular dynamics simulations reveal conformational variations, which regulate the solvent access to the intra- and extracellular half channels harbouring the primary proton donor E109 and the proposed proton release group E143. We provide a mechanism for the structural rearrangements allowing hydration of the intracellular half channel, which are triggered by changing the protonation state of E109. Functional characterization of selected mutants demonstrates the importance of the molecular organization around E109 and E143 for GPR activity. Furthermore, we present evidence that helices involved in the stabilization of the protomer interfaces serve as scaffolds for facilitating the motion of the other helices. Combined with the more constrained dynamics of the pentamer compared to the monomer, these observations illustrate the previously demonstrated functional significance of GPR oligomerization. Overall, this work provides molecular insights into the structure, dynamics and function of the proteorhodopsin family that will benefit the large scientific community employing GPR as a model protein.