Photochemistry of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2 and Its Implications on Microbial Rhodopsin Research: Retrospective and Perspective

Abstract

The discovery of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) in 2013 has changed the paradigm that cation transport in microbial rhodopsins is restricted to the translocation of protons. Even though this finding is already remarkable by itself, it also reignited more general discussions about the functional mechanism of ion transport. The unique composition of the retinal binding pocket in KR2 with a tight interaction between the retinal Schiff base and its respective counterion D116 also has interesting implications on the photochemical pathway of the chromophore. Here, we discuss the most recent advances in our understanding of the KR2 functionality from the primary event of photon absorption by all-trans retinal up to the actual protein response in the later phases of the photocycle, mainly from the point of view of optical spectroscopy. In this context, we furthermore highlight some of the ongoing debates on the photochemistry of microbial rhodopsins and give some perspectives for promising future directions in this field of research.

Na+ Binding and Transport: Insights from Light-Driven Na+-Pumping Rhodopsin

“…Molecular dynamics simulations and large-scale XMCQDPT2-based QM/MM modeling further support these findings, linking KR2's reactive and non-reactive states to three distinct retinal pocket conformations [56]. While this specific topic lies beyond the scope of our current discussion, a comprehensive review by Asido et al provides further insights [57].…”

A subgroup of light-driven sodium pumps with an additional Schiff base counterion

“…First, the spectral shift upon the pH decrease in Er NaR is small, being <10 nm between pH 8.0 and 2.3 and only 3 nm between pH 8.0 and 4.3. We suggest that these small spectral shifts of Er NaR are not connected to the protonation of the main RSB counterion, D105, since its protonation is expected to cause much larger spectral changes 1 , 34 , 35 . Indeed, in KR2, the protonation of D116 upon pH decrease from 8.0 to 4.3 results in the red-shift of ~25 nm 1 .…”

A novel subgroup of light-driven sodium pumps with an additional Schiff base counterion

“…Analysis of time-resolved spectroscopic data was performed using OPTIMUS software. 18 The data of the ultrafast transient absorption and transient flash photolysis measurements were objected to the model-free lifetime distribution analysis (LDA) yielding the lifetime distributions of the individual photointermediate transitions, which are summarized in a lifetime density map (LDM).…”

“…Namely, there are the K, L, M, and O intermediates of a typical NDQ rhodopsin, where the O state was shown to be the only one associated with the transient sodium binding inside the protein 1 . For several NDQ rhodopsins, such as KR2 and the NaR from Indibacter alkaliphilus (IaNaR), the O state was demonstrated to consist of several sub-states [13][14][15][16][17][18] .…”