The light‐driven sodium ion pump: A new player in rhodopsin research

Abstract

Rhodopsins are one of the most studied photoreceptor protein families, and ion-translocating rhodopsins, both pumps and channels, have recently attracted broad attention because of the development of optogenetics. Recently, a new functional class of ion-pumping rhodopsins, an outward Na þ pump, was discovered, and following structural and functional studies enable us to compare three functionally different ion-pumping rhodopsins: outward proton pump, inward Cl À pump, and outward Na þ pump. Here, we review the current knowledge on structure-function relationships in these three light-driven pumps, mainly focusing on Na þ pumps. A structural and functional comparison reveals both unique and conserved features of these ion pumps, and enhances our understanding about how the structurally similar microbial rhodopsins acquired such diverse functions. We also discuss some unresolved questions and future perspectives in research of ion-pumping rhodopsins, including optogenetics application and engineering of novel rhodopsins.

Light-Driven Sodium-Pumping Rhodopsin: A New Concept of Active Transport

“…The overall structure of KR2 is very similar to that of microbial rhodopsins in general, such as lightdriven proton and chloride pumps, negative phototaxis and photochromic sensors, and a light-gated channel. 67,68 While the sodium ion was not clearly resolved by the structure of Kato et al, 65 it was observed in the structure of Gushchin et al 66 In the latter structure, KR2 forms pentamers in which the A−C helices are the interaction surface inside each pentamer (Figure 5A). The sodium binding site is located at the boundary of two molecules in the pentamer, where Y25, T83, and F86 of one monomer and D102 of another monomer participate in the binding, as do two internal water molecules (Figure 5A).…”

“…The X-ray structure of KR2 enlightened the location of the ion selectivity filter. A structural comparison between BR and KR2 suggests that relatively bulky residues on the cytoplasmic side of BR (F42, I45, and L224) are replaced by less bulky residues (N61, S64, and G263, respectively) in KR2 (Figure B). − This replacement makes the intracellular cavity larger, presumably allowing the entry of a sodium ion into the conducting pathway. Indeed, the shape and size of this pore are major determinants of ion selectivity in KR2, because N61 and G263 mutants are able to pump potassium ions. , Among these mutants, the most efficient potassium pump was N61P/G263W .…”

“…A hydrogen-bonding network involving N112 participates in transient binding . The binding of sodium to the Schiff base region accompanies reverse proton transfer from D116 to the Schiff base in the O intermediate, and reorganization of the ion pair at the Schiff base region prevents the backflow of sodium ions, , though the reverse proton transfer process from D116 has to be clarified.…”

Natronomonas salsuginis sp. nov., a New Inhabitant of a Marine Solar Saltern

“…Their rhodopsins and their applications have been deeply studied. Besides, several studies have focused on the biotechnological potential of its enzymes [7][8][9][10][11][12][13][14][15]. On the other hand, several culture-independent studies have also shown the presence of members of the genus Natronomonas in different environments from widely separated sites, such as hypersaline and alkaline lakes, solar salterns, saline-alkaline soils, and sediments or oil fields [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31], supporting the widespread distribution of species of this genus.…”

A Survey of Biological Building Blocks for Synthetic Molecular Communication Systems

“…This can be accomplished by further integrating light-driven sodium-pumps into the membrane of the vesicle (Fig. 7, R1, lower panel) [134]. Then, the light-driven sodium pumps can operate e.g.…”