Energetics and dynamics of a light-driven sodium-pumping rhodopsin

Abstract

The conversion of light energy into ion gradients across biological membranes is one of the most fundamental reactions in primary biological energy transduction. Recently, the structure of the first light-activated Na + pump, Krokinobacter eikastus rhodopsin 2 (KR2), was resolved at atomic resolution [Kato HE, et al. (2015) Nature 521: [48][49][50][51][52][53]. To elucidate its molecular mechanism for Na + pumping, we perform here extensive classical and quantum molecular dynamics (MD) simulations of transient photocycle states. Our simulations show how the dynamics of key residues regulate water and ion access between the bulk and the buried light-triggered retinal site. We identify putative Na + binding sites and show how protonation and conformational changes gate the ion through these sites toward the extracellular side. We further show by correlated ab initio quantum chemical calculations that the obtained putative photocycle intermediates are in close agreement with experimental transient optical spectroscopic data. The combined results of the ion translocation and gating mechanisms in KR2 may provide a basis for the rational design of novel light-driven ion pumps with optogenetic applications.bacterial ion pumps | bioenergetics | QM/MM | optogenetics | retinal P rimary biological energy conversion is based on the efficient capture and conversion of light and chemical energy into ion gradients across biological membranes (1, 2). The established gradients are used to thermodynamically drive energy-requiring processes, such as active transport and synthesis of adenosine triphosphate (ATP) (3, 4). The rhodopsin family of proteins catalyzes such reactions by harnessing the energy from retinal photoisomerization and deprotonation reactions, followed by conformational changes that further trigger the pumping of ions across the membrane (5). All previously known ion-pumping rhodopsins function either as inward chloride or outward proton pumps, but the structure of the first Na + pumping rhodopsin, Krokinobacter eikastus rhodopsin 2 (KR2) (6), was recently resolved (7,8). In the absence of Na + ions, KR2 functions as an outward proton pump, similarly to bacteriorhodopsin (bR), but under physiological conditions, KR2 pumps Na + out of the cell (6, 9).KR2 shares the heptahelical transmembrane (7TM) structure common to all microbial rhodopsins (Fig. 1A) (5,7,8). In contrast to bR, however, where a highly conserved Asp-Thr-Asp (DTD) motif is used to pump protons, KR2 employs a unique NDQ motif comprising residues Asn112, Asp116, and Gln123 (6). In bR, Asp85 and Asp96 function as proton acceptors and donors for the protonated Schiff base (PSB), respectively, whereas in KR2, Asn112 and Gln123 occupy these positions, and Asp116 replaces Thr89. In analogy to bR, it has been suggested that Gln123 aids in capturing ions from the solvent and that Asn112 might be part of a Na + binding site (6,10).Similarly to other microbial rhodopsins, four photocycle intermediates have been spectroscopically identified in KR2 (Fig. 1B) (6)...

Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation

“…4b) for the L555M/K mutants reveal that alteration of highly conserved residue L555 at the hydrophobic gate modifies the spatial volume of the gate, electrostatic charge and its pore size (Fig. 3e and f), that is in accordance with other ion channel pore diameters [34]. (Fig.…”

Absorption shifts of diastereotopically ligated chlorophyll dimers of photosystem I

“…The RVS approach that significantly speeds up the calculations has been successfully employed in previous studies of photobiological systems, including chlorophylls. 26,27,44,[63][64][65][66][67] Comparing the results from the SOS-ADC(2) and SOS-CC2 calculations with the corresponding values calculated at the unscaled CC2 and ADC(2) levels shows that the SOS approximation introduces errors of À0.13 to 0.39 eV for the lowest four excited states of the Chl monomer ( Table 5). The oscillator strengths are also affected by the SOS approach.…”

Temperature Dependence of theKrokinobacterrhodopsin 2 Kinetics

“…This result is in agreement with literature, where some of these equilibria could also be observed before. 12,22 Our result shows that the transition from the L to the M intermediate is the step most affected by the temperature. While the overall photocycle is accelerated by a factor of six, the L-M transition is increased by a factor of 40.…”

“…While at first, it was modeled as an unbranched unidirectional photocycle with five distinct photointermediates, 14 later on more complex models were proposed. 15,16,17 KR2's photocycle has already been studied extensively with various techniques [18][19][20][21][22][23] but still remains to be understood completely. Especially the spectral location of the photointermediates, as well as the equilibria within the photocycle remain elusive.…”