Factors That Differentiate the H-bond Strengths of Water Near the Schiff Bases in Bacteriorhodopsin and Anabaena Sensory Rhodopsin

Saito, Keisuke; Kandori, Hideki; Ishikita, Hiroshi

doi:10.1074/jbc.m112.388348

Cited by 21 publications

(32 citation statements)

References 54 publications

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“…There are two negative charges, D85 and D212, on the extracellular side of BR, producing strong electrostatic attraction of the protonated Schiff base before the primary H + transfer, leading to outward H + transport34. In contrast, the XeR family possesses only one negative charge in that region, as D212 of BR is replaced by proline, which makes the electrostatic interaction between the protonated Schiff base and the counterion (D74 in Po XeR) weaker35363738. Consequently, photoisomerization reorients the N–H group of the Schiff base toward the cytoplasmic side.…”

Section: Discussionmentioning

confidence: 99%

A natural light-driven inward proton pump

et al. 2016

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Light-driven outward H+ pumps are widely distributed in nature, converting sunlight energy into proton motive force. Here we report the characterization of an oppositely directed H+ pump with a similar architecture to outward pumps. A deep-ocean marine bacterium, Parvularcula oceani, contains three rhodopsins, one of which functions as a light-driven inward H+ pump when expressed in Escherichia coli and mouse neural cells. Detailed mechanistic analyses of the purified proteins reveal that small differences in the interactions established at the active centre determine the direction of primary H+ transfer. Outward H+ pumps establish strong electrostatic interactions between the primary H+ donor and the extracellular acceptor. In the inward H+ pump these electrostatic interactions are weaker, inducing a more relaxed chromophore structure that leads to the long-distance transfer of H+ to the cytoplasmic side. These results demonstrate an elaborate molecular design to control the direction of H+ transfers in proteins.

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Section: Discussionmentioning

confidence: 99%

A natural light-driven inward proton pump

et al. 2016

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“…Several models have been proposed for the manner of hydrogen bonding of the water molecules near SB 36–38 . However, none of them have been fully accepted.…”

Section: Discussionmentioning

confidence: 99%

“…As reported previously, water molecules in the proton path do not show the tetrahedral coordination that usually occurs in protein surfaces as well as bulk waters. Several models have been proposed for the manner of hydrogen bonding of the water molecules near SB 36 – 38 . However, none of them have been fully accepted.…”

Section: Discussionmentioning

confidence: 99%

X-ray structure analysis of bacteriorhodopsin at 1.3 Å resolution

Hasegawa

Jonotsuka

Miki

et al. 2018

Sci Rep

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Bacteriorhodopsin (bR) of Halobacterium salinarum is a membrane protein that acts as a light-driven proton pump. bR and its homologues have recently been utilized in optogenetics and other applications. Although the structures of those have been reported so far, the resolutions are not sufficient for elucidation of the intrinsic structural features critical to the color tuning and ion pumping properties. Here we report the accurate crystallographic analysis of bR in the ground state. The influence of X-rays was suppressed by collecting the data under a low irradiation dose at 15 K. Consequently, individual atoms could be separately observed in the electron density map at better than 1.3 Å resolution. Residues from Thr5 to Ala233 were continuously constructed in the model. The twist of the retinal polyene was determined to be different from those in the previous models. Two conformations were observed for the proton release region. We discuss the meaning of these fine structural features.

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“…These results suggest that deprotonation of Asp234, "the only residue directly interacting with the protonated Schiff base 6 ", is a prerequisite to stabilize the protonated Schiff base, as suggested by Dreier et al 11 . pK a (Asp234) = -5 (Table 2) is significantly low and even lower than pK a (Asp212) = -2 in BR 12 . The crystal structures show that the protein electrostatic environment at the Schiff base moiety is highly conserved between GtACR1 and BR.…”

Section: Resultsmentioning

confidence: 76%

Proton-mediated gating mechanism of anion channelrhodopsin-1

Tsujimura

Kojima

Kawanishi

et al. 2021

Preprint

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Anion channelrhodopsin from Guillardia theta (GtACR1) has Asp234 (3.2 Å) and Glu68 (5.3 Å) near the protonated Schiff base. Here we investigate mutant GtACR1s (e.g., E68Q/D234N) expressed in HEK293 cells. The influence of the acidic residues on the absorption wavelengths were also analyzed, using a quantum mechanical/molecular mechanical approach. The calculated protonation pattern indicates that Asp234 is deprotonated and Glu68 is protonated in the original crystal structures. The D234E mutation and the E68Q/D234N mutation shortens and lengthens the measured and calculated absorption wavelengths, respectively, which suggests that Asp234 is deprotonated in the wild type GtACR1. Molecular dynamics simulations show that upon mutation of deprotonated Asp234 to asparagine, deprotonated Glu68 reorients towards the Schiff base and the calculated absorption wavelength remains unchanged. The formation of the proton transfer pathway via Asp234 toward Glu68 and the disconnection of the anion conducting channel are likely a basis of the gating mechanism.

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Factors That Differentiate the H-bond Strengths of Water Near the Schiff Bases in Bacteriorhodopsin and Anabaena Sensory Rhodopsin

Cited by 21 publications

References 54 publications

A natural light-driven inward proton pump

A natural light-driven inward proton pump

X-ray structure analysis of bacteriorhodopsin at 1.3 Å resolution

Proton-mediated gating mechanism of anion channelrhodopsin-1

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