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Ion-pumping microbial rhodopsins.

Kandori H - Front Mol Biosci (2015)

Bottom Line: Ion-transporting proteins can be found in microbial rhodopsins, such as light-gated channels and light-driven pumps, which are the main tools in optogenetics.On the other hand, different kinds of H(+) and Cl(-) pumps have been found in marine bacteria, such as proteorhodopsin (PR) and Fulvimarina pelagi rhodopsin (FR), respectively.In addition, a light-driven Na(+) pump was found, Krokinobacter eikastus rhodopsin 2 (KR2).

View Article: PubMed Central - PubMed

Affiliation: Department of Frontier Materials and OptoBioTechnology Research Center, Nagoya Institute of Technology Nagoya, Japan.

ABSTRACT
Rhodopsins are light-sensing proteins used in optogenetics. The word "rhodopsin" originates from the Greek words "rhodo" and "opsis," indicating rose and sight, respectively. Although the classical meaning of rhodopsin is the red-colored pigment in our eyes, the modern meaning of rhodopsin encompasses photoactive proteins containing a retinal chromophore in animals and microbes. Animal and microbial rhodopsins possess 11-cis and all-trans retinal, respectively, to capture light in seven transmembrane α-helices, and photoisomerizations into all-trans and 13-cis forms, respectively, initiate each function. Ion-transporting proteins can be found in microbial rhodopsins, such as light-gated channels and light-driven pumps, which are the main tools in optogenetics. Light-driven pumps, such as archaeal H(+) pump bacteriorhodopsin (BR) and Cl(-) pump halorhodopsin (HR), were discovered in the 1970s, and their mechanism has been extensively studied. On the other hand, different kinds of H(+) and Cl(-) pumps have been found in marine bacteria, such as proteorhodopsin (PR) and Fulvimarina pelagi rhodopsin (FR), respectively. In addition, a light-driven Na(+) pump was found, Krokinobacter eikastus rhodopsin 2 (KR2). These light-driven ion-pumping microbial rhodopsins are classified as DTD, TSA, DTE, NTQ, and NDQ rhodopsins for BR, HR, PR, FR, and KR2, respectively. Recent understanding of ion-pumping microbial rhodopsins is reviewed in this paper.

No MeSH data available.


H+ transport pathway in bacteriorhodopsin (BR). Arrows indicate each H+ transfer, and the numbers indicate a temporal order; (1) Schiff base to D85, (2) H+ release, (3) D96 to Schiff base, (4) uptake, and (5) D85 to the H+ release group.
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Figure 8: H+ transport pathway in bacteriorhodopsin (BR). Arrows indicate each H+ transfer, and the numbers indicate a temporal order; (1) Schiff base to D85, (2) H+ release, (3) D96 to Schiff base, (4) uptake, and (5) D85 to the H+ release group.

Mentions: The H+ pathway across the membrane from the cytoplasmic to the extracellular side in BR is shown in Figure 8, together with protonatable groups and the order of respective H+ transfers. A summary of the photocycle is shown in Figure 9, which illustrates key intermediate states for most microbial rhodopsins. Although the photocycle of BR contains six intermediates, namely J, K, L, M, N, and O states that are named alphabetically, only three states (K, M, and N) are shown in Figure 7 to demonstrate the mechanism clearly. After light absorption, photoisomerization occurs from the all-trans- to 13-cis-form in 10−13 second. This ultrafast retinal isomerization yields the formation of red-shifted J and K intermediates, in which J is the precursor of the K state. The protein cavity, which accommodates retinal, cannot change its shape promptly, and the K intermediate contains twisted 13-cis retinal. An altered hydrogen-bonding network in the Schiff base region also contributes to higher free energy in K than in the original state, and such energy storage in the primary intermediate structure leads to subsequent protein structural changes upon relaxation.


Ion-pumping microbial rhodopsins.

Kandori H - Front Mol Biosci (2015)

H+ transport pathway in bacteriorhodopsin (BR). Arrows indicate each H+ transfer, and the numbers indicate a temporal order; (1) Schiff base to D85, (2) H+ release, (3) D96 to Schiff base, (4) uptake, and (5) D85 to the H+ release group.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585134&req=5

Figure 8: H+ transport pathway in bacteriorhodopsin (BR). Arrows indicate each H+ transfer, and the numbers indicate a temporal order; (1) Schiff base to D85, (2) H+ release, (3) D96 to Schiff base, (4) uptake, and (5) D85 to the H+ release group.
Mentions: The H+ pathway across the membrane from the cytoplasmic to the extracellular side in BR is shown in Figure 8, together with protonatable groups and the order of respective H+ transfers. A summary of the photocycle is shown in Figure 9, which illustrates key intermediate states for most microbial rhodopsins. Although the photocycle of BR contains six intermediates, namely J, K, L, M, N, and O states that are named alphabetically, only three states (K, M, and N) are shown in Figure 7 to demonstrate the mechanism clearly. After light absorption, photoisomerization occurs from the all-trans- to 13-cis-form in 10−13 second. This ultrafast retinal isomerization yields the formation of red-shifted J and K intermediates, in which J is the precursor of the K state. The protein cavity, which accommodates retinal, cannot change its shape promptly, and the K intermediate contains twisted 13-cis retinal. An altered hydrogen-bonding network in the Schiff base region also contributes to higher free energy in K than in the original state, and such energy storage in the primary intermediate structure leads to subsequent protein structural changes upon relaxation.

Bottom Line: Ion-transporting proteins can be found in microbial rhodopsins, such as light-gated channels and light-driven pumps, which are the main tools in optogenetics.On the other hand, different kinds of H(+) and Cl(-) pumps have been found in marine bacteria, such as proteorhodopsin (PR) and Fulvimarina pelagi rhodopsin (FR), respectively.In addition, a light-driven Na(+) pump was found, Krokinobacter eikastus rhodopsin 2 (KR2).

View Article: PubMed Central - PubMed

Affiliation: Department of Frontier Materials and OptoBioTechnology Research Center, Nagoya Institute of Technology Nagoya, Japan.

ABSTRACT
Rhodopsins are light-sensing proteins used in optogenetics. The word "rhodopsin" originates from the Greek words "rhodo" and "opsis," indicating rose and sight, respectively. Although the classical meaning of rhodopsin is the red-colored pigment in our eyes, the modern meaning of rhodopsin encompasses photoactive proteins containing a retinal chromophore in animals and microbes. Animal and microbial rhodopsins possess 11-cis and all-trans retinal, respectively, to capture light in seven transmembrane α-helices, and photoisomerizations into all-trans and 13-cis forms, respectively, initiate each function. Ion-transporting proteins can be found in microbial rhodopsins, such as light-gated channels and light-driven pumps, which are the main tools in optogenetics. Light-driven pumps, such as archaeal H(+) pump bacteriorhodopsin (BR) and Cl(-) pump halorhodopsin (HR), were discovered in the 1970s, and their mechanism has been extensively studied. On the other hand, different kinds of H(+) and Cl(-) pumps have been found in marine bacteria, such as proteorhodopsin (PR) and Fulvimarina pelagi rhodopsin (FR), respectively. In addition, a light-driven Na(+) pump was found, Krokinobacter eikastus rhodopsin 2 (KR2). These light-driven ion-pumping microbial rhodopsins are classified as DTD, TSA, DTE, NTQ, and NDQ rhodopsins for BR, HR, PR, FR, and KR2, respectively. Recent understanding of ion-pumping microbial rhodopsins is reviewed in this paper.

No MeSH data available.