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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.


Structure of the Schiff base region in bacteriorhodopsin (BR). This is the side view of the Protein Data Bank structure 1C3W, which has a resolution of 1.55 Å (Luecke et al., 1999). The membrane normal is approximately in the vertical direction of this figure. Hydrogen atoms and hydrogen bonds (dashed lines) are supposed from the structure, while the numbers indicate hydrogen-bonding distances in Å.
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Figure 7: Structure of the Schiff base region in bacteriorhodopsin (BR). This is the side view of the Protein Data Bank structure 1C3W, which has a resolution of 1.55 Å (Luecke et al., 1999). The membrane normal is approximately in the vertical direction of this figure. Hydrogen atoms and hydrogen bonds (dashed lines) are supposed from the structure, while the numbers indicate hydrogen-bonding distances in Å.

Mentions: In addition to the aromatic sidechain rings, electrostatic and hydrogen-bonding interactions in the proximal region of retinal are crucial in defining the functionality of microbial rhodopsins (Ernst et al., 2014). The sidechain of K216 in BR (or its homologs in other microbial rhodopsins) forms a covalent linkage with the retinal molecule through the Schiff base (Figure 7). As the Schiff base is usually protonated, K216 and super-conserved R82 of helix C in BR provide two positive charges within the protein (Figure 7), which requires two negative charges for electrostatic stabilization. This dictates the most common configuration of the Schiff base counterion, which includes two perfectly conserved carboxylic acids (D85 and D212 in BR) for H+-pumping microbial rhodopsins (Figure 7).


Ion-pumping microbial rhodopsins.

Kandori H - Front Mol Biosci (2015)

Structure of the Schiff base region in bacteriorhodopsin (BR). This is the side view of the Protein Data Bank structure 1C3W, which has a resolution of 1.55 Å (Luecke et al., 1999). The membrane normal is approximately in the vertical direction of this figure. Hydrogen atoms and hydrogen bonds (dashed lines) are supposed from the structure, while the numbers indicate hydrogen-bonding distances in Å.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 7: Structure of the Schiff base region in bacteriorhodopsin (BR). This is the side view of the Protein Data Bank structure 1C3W, which has a resolution of 1.55 Å (Luecke et al., 1999). The membrane normal is approximately in the vertical direction of this figure. Hydrogen atoms and hydrogen bonds (dashed lines) are supposed from the structure, while the numbers indicate hydrogen-bonding distances in Å.
Mentions: In addition to the aromatic sidechain rings, electrostatic and hydrogen-bonding interactions in the proximal region of retinal are crucial in defining the functionality of microbial rhodopsins (Ernst et al., 2014). The sidechain of K216 in BR (or its homologs in other microbial rhodopsins) forms a covalent linkage with the retinal molecule through the Schiff base (Figure 7). As the Schiff base is usually protonated, K216 and super-conserved R82 of helix C in BR provide two positive charges within the protein (Figure 7), which requires two negative charges for electrostatic stabilization. This dictates the most common configuration of the Schiff base counterion, which includes two perfectly conserved carboxylic acids (D85 and D212 in BR) for H+-pumping microbial rhodopsins (Figure 7).

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.