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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.


Highlighted BR structure with the retinal chromophore, W86, W182, and Y185 (PDB: 1QM8). Y83, W86, and W182 are strongly conserved among the microbial rhodopsins (orange). Aromatic residues are strongly conserved at the Y185, W189, and F219 positions (yellow). In BR, W86, W182, Y185, and W189 constitute the chromophore binding pocket for all-trans retinal (red).
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Figure 5: Highlighted BR structure with the retinal chromophore, W86, W182, and Y185 (PDB: 1QM8). Y83, W86, and W182 are strongly conserved among the microbial rhodopsins (orange). Aromatic residues are strongly conserved at the Y185, W189, and F219 positions (yellow). In BR, W86, W182, Y185, and W189 constitute the chromophore binding pocket for all-trans retinal (red).

Mentions: Despite a variety of sequences and functions, the structural and mechanistic principles of microbial rhodopsin architecture have one common structure, a tight alpha-helical bundle of seven transmembrane helices surrounding the retinal chromophore (Klare et al., 2008; Zhang et al., 2011; Brown, 2013; Ernst et al., 2014). Figure 5 illustrates the overall structure of BR, which highlights the conserved aromatic amino acids. The retinal binding pocket is the most conserved element of the structure. W86, W182, and Y185, which constitute an important part of the chromophore binding site, are perfectly conserved among ion-pumping microbial rhodopsins (Figure 6). The presence of these bulky groups possibly determines the isomerization pathway from the all-trans to the 13-cis form after light absorption. Moreover, the interaction of photoisomerized retinal with W182 may serve as a mechanical transducer for passing the energy stored in retinal deformation into functionally important changes of the helical tilts necessary for function (Luecke et al., 2000). Y185 in BR (Figure 6) participates in hydrogen-bonding stabilization of the Schiff base counterion for many rhodopsins.


Ion-pumping microbial rhodopsins.

Kandori H - Front Mol Biosci (2015)

Highlighted BR structure with the retinal chromophore, W86, W182, and Y185 (PDB: 1QM8). Y83, W86, and W182 are strongly conserved among the microbial rhodopsins (orange). Aromatic residues are strongly conserved at the Y185, W189, and F219 positions (yellow). In BR, W86, W182, Y185, and W189 constitute the chromophore binding pocket for all-trans retinal (red).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: Highlighted BR structure with the retinal chromophore, W86, W182, and Y185 (PDB: 1QM8). Y83, W86, and W182 are strongly conserved among the microbial rhodopsins (orange). Aromatic residues are strongly conserved at the Y185, W189, and F219 positions (yellow). In BR, W86, W182, Y185, and W189 constitute the chromophore binding pocket for all-trans retinal (red).
Mentions: Despite a variety of sequences and functions, the structural and mechanistic principles of microbial rhodopsin architecture have one common structure, a tight alpha-helical bundle of seven transmembrane helices surrounding the retinal chromophore (Klare et al., 2008; Zhang et al., 2011; Brown, 2013; Ernst et al., 2014). Figure 5 illustrates the overall structure of BR, which highlights the conserved aromatic amino acids. The retinal binding pocket is the most conserved element of the structure. W86, W182, and Y185, which constitute an important part of the chromophore binding site, are perfectly conserved among ion-pumping microbial rhodopsins (Figure 6). The presence of these bulky groups possibly determines the isomerization pathway from the all-trans to the 13-cis form after light absorption. Moreover, the interaction of photoisomerized retinal with W182 may serve as a mechanical transducer for passing the energy stored in retinal deformation into functionally important changes of the helical tilts necessary for function (Luecke et al., 2000). Y185 in BR (Figure 6) participates in hydrogen-bonding stabilization of the Schiff base counterion for many rhodopsins.

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.