Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms

تعليق: مقالة ممتازة عن الكيمياء في الشبكية وهي ذات صلة بمقالة عام 1992. والمؤلفين يصلحون ليكونوا شركاء في كتابة مقالتنا عن تأثير هذه الأدوية على مضخة البروتون في الشبكية. لكن مهم سؤال المختصين عن أهمية وتأثير مضخات البروتون في صبغيات عين البشر وليس البكتيريا.--احمد شوقي محمدين 19:10، 2 نوفمبر 2016 (ت ع م)

مقتطفات مهمة

كلام مهم: Animal rhodopsins, for example, are employed in visual and nonvisual phototransduction, in the maintenance of the circadian clock and as photoisomerases ربما له علاقة بمشاكل النوم مع الأوميبراز أو مع الهذيان. أيضاً The retinal Schiff base (RSB) is protonated (RSBH+) in most cases, and changes in protonation state are integral to the signaling or transport activity of rhodopsins. دور البروتون.

light-driven outward proton pump and inward chloride pump, respectively. As ion pumps, they contribute to the formation of a membrane potential and thus have their function in light–energy conversion. وبالتالي يمكن إجراء تجارب عليها بالأوميبراز وعائلته مثلاً.

similar rhodopsins have been found in Eubacteria and lower Eukaryota,

(A) light-driven inward chloride pump (halorhodopsin (HR), PDB ID: 1E12), (B) light-driven outward proton pump (bacteriorhodopsin (BR), PDB ID: 1C3W)

Thus, studies on microbial rhodopsins are beneficial not only for our basic understanding of retinal proteins, but also for providing a toolset to study neuronal signaling through optogenetics.

G-protein-coupled receptors (GPCRs)

Animal rhodopsins belong to the superfamily of GPCRs which detect extracellular signals, typically by binding small molecule ligands like hormones and neurotransmitters.

Vertebrate rhodopsin was discovered more than 130 years ago and has long been used as a prototypical GPCR.(22) Due to the relative ease of purification from native material, it has been studied extensively.(2)

Color Tuning: Light absorption initiates functions of both microbial and animal rhodopsins,(23, 24) and the wavelength dependence of the absorption efficiency determines the colors of the proteins (Figure 5). The length of the π-conjugated polyene chain in the retinal chromophore as well as the protonation' of the RSB linkage determine the energy gap of the π–π* transition,(25) so that the absorption of most rhodopsins is within the visible region (400–700 nm). 'Humans have a single photoreceptor for dim light vision (rhodopsin, λmax ∼500 nm) and three receptors for color vision (blue, λmax ∼425 nm; green, λmax ∼530 nm; red, λmax ∼560 nm),(26, 27) whereas some shrimp species contain up to 16 rhodopsins covering the spectral range from 300 to 700 nm.(28) While the chromophore molecule is usually the same in all pigments (retinal bound via a (protonated) Schiff base), the absorption maxima differ significantly, implying an active protein control of the energy gap between the ground and excited states of the retinal chromophore. The mechanism of color tuning has fascinated researchers for a long time, and several factors have been determined to be responsible for it.

The protonation state of the chromophore plays a crucial role in color tuning; the unprotonated RSB absorbs in the UV region (λmax ∼360–380 nm), and this absorption is quite insensitive to the environment in contrast to the RSBH+, which exhibits a large variation in absorption covering the entire visible light spectrum.

In fact, while absorbance spectra of protonated Schiff bases of all-trans- and 11-cis-retinal in solution are similar (λmax ∼450 nm),(49) most microbial and animal rhodopsins typically possess λmax in 520–580 nm and 480–525 nm ranges, respectively,(50) which can in part be explained by the differences in the C6–C7 bond conformation. ..............These facts reveal the complexity of color tuning mechanism in microbial and animal rhodopsins, and the importance of structural information in understanding the mechanistic basis of color tuning in rhodopsins.

Figure 8. Time scale related to activation of microbial and animal rhodopsins. Light absorption, retinal isomerization, proton transfer, and local and global protein structural changes take place hierarchically, leading to functional activity.

For many microbial and animal rhodopsins, such changes accompany deprotonation of the RSBH+, forming the “M intermediate” and “Meta-II intermediate”, respectively. These intermediates are the key states for function, which are described in detail in sections 3 and 4. Figure 8 also contains a time domain of evolution, the time of natural design of protein architecture, by which both microbial and animal rhodopsins have been functionally optimized.

These publications marked the genesis of what we term today, optogenetics. In optogenetics, researchers target well-defined neuronal cell subpopulations by using cell-specific promoters to express light-activatable proteins and thus are able to selectively activate or silence (depolarize or hyperpolarize) cells through the application of short light pulses. Most surprisingly, the mammalian brain contains sufficient retinoid levels to allow wild-type ChR2 to function without addition of exogenous retinal. The affinity of the apoprotein for retinal is in the nanomolar range but varies widely in ChR isotypes and mutants, partially explaining why some variants work better than others in neurons, even though expression and membrane targeting is equivalent.(365) More recently, channelrhodopsins from algal species other than Chlamydomonas, most notably, from Volvox, have been similarly adopted for use in optogenetics.(170, 366, 367)

من المقالة

Review

Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms

Oliver P. Ernst*†, David T. Lodowski‡, Marcus Elstner§, Peter Hegemann∥, Leonid S. Brown⊥, and Hideki Kandori#

Chem. Rev., 2014, 114 (1), pp 126–163 DOI: 10.1021/cr4003769

1 Introduction

Organisms of all domains of life use photoreceptor proteins to sense and respond to light. The light-sensitivity of photoreceptor proteins arises from bound chromophores such as retinal in retinylidene proteins, bilin in biliproteins, and flavin in flavoproteins. Rhodopsins found in Eukaryotes, Bacteria, and Archaea consist of opsin apoproteins and a covalently linked retinal which is employed to absorb photons for energy conversion or the initiation of intra- or intercellular signaling.(1) Both functions are important for organisms to survive and to adapt to the environment. While lower organisms utilize the family of microbial rhodopsins for both purposes, animals solely use a different family of rhodopsins, a specialized subset of G-protein-coupled receptors (GPCRs).(1, 2) Animal rhodopsins, for example, are employed in visual and nonvisual phototransduction, in the maintenance of the circadian clock and as photoisomerases.(3, 4) While sharing practically no sequence similarity, microbial and animal rhodopsins, also termed type-I and type-II rhodopsins, respectively, share a common architecture of seven transmembrane α-helices (TM) with the N- and C-terminus facing out- and inside of the cell, respectively (Figure 1).(1, 5) Retinal is attached by a Schiff base linkage to the ε-amino group of a lysine side chain in the middle of TM7 (Figures 1 and 2). The retinal Schiff base (RSB) is protonated (RSBH+) in most cases, and changes in protonation state are integral to the signaling or transport activity of rhodopsins.

Retinal, the aldehyde of vitamin A, is derived from β-carotene and is utilized in the all-trans/13-cis configurations in microbial rhodopsins and the 11-cis/all-trans configurations in animal rhodopsins (Figure 2).(1, 6) For optimal light to energy or light to signal conversion, defined chromophore–protein interactions in rhodopsins direct the unique photophysical and photochemical processes, which start with specific retinal isomerization and culminate with distinct protein conformational changes. The protein environment is typically optimized for light-induced retinal isomerization from all-trans → 13-cis in microbial rhodopsins and for 11-cis → all-trans in animal rhodopsins. Variations in this isomerization pattern are discussed in sections 3 and 4.

bacteriorhodopsin (BR) a light-driven outward proton pump

The 7TM protein scaffold of microbial rhodopsins is designed for light-driven ion pumps, light-gated ion channels, and light sensors which couple to transducer proteins (Figure 3).(7) Microbial rhodopsins were first found in the Archaea (Halobacterium salinarum, historically referred to as Halobacterium halobium)(8) and were therefore initially termed archaeal rhodopsins. H. salinarum contains bacteriorhodopsin (BR)(8) and halorhodopsin (HR)(9) that act as a light-driven outward proton pump and inward chloride pump, respectively. As ion pumps, they contribute to the formation of a membrane potential and thus have their function in light–energy conversion. The other two H. salinarum rhodopsins are sensory rhodopsin I and II (SRI and SRII),(10) which act as positive and negative phototaxis sensors, respectively. Since the original discovery of BR in H. salinarum, similar rhodopsins have been found in Eubacteria and lower Eukaryota, leading to the name microbial rhodopsins. For example, Anabaena sensory rhodopsin (ASR), the first sensory rhodopsin observed in the Eubacteria,(11) is a sensor that activates a soluble transducer (Figure 3).

light-driven outward proton pump

Figure 3. Microbial rhodopsins can function as pumps, channels, and light-sensors. Arrows indicate the direction of transport or flow of signal: (A) light-driven inward chloride pump (halorhodopsin (HR), PDB ID: 1E12), (B) light-driven outward proton pump (bacteriorhodopsin (BR), PDB ID: 1C3W), (C) light-gated cation channel (channelrhodopsin (ChR), PDB ID: 3UG9), (D) light-sensor activating transmembrane transducer protein (sensory rhodopsin II (SRII), PDB ID: 1JGJ), (E) light-sensor activating soluble transducer protein (Anabaena sensory rhodopsin (ASR), PDB ID: 1XIO).

studies on microbial rhodopsins are beneficial

.......................Thus, studies on microbial rhodopsins are beneficial not only for our basic understanding of retinal proteins, but also for providing a toolset to study neuronal signaling through optogenetics.

G-protein-coupled receptors (GPCRs)

Animal rhodopsins belong to the superfamily of GPCRs which detect extracellular signals, typically by binding small molecule ligands like hormones and neurotransmitters.

Vertebrate rhodopsin

Vertebrate rhodopsin was discovered more than 130 years ago and has long been used as a prototypical GPCR.(22) Due to the relative ease of purification from native material, it has been studied extensively.(2)

Color Tuning

Light absorption initiates functions of both microbial and animal rhodopsins,(23, 24) and the wavelength dependence of the absorption efficiency determines the colors of the proteins (Figure 5). The length of the π-conjugated polyene chain in the retinal chromophore as well as the protonation' of the RSB linkage determine the energy gap of the π–π* transition,(25) so that the absorption of most rhodopsins is within the visible region (400–700 nm). 'Humans have a single photoreceptor for dim light vision (rhodopsin, λmax ∼500 nm) and three receptors for color vision (blue, λmax ∼425 nm; green, λmax ∼530 nm; red, λmax ∼560 nm),(26, 27) whereas some shrimp species contain up to 16 rhodopsins covering the spectral range from 300 to 700 nm.(28) While the chromophore molecule is usually the same in all pigments (retinal bound via a (protonated) Schiff base), the absorption maxima differ significantly, implying an active protein control of the energy gap between the ground and excited states of the retinal chromophore. The mechanism of color tuning has fascinated researchers for a long time, and several factors have been determined to be responsible for it.

protonation state of the chromophore

The protonation state of the chromophore plays a crucial role in color tuning; the unprotonated RSB absorbs in the UV region (λmax ∼360–380 nm), and this absorption is quite insensitive to the environment in contrast to the RSBH+, which exhibits a large variation in absorption covering the entire visible light spectrum.

protonated Schiff bases

In fact, while absorbance spectra of protonated Schiff bases of all-trans- and 11-cis-retinal in solution are similar (λmax ∼450 nm),(49) most microbial and animal rhodopsins typically possess λmax in 520–580 nm and 480–525 nm ranges, respectively,(50) which can in part be explained by the differences in the C6–C7 bond conformation. ..............These facts reveal the complexity of color tuning mechanism in microbial and animal rhodopsins, and the importance of structural information in understanding the mechanistic basis of color tuning in rhodopsins.

proton transfer

Figure 8. Time scale related to activation of microbial and animal rhodopsins. Light absorption, retinal isomerization, proton transfer, and local and global protein structural changes take place hierarchically, leading to functional activity.

deprotonation of the RSBH+,

For many microbial and animal rhodopsins, such changes accompany deprotonation of the RSBH+, forming the “M intermediate” and “Meta-II intermediate”, respectively. These intermediates are the key states for function, which are described in detail in sections 3 and 4. Figure 8 also contains a time domain of evolution, the time of natural design of protein architecture, by which both microbial and animal rhodopsins have been functionally optimized.

optogenetics

These publications marked the genesis of what we term today, optogenetics. In optogenetics, researchers target well-defined neuronal cell subpopulations by using cell-specific promoters to express light-activatable proteins and thus are able to selectively activate or silence (depolarize or hyperpolarize) cells through the application of short light pulses. Most surprisingly, the mammalian brain contains sufficient retinoid levels to allow wild-type ChR2 to function without addition of exogenous retinal. The affinity of the apoprotein for retinal is in the nanomolar range but varies widely in ChR isotypes and mutants, partially explaining why some variants work better than others in neurons, even though expression and membrane targeting is equivalent.(365) More recently, channelrhodopsins from algal species other than Chlamydomonas, most notably, from Volvox, have been similarly adopted for use in optogenetics.(170, 366, 367)

لكن مهم سؤال المختصين عن أهمية وتأثير مضخات البروتون في صبغيات عين البشر وليس البكتيريا.

رابط

http://pubs.acs.org/doi/full/10.1021/cr4003769