Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2014 Jan 8;114(1):126-63.
doi: 10.1021/cr4003769. Epub 2013 Dec 23.

Microbial and animal rhodopsins: structures, functions, and molecular mechanisms

Oliver P Ernst  1 , David T Lodowski, Marcus Elstner, Peter Hegemann, Leonid S Brown, Hideki Kandori
Affiliations
Review

Microbial and animal rhodopsins: structures, functions, and molecular mechanisms

Oliver P Ernst et al. Chem Rev. .
No abstract available

PubMed Disclaimer

Figures

Figure 1
Figure 1
Topology of the retinal proteins. (A) These membrane proteins contain seven α-helices (typically denoted helix A to G in microbial opsins and TM1 to 7 in the animal opsins) spanning the lipid bilayer. The N-terminus faces the outside of the cell and the C-terminus the inside. Retinal is covalently attached to a lysine side chain on helix G or TM7, respectively. (B) Cartoon representation of the helical arrangement of a microbial rhodopsin with attached all-trans-retinal (bacteriorhodopsin, PDB ID: 1C3W).
Figure 2
Figure 2
Genesis of the chromophore of microbial and animal rhodopsins. Cleavage of β-carotene is the source of the chromophore. The ground state of microbial and animal rhodopsins possesses all-trans- and 11-cis-retinal as its chromophore, respectively, bound to a Lys residue via a Schiff base, which is normally protonated and exists in the 15-anti configuration. It should be noted that microbial rhodopsins depend exclusively on all-trans-retinal, while some animal rhodopsins possess vitamin A2 (C3=C4 double bond for fish visual pigments) and hydroxyl (C3—OH for insect visual pigments) forms of 11-cis-retinal. Usually, photoactivation isomerizes microbial rhodopsin selectively at the C13=C14 double bond and animal rhodopsin at the C11=C12 double bond.
Figure 3
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).
Figure 4
Figure 4
Animal rhodopsins are specialized G-protein-coupled receptors (GPCRs). (A) Binding of extracellular ligands stabilizes certain GPCR conformations which enable the GPCR to catalyze GDP/GTP exchange in heterotrimeric G proteins (Gαβγ) and/or to induce G-protein-independent, arrestin-mediated signaling. (B) Typical GPCR fold shown in cartoon representation for bovine rhodopsin (PDB ID: 1U19). Structures of animal and microbial rhodopsins differ largely (cf. Figure 1B) and are drawn in opposite orientations with respect to the membrane. As model for the GPCR family, animal rhodopsin is shown in the orientation commonly used for GPCRs. In a large number of publications, animal rhodopsins are shown for historical reasons in the orientation of microbial rhodopsins (C-terminus up).
Figure 5
Figure 5
Microbial rhodopsins exhibit a wide range of absorption maxima. Colors of microbial rhodopsins (A) and their absorption spectra (B). The following rhodopsins are shown: (1) a blue-proteorhodopsin (LC1-200, pH 7), (2) Q105L mutant of LC1-200 (pH 7), (3) a green-proteorhodopsin (EBAC31A08, pH 7), (4) A178R mutant of green-proteorhodopsin (pH 7), (5) bacteriorhodopsin (pH 7), (6) H. salinarum sensory rhodopsin I (pH 4).
Figure 6
Figure 6
Color tuning exemplified by visual rhodopsins (containing 11-cis-retinal and RSBH+). Photoexcitation causes bond alteration, which leads in the electronically excited state to the movement of the positive charge from the RSBH+ to the β-ionone ring. (A) Excitation when a negatively charged counterion is close to the positively charged RSBH+. (B) Excitation in the absence of a negatively charged counterion. (C) Excitation when the chromophore counterion is located near the β-ionone ring. (D) Electrostatic interactions with the counterion lower the energy level of the ground state (case [A]) or excited state (case [C]), yielding a spectral blue- or red-shift, respectively.
Figure 7
Figure 7
Suggested mechanism of retinal photoisomerization in rhodopsins. Potential energy profiles along the reaction coordinate (the dihedral angle of C11=C12 and C13=C14 bonds of animal (left) and microbial (right) rhodopsins): S0, ground state; S1, the first electronic excited state. Colored arrows represent excitation by visible light. C.I. represents conical intersection, the point of the closest approach of the energy surfaces of the ground and the excited states, through which transitions are the most probable.
Figure 8
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.
Figure 9
Figure 9
Phylogenetic tree of selected microbial rhodopsins. Four main functions of microbial rhodopsins are shown in different colors: blue, proton pumps; green, chloride ion pumps; red, light-gated cation channels; yellow, photosensors. Proton pumps are widely distributed among Archaea, Eubacteria, and Eukaryota. Two additional poorly studied functional groups (sodium ion pumps and enzymerhodopsins) are not included. See Supporting Information Figure 1 for additional information on genus and species of the microbial rhodopsins.
Figure 10
Figure 10
(A) Structure of bacteriorhodopsin (BR), with conserved aromatic residues highlighted (PDB ID: 1QM8). Tyr83, Trp86, and Trp182 are strongly conserved among microbial rhodopsins (orange). Aromatic amino acids are strongly conserved at the position of Tyr185, Trp189, and Phe219 (yellow). In BR, Trp86, Trp182, Tyr185, and Trp189 constitute the chromophore binding pocket for all-trans-retinal (gray). (B) Crystallographically observed internal water molecules of BR (shown as green spheres). Note much higher hydration of the extracellular half compared to the cytoplasmic one.
Figure 11
Figure 11
X-ray crystallographic structures of the RSB region for eight representative microbial rhodopsins with various transport/signaling functions. BR, AR2 (archaerhodopsin 2), and XR function as proton pumps. NpSRII is a phototaxis sensor, but pumps protons in the absence of its transmembrane transducer. HsHR and NpHR are chloride pumps, ASR is a photochromic sensor, and ChR is a light-gated cation channel. Membrane normal is approximately in the vertical direction of the figure. Upper and lower regions correspond to the cytoplasmic and extracellular sides, respectively. Green spheres denote ordered water molecules observed crystallographically. For abbreviations of microbial rhodopsins, see Supporting Information Figure 1.
Figure 12
Figure 12
Typical photocycle of microbial rhodopsins showing isomeric and protonation state of the retinal. Names of the photocycle intermediates and their characteristics were originally established for BR. In the case of BR, K and O are the red-shifted intermediates, while L, M, and N are all blue-shifted intermediates. The primary photoreaction is the retinal isomerization from the all-trans,15-anti- to 13-cis,15-anti-isomer. The RSBH+ deprotonates upon M formation and is reprotonated upon M decay. Thermal reisomerization occurs upon O formation from the 13-cis,15-anti- to reform the all-trans,15-anti-state.
Figure 13
Figure 13
Main proton transfers in the bacteriorhodopsin photocycle. Protonatable groups and bound water molecules important for transport activity are shown as stick representation and blue spheres, respectively (PDB ID: 1C3W). Numbers with arrows represent the sequence of proton transfer reactions, the corresponding transitions between the photointermediates are indicated in the inset. The TM helices are shown in the following colors: A, blue; B, teal; C, green; D, lime green; E, yellow; F, orange; G, red; and the chromophore is depicted as black sticks. ① Proton transfer from the RSBH+ to the primary proton acceptor Asp85; ② proton release to the extracellular medium from the proton-releasing complex; ③ reprotonation of the RSB from the primary proton donor Asp96; ④ reprotonation of Asp96 from the cytoplasmic medium; ⑤ proton transfer from Asp85 to the proton-releasing complex.
Figure 14
Figure 14
Sequence of the main molecular events in the bacteriorhodopsin photocycle and accessibility of RSB: ① absorption of a photon by all-trans-retinal, photoisomerization to twisted 13-cis form; ② relaxation of retinal twist, strengthening of water-mediated hydrogen-bonding between RSBH+ and Asp85; ③ proton transfer from RSBH+ to the primary proton acceptor Asp85; ④ proton release to the extracellular medium from the proton-releasing complex and switch of the accessibility of RSB to the cytoplasmic side; ⑤ conformational change of the backbone in the cytoplasmic half and reprotonation of RSB from the primary proton donor Asp96; ⑥ reprotonation of Asp96 from the cytoplasmic medium and thermal reisomerization of retinal to all-trans; ⑦ proton transfer from Asp85 to the proton-releasing complex and restoration of the initial conformation.
Figure 15
Figure 15
(A) Photocycle of Natronomonas pharaonis halorhodopsin (NpHR). (B) Light-induced hydrogen-bonding alteration in the RSB region of NpHR (left) and bacteriorhodopsin (BR, right), suggesting the mechanism of proton and chloride ion translocation (refs (306, 566), respectively).
Figure 16
Figure 16
X-ray crystallographic structure of the transmembrane part of the NpSRII–NpHtrII complex (PDB ID: 1H2S). NpSRII helices are shown in purple, and NpHtrII helices are shown in green. (A) Side view of the complex. (B) Complex viewed from the cytoplasmic side. Inset: Illustration of the light-induced conformational changes of helix F of SRII and TM2 of HtrII. Because of the tight interaction between helix F and TM2, the outward movement of helix F in the receptor (arrow) causes a clockwise rotary motion of TM2 in the transducer.
Figure 17
Figure 17
Structural model of ChR2 based on the C1C2 chimera crystal structure as derived from extensive MD simulations. Shown are the relevant amino acids as discussed in the text and the calculated water (blue) and sodium ion (yellow) distributions averaged over the course of MD simulations. Insets: cation binding site (top) and cation uptake pathway observed in MD simulations with sodium trajectory (bottom). Cytoplasmic side of ChR2 is facing up.
Figure 18
Figure 18
Simplified scheme of the ChR2 photocycle with D470 as dark-adapted state and P520 as conducting state based on data from refs (369, 370, 379, 386). It is worth noting that during bright continuous illumination or repetitive flashing the photocycle is fed by photoconversion of the late photocycle intermediate Des480, the so-called desensitized or light-adapted state (blue dotted arrow). Green and UV light photoconverts the conducting state P520 and the early state P390, respectively, back to the light-adapted state (green and purple dotted arrows).
Figure 19
Figure 19
Global changes in the structure of rhodopsin and other GPCRs upon attainment of the active state. (A) Structural superposition of inactive and active G-protein-interacting state of bovine Rho reveals structural rearrangement of TM5 and TM6 to accommodate binding of the C-terminus of the α-subunit of transducin (Gtα peptide, shown in gray). Inactive rhodopsin (dark state; PDB ID: 1U19) is denoted in red, and active rhodopsin (Meta II; PDB ID: 3PQR) is denoted in yellow. (B) Model of the complex between a rhodopsin dimer and transducin built into electron microscopy map derived from native source purified bovine rhodopsin/transducin complex. GDP/GTP binding site is denoted by a yellow hexagon in parts B and D although both structures are solved in the nucleotide-free state. (C) Structural superposition of antagonist bound (inactive state, denoted in green) and agonist bound (active state, denoted in orange) β2-adrenergic receptors (β2AR). Structural displacement of TM5 and TM6 is similar to that seen in the comparison shown in part A. A nanobody (shown in gray) was utilized to stabilize the agonist bound state, and a nanobody loop protrudes into a similar position as seen for the Gtα peptide which stabilizes the Meta II state in part A. A T4 lysozyme (T4L) domain used to facilitate crystallization is not shown for clarity. The antagonist bound structure is the carazolol bound β2AR-T4L fusion (PDB ID: 2RH1), and the agonist bound structure is the nanobody stabilized, BI-167107 high affinity agonist bound structure (PDB ID: 3POG). (D) Crystal structure of an agonist bound β2AR-T4L fusion (T4L not shown) in complex with its cognate heterotrimeric G protein, Gsαβγ, and a stabilizing nanobody (not shown) reveals the mode of Gs binding to monomeric β2AR (PDB ID: 3SN6). In this complex, the Gsα C-terminus also binds in the cleft formed by the outward movement of TM5 and TM6. All representations are in approximately the same orientations, and all superpositions were performed with TM1 to TM4, TM7, and cytoplasmic helix H8 to accurately portray the differences in the positions of TM5 and TM6.
Figure 20
Figure 20
Sequence and motif conservation in GPCRs extends to ordered bound water molecules. Sequence conservation among rhodopsin-like (class A) GPCR sequences was mapped onto the backbone of rhodopsin as reported in ref (463); greater “tube” thickness and ramping from blue to red indicate greater residue conservation at that position. Because of considerably lower sequence conservation outside of the TM region, these regions were not included in the analysis and are denoted in white. Structural superposition of all antagonist bound structures of GPCRs with a resolution 2.7 Å or higher reveals a subset of ordered water molecules that are found within the transmembrane bundle (shown in light blue). As indicated by the color and thickness of the cartoon representation, these waters are found in close proximity to positions within the TM region that have high homology throughout all class A GPCRs. Water molecules shared among four or more different receptor structures are shown here. In addition, density best represented by a bound octahedrally coordinated sodium ion has been found within the TM bundle of A2A-adenosine and PAR1 receptor structures (PDB ID: 4EIY, 3VW7; shown as a black sphere) in a similar position to a water observed in the bovine Rho structure (PDB ID: 1U19). Three motifs important for GPCR activation are denoted by shaded ovals.
Figure 21
Figure 21
Activation states of rhodopsin and GPCRs. (A) In the photochemical core process, photon energy is used to convert the inverse agonist 11-cis-retinal into the full agonist all-trans-retinal. Energy stored in the initially twisted all-trans-retinylidene-Lys296 chromophore is gradually released via local protein (side chain) conformational changes in the Batho and Lumi photoproducts. Conformational changes in more distant parts of the protein begin within microseconds of when Meta I forms, the first intermediate of several Meta states in equilibrium, which as GPCR funtional states interact with G protein, GRK1 (rhodopsin kinase), and arrestin. Deprotonation of the RSBH+ and protonation of its counterion Glu113 lead to the formation of Meta II substates which develop sequentially. The largest conformational changes (inset and Figure 19A) are observed in the transition from Meta IIa to Meta IIb; the latter intermediate is further stabilized by proton uptake to Glu134 of the (D/E)RY motif at the cytoplasmic end of TM3. The retinal-free apoprotein opsin exists also in an equilibrium between inactive (rhodopsin-like) and active (Meta-II-like) conformations,,, termed Ops and Ops*. (B) Diffusible ligand activated GPCRs similarly exist in equilibrium between inactive and active conformations in which similar activating conformational changes as in the Meta states are thought to occur. Ligand binding shifts the equilibrium toward ligand type specific energetic states.,
Figure 22
Figure 22
Spectroscopically detected intermediates of photoactivated bovine rhodopsin. Photoisomerization of the retinal 11-cis double bond leads within femtoseconds to photorhodopsin with a highly distorted 11-trans bond. Via thermal relaxation, several intermediates form with distinct λmax values, distinguishable by low-temperature or time-resolved spectroscopy., Gradual release of the strain in the chromophore leads through Batho and Lumi to Meta I, as seen by the different absorption maxima that arise from changes in chromophore/protein interaction. A transient blue-shifted intermediate (BSI) cannot be trapped at low temperatures. Time-resolved UV–vis measurements revealed the existence of additional transient forms of Lumi (Lumi II),, and Meta I (Meta I380;, Meta Ib). The RSBH+ remains protonated up through Meta I, probably due to the low pKa of the stabilizing counterion Glu113. Larger protein conformational changes lead to Meta II (comprising substates Meta IIa and Meta IIb) which is in equilibrium with its predecessor Meta I. Meta II is the agonist-bound active receptor state capable of catalyzing GDP/GTP nucleotide exchange in the G protein transducin. Meta II is characterized by a deprotonated RSB resulting in a large blue-shifted value for λmax (380 nm). As a result of RSB hydrolysis Meta II decays to the apoprotein opsin and all-trans-retinal. Meta I can also form Meta III, involving thermal isomerization of the RSBH+ (λmax = 465 nm) from all-trans,15-anti to all-trans,15-syn. Meta III decays to opsin and all-trans-retinal, but can also be photoconverted to Meta I and Meta II. Unlike in invertebrates, bovine rhodopsin cannot be regenerated in situ by reisomerization of retinal with a second photon. All-trans-retinal is reduced to retinol by retinol dehydrogenase and transported out of the photoreceptor cell to adjacent retinal pigment epithelial cells, where 11-cis-retinal is regenerated (for details, see ref (551)). Adapted with permission from ref (576). Copyright 2002 John Wiley & Sons, Inc.
Figure 23
Figure 23
Isomerization, elongation, and rotation of retinal upon light activation of rhodopsin. (A) Superposition of retinal and the Lys296 and Trp265 side chains in bovine Rho (11-cis-retinal, PDB ID: 1U19, red sticks), Batho (twisted all-trans-retinal, PDB ID: 2G87, gray sticks), Lumi (partially relaxed all-trans-retinal, PDB ID: 2HPY, white sticks), and Meta II (relaxed all-trans-retinal, PDB ID: 3PXO, yellow sticks) structures. Note that from Lumi to Meta II retinal undergoes a large rotation along its long axis. (B) Overlay of rhodopsin and Meta II structures showing differences in the positions of the TM helices. Note that retinal movement induces TM5 motion and rotational tilt of TM6., View from cytoplasmic side.
Figure 24
Figure 24
Conformational changes upon rhodopsin activation leading to the Meta II activated state. ① Photon absorption causes retinal cis → trans isomerization and small scale changes in structure in the immediate vicinity of the retinal, driving all subsequent activation steps. ② Deprotonation of the RSBH+ along with further small-scale changes within the TM region. ③ Signal propagation to two regions almost universally conserved in class A GPCRs, the (D/E)RY and NPxxY(x)5,6F motifs. Changes in the (D/E)RY motif (in TM3; Glu134, Arg135, Tyr136 of bovine Rho), resulting in disruption of the “ionic lock” between Arg135 and Glu247 (on TM6), and changes in the NPxxY(x)5,6F region (TM7/H8) which rearranges. ④ Proton uptake from the cytoplasm onto Glu134. The TM helices are depicted in the following colors: TM1, blue; TM2, teal; TM3, green; TM4, lime green; TM5, yellow; TM6, orange; TM7, red; and H8, purple.
Figure 25
Figure 25
Structural changes in the chromophore binding site and conserved motifs that accompany bovine Rho activation. Upon light-induced activation of Rho a series of small scale structural changes result in the release of restraints enabling attainment of the fully active Meta II state. (A, B) Glu181 is found hydrogen bonded to a water molecule in both the dark state and Meta II structures, and it appears that this water functions as a noncovalently bound cofactor which moves along with Glu181 to stabilize the deprotonated RSB in Meta II. (C, D) TM3/TM6 restraints in the dark state due to the “ionic lock” formed by Arg135, Glu134, Glu247, and Thr251 are released upon Rho activation. In Meta II new interactions are formed between TM3–TM5 (Arg135–Tyr223) and TM6–TM5 (Glu247–Lys231). (E, F) Structural changes within the NPxxY(x)5,6F motif upon activation of Rho entail a remodeling of solvent-mediated hydrogen bonding of two water molecules as well as a 180° change of rotamer for Tyr306 and a concomitant shift of the conserved Phe313 residue. For ease of interpretation, helices are depicted in the following colors: TM1, blue; TM2, teal; TM3, green; TM4, lime green; TM5, yellow; TM6, orange; TM7, red; and H8, purple. For all comparisons, PDB ID: 1U19 was used for dark state and PDB ID: 3PQR was used for Meta II state.
Figure 26
Figure 26
Structural and functional changes in the activation pathway of bovine Rho based on structural and complementary biophysical data discussed in the text and ref (490) and described in Figures 23 and 24.
Figure 27
Figure 27
Retinal channel in the Ops*/Meta II conformation. (A) Meta II structure (PDB ID: 3PXO) with the putative retinal channel indicated, rotated to face opening one (red arrow and half channel indicated in red mesh) which is located between TM1 and TM7, and (B) rotated to face opening two (green arrow and half channel indicated in green mesh) which is located between TM5 and TM6. Channels were determined using MOLE on the Ops* structure (PDB ID: 3CAP). The Meta II structure was used for the figure so that the retinal could be shown as it is absent in the Ops* structure.
Figure 28
Figure 28
Retinal binding site of bovine rhodopsin. (A) Crystal structure of inactive dark state (PDB ID: 1U19) where 11-cis-retinal is tightly bound deep in the protein with no openings of the retinal binding site toward the lipidic environment. (B) In the active Ops* (or Meta II) conformation the retinal channel allows all-trans-retinal access and egress, and some detergents like β-d-octylglucoside, mimicking the all-trans-retinal chromophore, to enter the retinal binding site. Shown is an overlay of the two ligands in the retinal binding pocket as observed in the crystal structures of Meta II (all-trans-retinal depicted in yellow; PDB ID: 3PXO) and Ops* in complex with β-d-octylglucoside (depicted in green/red; two rotamers of Lys296 are shown in red; PDB ID: 4J4Q). Note that the ring moieties of chromophore and detergent are oriented in opposite directions. Whereas all-trans-retinal is covalently linked by the RSB to Lys296, β-d-octylglucoside is fixed in the ligand binding site by hydrogen bonding of its hydroxyl groups to the opsin environment.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Spudich J. L.; Yang C. S.; Jung K. H.; Spudich E. N. Annu. Rev. Cell Dev. Biol. 2000, 16, 365. - PubMed
    1. Palczewski K. Annu. Rev. Biochem. 2006, 75, 743. - PMC - PubMed
    1. Shichida Y.; Matsuyama T. Philos. Trans. R. Soc., B 2009, 364, 2881. - PMC - PubMed
    1. Schmidt T. M.; Chen S. K.; Hattar S. Trends Neurosci. 2011, 34, 572. - PMC - PubMed
    1. Soppa J. FEBS Lett. 1994, 342, 7. - PubMed

Publication types

MeSH terms