BBA - Bioenergetics (v.1837, #5)

Retinal proteins — You can teach an old dog new tricks by Joachim Heberle; Xavier Deupi; Gebhard Schertler (531-532).

We present a historical overview of research on microbial rhodopsins ranging from the 1960s to the present date. Bacteriorhodopsin (BR), the first identified microbial rhodopsin, was discovered in the context of cell and membrane biology and shown to be an outward directed proton transporter. In the 1970s, BR had a big impact on membrane structural research and bioenergetics, that made it to a model for membrane proteins and established it as a probe for the introduction of various biophysical techniques that are widely used today. Halorhodopsin (HR), which supports BR physiologically by transporting negatively charged Cl into the cell, is researched within the microbial rhodopsin community since the late 1970s. A few years earlier, the observation of phototactic responses in halobacteria initiated research on what are known today as sensory rhodopsins (SR). The discovery of the light-driven ion channel, channelrhodopsin (ChR), serving as photoreceptors for behavioral responses in green alga has complemented inquiries into this photoreceptor family. Comparing the discovery stories, we show that these followed quite different patterns, albeit the objects of research being very similar. The stories of microbial rhodopsins present a comprehensive perspective on what can nowadays be considered one of nature's paradigms for interactions between organisms and light. Moreover, they illustrate the unfolding of this paradigm within the broader conceptual and instrumental framework of the molecular life sciences. This article is part of a Special Issue entitled: Retinal proteins — You can teach an old dog new tricks.
Keywords: Bacteriorhodopsin; Sensory rhodopsin; Channelrhodopsin; Membrane research; History;

Mechanism divergence in microbial rhodopsins by John L. Spudich; Oleg A. Sineshchekov; Elena G. Govorunova (546-552).
A fundamental design principle of microbial rhodopsins is that they share the same basic light-induced conversion between two conformers. Alternate access of the Schiff base to the outside and to the cytoplasm in the outwardly open “E” conformer and cytoplasmically open “C” conformer, respectively, combined with appropriate timing of pKa changes controlling Schiff base proton release and uptake make the proton path through the pumps vectorial. Phototaxis receptors in prokaryotes, sensory rhodopsins I and II, have evolved new chemical processes not found in their proton pump ancestors, to alter the consequences of the conformational change or modify the change itself. Like proton pumps, sensory rhodopsin II undergoes a photoinduced E → C transition, with the C conformer a transient intermediate in the photocycle. In contrast, one light-sensor (sensory rhodopsin I bound to its transducer HtrI) exists in the dark as the C conformer and undergoes a light-induced C → E transition, with the E conformer a transient photocycle intermediate. Current results indicate that algal phototaxis receptors channelrhodopsins undergo redirected Schiff base proton transfers and a modified E → C transition which, contrary to the proton pumps and other sensory rhodopsins, is not accompanied by the closure of the external half-channel. The article will review our current understanding of how the shared basic structure and chemistry of microbial rhodopsins have been modified during evolution to create diverse molecular functions: light-driven ion transport and photosensory signaling by protein–protein interaction and light-gated ion channel activity.This article is part of a Special Issue entitled: Retinal Proteins — You can teach an old dog new tricks.
Keywords: Microbial rhodopsins; Schiff base connectivity; Proton transfer; Photosensory transduction; Phototaxis; Optogenetics;

Since the discovery of proteorhodopsins, the ubiquitous marine light-driven proton pumps of eubacteria, a large number of other eubacterial rhodopsins with diverse structures and functions have been characterized. Here, we review the body of knowledge accumulated on the four major groups of eubacterial rhodopsins, with the focus on their biophysical characterization. We discuss advances and controversies on the unique eubacterial sensory rhodopsins (as represented by Anabaena sensory rhodopsin), proton-pumping proteorhodopsins and xanthorhodopsins, as well as novel non-proton ion pumps. This article is part of a Special Issue entitled: Retinal Proteins — You can teach an old dog new tricks.
Keywords: Eubacterial rhodopsins; Retinal-binding proteins; Photosensory transduction; Proton pumping; Biospectroscopy;

Molecular and evolutionary aspects of microbial sensory rhodopsins by Keiichi Inoue; Takashi Tsukamoto; Yuki Sudo (562-577).
Retinal proteins (~ rhodopsins) are photochemically reactive membrane-embedded proteins, with seven transmembrane α-helices which bind the chromophore retinal (vitamin A aldehyde). They are widely distributed through all three biological kingdoms, eukarya, bacteria and archaea, indicating the biological significance of the retinal proteins. Light absorption by the retinal proteins triggers a photoisomerization of the chromophore, leading to the biological function, light-energy conversion or light-signal transduction. This article reviews molecular and evolutionary aspects of the light-signal transduction by microbial sensory receptors and their related proteins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
Keywords: Retinal; Signal transfer; Membrane protein; Phototaxis;

The biochemical processes of living cells involve a numerous series of reactions that work with exceptional specificity and efficiency. The tight control of this intricate reaction network stems from the architecture of the proteins that drive the chemical reactions and mediate protein–protein interactions. Indeed, the structure of these proteins will determine both their function and interaction partners. A detailed understanding of the proximity and orientation of pivotal functional groups can reveal the molecular mechanistic basis for the activity of a protein. Together with X-ray crystallography and electron microscopy, NMR spectroscopy plays an important role in solving three-dimensional structures of proteins at atomic resolution. In the challenging field of membrane proteins, retinal-binding proteins are often employed as model systems and prototypes to develop biophysical techniques for the study of structural and functional mechanistic aspects. The recent determination of two 3D structures of seven-helical trans-membrane retinal proteins by solution-state NMR spectroscopy highlights the potential of solution NMR techniques in contributing to our understanding of membrane proteins. This review summarizes the multiple strategies available for expression of isotopically labeled membrane proteins. Different environments for mimicking lipid bilayers will be presented, along with the most important NMR methods and labeling schemes used to generate high-quality NMR spectra. The article concludes with an overview of types of conformational restraints used for generation of high-resolution structures of membrane proteins. This article is part of a Special Issue entitled: Retinal Proteins — You can teach an old dog new tricks.
Keywords: Solution-state NMR; Membrane proteins; Protein structure determination; Expression systems; Isotope labeling;

Light induced isomerization of the retinal chromophore activates biological function in all retinal protein (RP) driving processes such as ion-pumping, vertebrate vision and phototaxis in organisms as primitive as archea, or as complex as mammals. This process and its consecutive reactions have been the focus of experimental and theoretical research for decades. The aim of this review is to demonstrate how the experimental and theoretical research efforts can now be combined to reach a more comprehensive understanding of the excited state process on the molecular level. Using the Anabaena Sensory Rhodopsin as an example we will show how contemporary time-resolved spectroscopy and recently implemented excited state QM/MM methods consistently describe photochemistry in retinal proteins. This article is part of a Special Issue entitled: Retinal Proteins — You can teach an old dog new tricks.
Keywords: Anabaena Sensory Rhodopsin; Retinal chromophore; Photoisomerization; Photochromism; Time resolved spectroscopy; Excited state molecular dynamics;

Microbial rhodopsins are classified into type-I rhodopsins, which utilize light energy to perform wide varieties of function, such as proton pumping, ion pumping, light sensing, cation channels, and so on. The crystal structures of several type-I rhodopsins were solved and the molecular mechanisms have been investigated based on the atomic structures. However, the crystal structures of proteins of interest are not always available and the basic architectures are sometimes quite similar, which obscures how the proteins achieve different functions. Stimulus-induced difference FTIR spectroscopy is a powerful tool to detect minute structural changes providing a clue for elucidating the molecular mechanisms. In this review, the studies on type-I rhodopsins from fungi and marine bacteria, whose crystal structures have not been solved yet, were summarized. Neurospora rhodopsin and Leptosphaeria rhodopsin found from Fungi have sequence similarity. The former has no proton pumping function, while the latter has. Proteorhodopsin is another example, whose proton pumping machinery is altered at alkaline and acidic conditions. We described how the structural changes of protein were different and how water molecules were involved in them. We reviewed the results on dynamics of the internal water molecules in pharaonis halorhodopsin as well. This article is part of a Special Issue entitled: Retinal Proteins — You can teach an old dog new tricks.
Keywords: Light-energy conversion; Proton pump; Hydrogen bond; Ion–protein interaction; Vibrational spectroscopy;

The role of protein-bound water molecules in microbial rhodopsins by Klaus Gerwert; Erik Freier; Steffen Wolf (606-613).
Protein-bound internal water molecules are essential features of the structure and function of microbial rhodopsins. Besides structural stabilization, they act as proton conductors and even proton storage sites. Currently, the most understood model system exhibiting such features is bacteriorhodopsin (bR). During the last 20 years, the importance of water molecules for proton transport has been revealed through this protein. It has been shown that water molecules are as essential as amino acids for proton transport and biological function. In this review, we present an overview of the historical development of this research on bR. We furthermore summarize the recently discovered protein-bound water features associated with proton transport. Specifically, we discuss a pentameric water/amino acid arrangement close to the protonated Schiff base as central proton-binding site, a protonated water cluster as proton storage site at the proton-release site, and a transient linear water chain at the proton uptake site. We highlight how protein conformational changes reposition or reorient internal water molecules, thereby guiding proton transport. Last, we compare the water positions in bR with those in other microbial rhodopsins to elucidate how protein-bound water molecules guide the function of microbial rhodopsins. This article is part of a Special Issue entitled: Retinal Proteins — You can teach an old dog new tricks.
Keywords: Protein-bound water molecules; Microbial rhodopsins; Grotthuss proton transfer; Fourier transform infrared spectroscopy; Biomolecular simulations;

Proteorhodopsin by Christian Bamann; Ernst Bamberg; Josef Wachtveitl; Clemens Glaubitz (614-625).
Proteorhodopsins are the most abundant retinal based photoreceptors and their phototrophic function might be relevant in marine ecosystems. Here, we describe their remarkable molecular properties with a special focus on the green absorbing variant. Its distinct features include a high pKa value of the primary proton acceptor stabilized through an interaction with a conserved histidine, a long-range interaction between the cytoplasmic EF loop and the chromophore entailing a particular mode of color tuning and a variable proton pumping vectoriality with complex voltage-dependence. The proteorhodopsin family represents a profound example for structure–function relationships. Especially the development of a biophysical understanding of green proteorhodopsin is an excellent example for the unique opportunities offered by a combined approach of advanced spectroscopic and electrophysiological methods. This article is part of a Special Issue entitled: Retinal Proteins—You can teach an old dog new tricks.Display Omitted
Keywords: Photocycle; NMR spectroscopy; Photoisomerization; Charge transfer; Electrophysiology;

Channelrhodopsin unchained: Structure and mechanism of a light-gated cation channel by Víctor A. Lórenz-Fonfría; Joachim Heberle (626-642).
The new and vibrant field of optogenetics was founded by the seminal discovery of channelrhodopsin, the first light-gated cation channel. Despite the numerous applications that have revolutionised neurophysiology, the functional mechanism is far from understood on the molecular level. An arsenal of biophysical techniques has been established in the last decades of research on microbial rhodopsins. However, application of these techniques is hampered by the duration and the complexity of the photoreaction of channelrhodopsin compared with other microbial rhodopsins. A particular interest in resolving the molecular mechanism lies in the structural changes that lead to channel opening and closure. Here, we review the current structural and mechanistic knowledge that has been accomplished by integrating the static structure provided by X-ray crystallography and electron microscopy with time-resolved spectroscopic and electrophysiological techniques. The dynamical reactions of the chromophore are effectively coupled to structural changes of the protein, as shown by ultrafast spectroscopy. The hierarchical sequence of structural changes in the protein backbone that spans the time range from 10− 12  s to 10− 3  s prepares the channel to open and, consequently, cations can pass. Proton transfer reactions that are associated with channel gating have been resolved. In particular, glutamate 253 and aspartic acid 156 were identified as proton acceptor and donor to the retinal Schiff base. The reprotonation of the latter is the critical determinant for channel closure. The proton pathway that eventually leads to proton pumping is also discussed. This article is part of a Special Issue entitled: Retinal Proteins — You can teach an old dog new tricks.
Keywords: Vibrational spectroscopy; Bacteriorhodopsin; Electrophysiology; Proton transfer; Optogenetics;

Channelrhodopsins: A bioinformatics perspective by Coral del Val; José Royuela-Flor; Stefan Milenkovic; Ana-Nicoleta Bondar (643-655).
Channelrhodopsins are microbial-type rhodopsins that function as light-gated cation channels. Understanding how the detailed architecture of the protein governs its dynamics and specificity for ions is important, because it has the potential to assist in designing site-directed channelrhodopsin mutants for specific neurobiology applications. Here we use bioinformatics methods to derive accurate alignments of channelrhodopsin sequences, assess the sequence conservation patterns and find conserved motifs in channelrhodopsins, and use homology modeling to construct three-dimensional structural models of channelrhodopsins. The analyses reveal that helices C and D of channelrhodopsins contain Cys, Ser, and Thr groups that can engage in both intra- and inter-helical hydrogen bonds. We propose that these polar groups participate in inter-helical hydrogen-bonding clusters important for the protein conformational dynamics and for the local water interactions. This article is part of a Special Issue entitled: Retinal Proteins — You can teach an old dog new tricks.
Keywords: Channelrhodopsin; Bioinformatics; Membrane protein; Protein structure and dynamics;

Retinal proteins as model systems for membrane protein folding by Oznur Tastan; Arpana Dutta; Paula Booth; Judith Klein-Seetharaman (656-663).
Experimental folding studies of membrane proteins are more challenging than water-soluble proteins because of the higher hydrophobicity content of membrane embedded sequences and the need to provide a hydrophobic milieu for the transmembrane regions. The first challenge is their denaturation: due to the thermodynamic instability of polar groups in the membrane, secondary structures in membrane proteins are more difficult to disrupt than in soluble proteins. The second challenge is to refold from the denatured states. Successful refolding of membrane proteins has almost always been from very subtly denatured states. Therefore, it can be useful to analyze membrane protein folding using computational methods, and we will provide results obtained with simulated unfolding of membrane protein structures using the Floppy Inclusions and Rigid Substructure Topography (FIRST) method. Computational methods have the advantage that they allow a direct comparison between diverse membrane proteins. We will review here both, experimental and FIRST studies of the retinal binding proteins bacteriorhodopsin and mammalian rhodopsin, and discuss the extension of the findings to deriving hypotheses on the mechanisms of folding of membrane proteins in general. This article is part of a Special Issue entitled: Retinal Proteins—You can teach an old dog new tricks.
Keywords: Rhodopsin; Bacteriorhodopsin; Membrane protein folding; Denatured states;

Cone visual pigments by Yasushi Imamoto; Yoshinori Shichida (664-673).
Cone visual pigments are visual opsins that are present in vertebrate cone photoreceptor cells and act as photoreceptor molecules responsible for photopic vision. Like the rod visual pigment rhodopsin, which is responsible for scotopic vision, cone visual pigments contain the chromophore 11-cis-retinal, which undergoes cis–trans isomerization resulting in the induction of conformational changes of the protein moiety to form a G protein-activating state. There are multiple types of cone visual pigments with different absorption maxima, which are the molecular basis of color discrimination in animals. Cone visual pigments form a phylogenetic sister group with non-visual opsin groups such as pinopsin, VA opsin, parapinopsin and parietopsin groups. Cone visual pigments diverged into four groups with different absorption maxima, and the rhodopsin group diverged from one of the four groups of cone visual pigments. The photochemical behavior of cone visual pigments is similar to that of pinopsin but considerably different from those of other non-visual opsins. G protein activation efficiency of cone visual pigments is also comparable to that of pinopsin but higher than that of the other non-visual opsins. Recent measurements with sufficient time-resolution demonstrated that G protein activation efficiency of cone visual pigments is lower than that of rhodopsin, which is one of the molecular bases for the lower amplification of cones compared to rods. In this review, the uniqueness of cone visual pigments is shown by comparison of their molecular properties with those of non-visual opsins and rhodopsin. This article is part of a Special Issue entitled: Retinal Proteins — You can teach an old dog new tricks.Display Omitted
Keywords: Rhodopsin; Color vision; Molecular evolution; G-protein coupled receptors; Opsin family; Retina;

Rhodopsin, the dim-light photoreceptor present in the rod cells of the retina, is both a retinal-binding protein and a G protein-coupled receptor (GPCR). Due to this conjunction, it benefits from an arsenal of spectroscopy techniques that can be used for its characterization, while being a model system for the important family of Class A (also referred to as “rhodopsin-like”) GPCRs. For instance, rhodopsin has been a crucial player in the field of GPCR structural biology. Until 2007, it was the only GPCR for which a high-resolution crystal structure was available, so all structure–activity analyses on GPCRs, from structure-based drug discovery to studies of structural changes upon activation, were based on rhodopsin. At present, about a third of currently available GPCR structures are still from rhodopsin. In this review, I show some examples of how these structures can still be used to gain insight into general aspects of GPCR activation. First, the analysis of the third intracellular loop in rhodopsin structures allows us to gain an understanding of the structural and dynamic properties of this region, which is absent (due to protein engineering or poor electron density) in most of the currently available GPCR structures. Second, a detailed analysis of the structure of the transmembrane domains in inactive, intermediate and active rhodopsin structures allows us to detect early conformational changes in the process of ligand-induced GPCR activation. Finally, the analysis of a conserved ligand-activated transmission switch in the transmembrane bundle of GPCRs in the context of the rhodopsin activation cycle, allows us to suggest that the structures of many of the currently available agonist-bound GPCRs may correspond to intermediate active states. While the focus in GPCR structural biology is inevitably moving away from rhodopsin, in other aspects rhodopsin is still at the forefront. For instance, the first studies of the structural basis of disease mutants in GPCRs, or the most detailed analysis of cellular GPCR signal transduction networks using a systems biology approach, have been carried out in rhodopsin. Finally, due again to its unique properties among GPCRs, rhodopsin will likely play an important role in the application of X-ray free electron laser crystallography to time-resolved structural biology in membrane proteins. Rhodopsin, thus, still remains relevant as a model system to study the molecular mechanisms of GPCR activation. This article is part of a Special Issue entitled: Retinal Proteins—You can teach an old dog new tricks.
Keywords: Rhodopsin; G protein-coupled receptors; GPCR activation; Structural biology; Structural bioinformatics;

Amino acid conservation and interactions in rhodopsin: Probing receptor activation by NMR spectroscopy by Andreyah Pope; Markus Eilers; Philip J. Reeves; Steven O. Smith (683-693).
Rhodopsin is a classical two-state G protein-coupled receptor (GPCR). In the dark, its 11-cis retinal chromophore serves as an inverse agonist to lock the receptor in an inactive state. Retinal–protein and protein–protein interactions have evolved to reduce the basal activity of the receptor in order to achieve low dark noise in the visual system. In contrast, absorption of light triggers rapid isomerization of the retinal, which drives the conversion of the receptor to a fully active conformation. Several specific protein–protein interactions have evolved that maintain the lifetime of the active state in order to increase the sensitivity of this receptor for dim-light vision in vertebrates. In this article, we review the molecular interactions that stabilize rhodopsin in the dark-state and describe the use of solid-state NMR spectroscopy for probing the structural changes that occur upon light-activation. Amino acid conservation provides a guide for those interactions that are common in the class A GPCRs as well as those that are unique to the visual system. This article is part of a Special Issue entitled: Retinal Proteins — You can teach an old dog new tricks.
Keywords: Solid-state NMR spectroscopy; GPCR; Visual pigment;

Fluorescence spectroscopy of rhodopsins: Insights and approaches by Ulrike Alexiev; David L. Farrens (694-709).
Fluorescence spectroscopy has become an established tool at the interface of biology, chemistry and physics because of its exquisite sensitivity and recent technical advancements. However, rhodopsin proteins present the fluorescence spectroscopist with a unique set of challenges and opportunities due to the presence of the light-sensitive retinal chromophore. This review briefly summarizes some approaches that have successfully met these challenges and the novel insights they have yielded about rhodopsin structure and function. We start with a brief overview of fluorescence fundamentals and experimental methodologies, followed by more specific discussions of technical challenges rhodopsin proteins present to fluorescence studies. Finally, we end by discussing some of the unique insights that have been gained specifically about visual rhodopsin and its interactions with affiliate proteins through the use of fluorescence spectroscopy. This article is part of a Special Issue entitled: Retinal Proteins — You can teach an old dog new tricks.
Keywords: Retinal protein; Fluorescence spectroscopy; Site-directed fluorescence labeling; Visual rhodopsin;

Diversity of animal opsin-based pigments and their optogenetic potential by Mitsumasa Koyanagi; Akihisa Terakita (710-716).
Most animal opsin-based pigments are typical G protein-coupled receptors (GPCR) and consist of a protein moiety, opsin, and 11-cis retinal as a chromophore. More than several thousand opsins have been identified from a wide variety of animals, which have multiple opsin genes. Accumulated evidence reveals the molecular property of opsin-based pigments, particularly non-conventional visual pigments including non-visual pigments. Opsin-based pigments are generally a bistable pigment having two stable and photointerconvertible states and therefore are bleach-resistant and reusable, unlike vertebrate visual pigments which become bleached. The opsin family contains Gt-coupled, Gq-coupled, Go-coupled, Gs-coupled, Gi-coupled, and Gi/Go-coupled opsins, indicating the existence of a large diversity of light-driven GPCR-signaling cascades. It is suggested that these molecular properties might contribute to different physiologies. In addition, various opsin based-pigments, especially nonconventional visual pigments having different molecular characteristics would facilitate the design and development of promising optogenetic tools for modulating GPCR-signaling, which is involved in a wide variety of physiological responses. We here introduce molecular and functional properties of various kinds of opsins and discuss their physiological function and also their potentials for optogenetic applications. This article is part of a Special Issue entitled: Retinal proteins — you can teach an old dog new tricks.
Keywords: Non-visual pigment; Phototransduction; Opsin diversity; Optogenetics;