High-resolution structural insights into the heliorhodopsin family

Kovalev, Kirill; Volkov, Dmytro; Astashkin, Roman; Alekseev, Alexey; Gushchin, Ivan; Haro-Moreno, José M.; Chizhov, Igor; Siletsky, Sergey A.; Mamedov, Mahir D.; Rogachev, Andrey; Balandin, Taras; Borshchevskiy, Valentin; Popov, A.; Bourenkov, Gleb; Bamberg, Ernst; Rodrı́guez-Valera, Francisco; Büldt, Georg; Gordeliy, Valentin

doi:10.1073/pnas.1915888117

“…The vibrational coupling of the ν(C=C) and δ(N-H) modes indicates different Schiff base geometry in HeRs and other known microbial rhodopsins. These results agree with structural data, which demonstrated distinct retinal pocket organization of HeRs [296]. Nevertheless, Figure 13 shows that the RR spectra of heliorhodopsin HeR 48C12 have a lot of similarities with other microbial rhodopsin spectra although the protein has unique structural features and unclear function.…”

Section: Rs Of Microbial Rhodopsinssupporting

confidence: 85%

“…At this moment, the conception of optogenetics covers a lot of applications, i.e., fundamental study of inner membrane structures of the cell, peripheral nervous system investigation, degenerative retina prosthetics, and a lot more. Robust development in this field opened new era of microbial rhodopsins study [292,293] and generated a tsunami of structural-functional studies of retinal proteins that aimed at the development of new optogenetic tools [19,[293][294][295][296][297][298][299][300]. Advanced RS, such as resonance, time-resolved, SRS provide exclusive information regarding their functional and structural peculiarities, thus facilitating the design of novel optogenetic tools.…”

Section: Rs Of Microbial Rhodopsinsmentioning

confidence: 99%

Raman Scattering: From Structural Biology to Medical Applications

Vlasov

¹

,

Maliar

²

,

Bazhenov

³

et al. 2020

View full text Add to dashboard Cite

This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.

show abstract

“…Recently, a distinct and abundant group of microbial rhodopsins, HeRs, has been discovered 37 – 39 . Although HeRs share low sequence identity with the other rhodopsins and adopt the inverted membrane topology, the crystal structures revealed that HeR comprises seven TMs with the retinal chromophore, as in the other rhodopsins 40 – 42 . Unlike these rhodopsins, the enzyme rhodopsins have long N-termini, and are predicted to have 1–2 additional transmembrane helices 11 , 12 , 43 , while the existence of TM0 and its function still have remained to be elucidated.…”

Section: Discussionmentioning

confidence: 96%

Structural insights into the mechanism of rhodopsin phosphodiesterase

Ikuta

¹

,

Shihoya

²

,

Sugiura

³

et al. 2020

View full text Add to dashboard Cite

Rhodopsin phosphodiesterase (Rh-PDE) is an enzyme rhodopsin belonging to a recently discovered class of microbial rhodopsins with light-dependent enzymatic activity. Rh-PDE consists of the N-terminal rhodopsin domain and C-terminal phosphodiesterase (PDE) domain, connected by 76-residue linker, and hydrolyzes both cAMP and cGMP in a light-dependent manner. Thus, Rh-PDE has potential for the optogenetic manipulation of cyclic nucleotide concentrations, as a complementary tool to rhodopsin guanylyl cyclase and photosensitive adenylyl cyclase. Here we present structural and functional analyses of the Rh-PDE derived from Salpingoeca rosetta. The crystal structure of the rhodopsin domain at 2.6 Å resolution revealed a new topology of rhodopsins, with 8 TMs including the N-terminal extra TM, TM0. Mutational analyses demonstrated that TM0 plays a crucial role in the enzymatic photoactivity. We further solved the crystal structures of the rhodopsin domain (3.5 Å) and PDE domain (2.1 Å) with their connecting linkers, which showed a rough sketch of the full-length Rh-PDE. Integrating these structures, we proposed a model of full-length Rh-PDE, based on the HS-AFM observations and computational modeling of the linker region. These findings provide insight into the photoactivation mechanisms of other 8-TM enzyme rhodopsins and expand the definition of rhodopsins.

show abstract

“…TMs with the retinal chromophore, as in the other rhodopsins [39][40][41] . Unlike these rhodopsins, the enzyme rhodopsins have long N-termini, and are predicted to have 1-2 additional transmembrane helices 11,12,42 , while the existence of TM0 and its function still have remained to be elucidated.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, a distinct and abundant group of microbial rhodopsins, the heliorhodopsins (HeRs) has been discovered [36][37][38] . Although HeRs share low sequence identity with the other rhodopsins and adopt the inverted membrane topology, the crystal structures revealed that HeR comprises 7TMs with the retinal chromophore, as in the other rhodopsins [39][40][41] . Unlike these rhodopsins, the enzyme rhodopsins have long N-termini, and are predicted to have 1-2 additional transmembrane helices 11,12,42 , while the existence of TM0 and its function still have remained to be elucidated.…”

mentioning

confidence: 94%

Structural insights into the mechanism of rhodopsin phosphodiesterase

Ikuta

¹

,

Shihoya

²

,

Sugiura

³

et al. 2020

Preprint

View full text Add to dashboard Cite

Rhodopsin phosphodiesterase (Rh-PDE) is an enzyme rhodopsin belonging to a recently discovered class of microbial rhodopsins with light-dependent enzymatic activity. Rh-PDE consists of the N-terminal rhodopsin domain and C-terminal phosphodiesterase (PDE) domain, connected by 76-residue linker, and hydrolyzes both cAMP and cGMP in a light-dependent manner. Thus, Rh-PDE has potential for the optogenetic manipulation of cyclic nucleotide concentrations, as a complementary tool to rhodopsin guanylyl cyclase (Rh-GC) and photosensitive adenylyl cyclase (PAC). Here we present structural and functional analyses of the Rh-PDE derived from Salpingoeca rosetta. The 2.6 Å resolution crystal structure of the transmembrane domain revealed a new topology of rhodopsin, with 8 TMs including the N-terminal extra TM, TM0. Mutational analyses demonstrated that TM0 plays a crucial role in the enzymatic photoactivity. We further solved the crystal structures of the transmembrane and PDE domain (2.1 Å) with their connecting linkers. Integrating these structures, we proposed a model of full-length Rh-PDE, based on the HS-AFM observations and computational modeling of the linker region. These findings provide insight into the photoactivation mechanisms of other 8-TM enzyme rhodopsins and expand the definition of rhodopsins. -3 - Main text IntroductionMicrobial rhodopsins are photoreceptive membrane proteins with an all-trans retinylidene chromophore 1,2 (all-trans retinal). All microbial rhodopsins share a seven transmembrane topology, in which all-trans retinal chromophore is bound to a conserved lysine residue via Schiff base in the transmembrane helix (TM) 7. Most microbial rhodopsins function as light-driven ion pumps that actively transport various ions 1 (H + , Na + , Cl -, etc.). Some microbial rhodopsins function as light-gated ion channels (channelrhodopsins 3,4 ), which are used as optogenetic tools in neuroscience 5,6 . Enzyme rhodopsins are a group of newly discovered microbial rhodopsins 7 , found in eukaryotes such as fungi and green algae, and choanoflagellates. Enzyme rhodopsins comprise the N-terminal rhodopsin domain and C-terminal enzyme domain, connected by a linker, and function as light-activated enzymes. Two types of enzyme rhodopsins were initially discovered, the histidine kinase rhodopsins 8 (HKRs) and rhodopsin guanylyl cyclase 9 (Rh-GC). While HKRs function as ATP-dependent light-inhibited guanylyl cyclase 10 , Rh-GC from Blastocladiella emersonii (BeGC1) induces a rapid light-triggered cGMP increase in heterologous cells (~5,000-fold) and could be utilized as an optogenetic tool to rapidly manipulate cGMP levels in cells and animals 11,12 .In 2017, rhodopsin phosphodiesterase 13 (Rh-PDE), a novel type of enzyme rhodopsin, was discovered. Rh-PDE derived from Salpingoeca rosetta (SrRh-PDE) was first identified and exhibits light-dependent hydrolytic activity for both of cAMP and cGMP, whereas it lacks pump or channel activity. Moreover, four Rh-PDE homologs were recently discovered in Choanoeca flexa 14 . Thes...

show abstract

High-resolution structural insights into the heliorhodopsin family

Cited by 68 publications

References 75 publications

Raman Scattering: From Structural Biology to Medical Applications

Raman Scattering: From Structural Biology to Medical Applications

Structural insights into the mechanism of rhodopsin phosphodiesterase

Structural insights into the mechanism of rhodopsin phosphodiesterase

Contact Info

Product

Resources

About