Discovering Key Activation Hotspots in the M2 Muscarinic Receptor

The M2 muscarinic receptor (M2R) is a prototypical G protein-coupled receptor (GPCR) that serves as a model system for understanding ligand recognition and GPCR activation. Here, using vibrational spectroscopy, we identify the mechanisms governing M2R activation by its native agonist, acetylcholine. Combined with mutagenesis, computational chemistry, and organic synthetic chemistry, our analyses found that the precise distance between acetylcholine and Asn404, one of the amino acids constituting the ligand-binding site, is important for M2R activation and that the N404Q mutant undergoes partial active state-like conformational changes. We discovered that a water molecule bridging acetylcholine and Asn404 forms a precise and flexible hydrogen bond network, triggering the outward movement of transmembrane helix 6 in M2R. Consistent with this observation, disruptions in this hydrogen bond network via chemical modification at the α- or β-position of acetylcholine failed to activate M2R. Collectively, our findings pinpoint Asn404 as a critical residue that both senses acetylcholine binding and induces M2R activation.

FTIR study of light-induced proton transfer and Ca2+ binding in T82D mutant of TAT rhodopsin

Proton transfer reactions play important functional roles in many proteins, such as enzymes and transporters, which is also the case in rhodopsins. In fact, functional expression of rhodopsins accompanies intramolecular proton transfer reactions in many cases. One of the exceptional cases can be seen in the protonated form of marine bacterial TAT rhodopsin, which isomerizes the retinal by light but returns to the original state within 10-5 s. Thus, light energy is converted into heat without any function. In contrast, the T82D mutant of TAT rhodopsin conducts the light-induced deprotonation of the Schiff base at high pH. In this article, we report the structural analysis of T82D by means of difference Fourier transform infrared (FTIR) spectroscopy. In the light-induced difference FTIR spectra at 77 K, we observed little hydrogen out-of-plane vibrations for T82D as well as the wild-type (WT), suggesting that the planar chromophore structure itself is not the origin of the reversion from the K intermediate in WT TAT rhodopsin. Upon relaxation of the K intermediate, T82D forms the following intermediate, such as M, whereas K of WT returns to the original state. Present FTIR analysis revealed the proton transfer from the Schiff base to D82 in T82D upon formation of the M intermediate. It is accompanied by the second proton transfer from E54 to the Schiff base, forming the N intermediate, particularly in membranes. The equilibrium between the M and N intermediates corresponds to the protonation equilibrium between E54 and the Schiff base. We also found that Ca2+ binding takes place in T82D as well as WT but with 6 times lower affinity. An altered hydrogen-bonding network would be the origin of low affinity in T82D, where deprotonation of E54 is involved in the Ca2+ binding.

Origin of the Difference in Proton Transport Direction between Inward and Outward Proton-Pumping Rhodopsins

Active transport is a vital and ubiquitous process in biological phenomena. Ion-pumping rhodopsins are light-driven active ion transporters that share a heptahelical transmembrane structural scaffold in which the all-trans retinal chromophore is covalently bonded through a Schiff base to a conserved lysine residue in the seventh transmembrane helix. Bacteriorhodopsin from Halobacterium salinarum was the first ion-pumping rhodopsin to be discovered and was identified as an outward proton-pumping rhodopsin. Since the discovery of bacteriorhodopsin in 1971, many more ion-pumping rhodopsins have been isolated from diverse microorganisms spanning three domains (bacteria, archaea, and eukaryotes) and giant viruses. In addition to proton-pumping rhodopsins, chloride ion- and sodium ion-pumping rhodopsins have also been discovered. Furthermore, diversity of ion-pumping rhodopsins was found in the direction of ion transport; i.e., rhodopsins that pump protons inward have recently been discovered. Very intriguingly, the inward proton-pumping rhodopsins share structural features and many conserved key residues with the outward proton-pumping rhodopsins. However, a central question remains unchanged despite the increasing variety: how and why do the ion-pumping rhodopsins undergo interlocking conformational changes that allow unidirectional ion transfer within proteins? In this regard, it is an effective strategy to compare the structures and their evolutions in the proton-pumping processes of both inward and outward proton-pumping rhodopsins because the comparison sheds light on key elements for the unidirectional proton transport. We elucidated the proton-pumping mechanism of the inward and outward proton-pumping rhodopsins by time-resolved resonance Raman spectroscopy, a powerful technique for tracking the structural evolutions of proteins at work that are otherwise inaccessible. In this Account, we primarily review our endeavors in the elucidation of the proton-pumping mechanisms and determination factors for the transport directions of inward and outward proton-pumping rhodopsins. We begin with a brief summary of previous findings on outward proton-pumping rhodopsins revealed by vibrational spectroscopy. Next, we provide insights into the mechanism of inward proton-pumping rhodopsins, schizorhodopsins, obtained in our studies. Time-resolved resonance Raman spectroscopy provided valuable information about the structures of the retinal chromophore in the unphotolyzed state and intermediates of schizorhodopsins. As we ventured further into our investigations, we succeeded in uncovering the factors determining the directions of proton release and uptake in the retinal Schiff base. While it is intriguing that the proton-pumping rhodopsins actively transport protons against a concentration gradient, it is even more curious that proteins with structural similarities transport protons in opposite directions. Solving the second mystery led to solving the first. When we considered our findings, we realized that we would probably not have been able to elucidate the mechanism if we had studied only the outward pump. Our Account concludes by outlining future opportunities and challenges in the growing research field of ion-pumping rhodopsins, with a particular emphasis on elucidating their sequence-structure-function relationships. We aim to inspire further advances toward the understanding and creation of light-driven active ion transporters.

Unique hydrogen-bonding network in a viral channelrhodopsin

Channelrhodopsins (CRs) are used as key tools in optogenetics, and novel CRs, either found from nature or engineered by mutation, have greatly contributed to the development of optogenetics. Recently CRs were discovered from viruses, and crystal structure of a viral CR, OLPVR1, reported a very similar water-containing hydrogen-bonding network near the retinal Schiff base to that of a light-driven proton-pump bacteriorhodopsin (BR). In both OLPVR1 and BR, nearly planar pentagonal cluster structures are comprised of five oxygen atoms, three oxygens from water molecules and two oxygens from the Schiff base counterions. The planar pentagonal cluster stabilizes a quadrupole, two positive charges at the Schiff base and an arginine, and two negative charges at the counterions, and thus plays important roles in light-gated channel function of OLPVR1 and light-driven proton pump function of BR. Despite similar pentagonal cluster structures, present FTIR analysis revealed different hydrogen-bonding networks between OLPVR1 and BR. The hydrogen bond between the protonated Schiff base and a water is stronger in OLPVR1 than in BR, and internal water molecules donate hydrogen bonds much weaker in OLPVR1 than in BR. In OLPVR1, the bridged water molecule between the Schiff base and counterions forms hydrogen bonds to D76 and D200 equally, while the hydrogen-bonding interaction is much stronger to D85 than to D212 in BR. The present interpretation is supported by the mutation results, where D76 and D200 equally work as the Schiff base counterions in OLPVR1, but D85 is the primary counterion in BR. This work reports highly sensitive hydrogen-bonding network in the Schiff base region, which would be closely related to each function through light-induced alterations of the network.

Light-driven anion-pumping rhodopsin with unique cytoplasmic anion-release mechanism

Microbial rhodopsins are photoreceptive membrane proteins found in microorganisms with an all-trans-retinal chromophore. The function of many microbial rhodopsins is determined by three residues in the third transmembrane helix called motif residues. Here, we report a group of microbial rhodopsins with a novel Thr-Thr-Gly (TTG) motif. The ion-transport assay revealed that they function as light-driven inward anion pumps similar to halorhodopsins previously found in archaea and bacteria. Based on the characteristic glycine residue in their motif and light-driven anion-pumping function, these new rhodopsins are called glycylhalorhodopsins (GHRs). X-ray crystallographic analysis found large cavities on the cytoplasmic side, which are produced by the small side-chain volume of the glycine residue in the motif. The opened structure of GHR on the cytoplasmic side is related to the anion releasing process to the cytoplasm during the photoreaction compared to canonical halorhodopsin from Natronomonas pharaonis (NpHR). GHR also transports SO42- and the extracellular glutamate residue plays an essential role in extracellular SO42- uptake. In summary, we have identified TTG motif-containing microbial rhodopsins that display an anion-releasing mechanism.

Low-temperature FTIR spectroscopy of the L/Q switch of proteorhodopsin

Rhodopsins are photoreceptive membrane proteins containing a retinal chromophore, and the color tuning mechanism in rhodopsins is one of the important topics. Color switch is a color-determining residue at the same position, where replacement of red- and blue-shifting amino acids in two wild-type rhodopsins causes spectral blue- and red-shifts, respectively. The first and most famous color switch in microbial rhodopsins is the L/Q switch in proteorhodopsins (PRs). Green- or blue-absorbing PR (GPR or BPR) contains Leu and Gln at position 105 of the C-helix (TM3), respectively, and their replacement converted absorbing colors. The L/Q switch enables bacteria to absorb green or blue light in shallow or deep ocean waters, respectively. Although Gln and Leu are hydrophilic and hydrophobic residues, respectively, a comprehensive mutation study of position 105 in GPR revealed that the λmax correlated with the volume of residues, not the hydropathy index. To gain structural insights into the mechanism, we applied low-temperature FTIR spectroscopy of L105Q GPR, and the obtained spectra were compared with those of GPR and BPR. The difference FTIR spectra of L105Q GPR were similar to those of BPR, not GPR, implying that the L/Q switch converts the GPR structure into a BPR structure in terms of the local environments of the retinal chromophore. It includes retinal skeletal vibration, hydrogen-bonding strength of the protonated Schiff base, amide-A vibration (peptide backbone), and protein-bound water molecules. Consequently color is switched accompanying such structural alterations, and known as the L/Q switch.

Photoisomerization pathway of the microbial rhodopsin chromophore in solution

Photoisomerization is a key photochemical reaction in microbial and animal rhodopsins. It is well established that such photoisomerization is highly selective; all-trans to 13-cis, and 11-cis to all-trans forms in microbial and animal rhodopsins, respectively. Nevertheless, unusual photoisomerization pathways have been discovered recently in microbial rhodopsins. In an enzymerhodopsin NeoR, the all-trans chromophore is isomerized into the 7-cis form exclusively, which is stable at room temperature. Although, the 7-cis form is produced by illumination of retinal, formation of the 7-cis form was never reported for a protonated Schiff base of all-trans retinal in solution. Present HPLC analysis of retinal oximes prepared by hydroxylamine reaction revealed that all-trans and 7-cis forms cannot be separated from the syn peaks under the standard HPLC conditions, while it is possible by the analysis of the anti-peaks. Consequently, we found formation of the 7-cis form by the photoreaction of all-trans chromophore in solution, regardless of the protonation state of the Schiff base. Upon light absorption of all-trans protonated retinal Schiff base in solution, excited-state relaxation accompanies double-bond isomerization, producing 7-cis, 9-cis, 11-cis, or 13-cis form. In contrast, specific chromophore-protein interaction enforces selective isomerization into the 13-cis form in many microbial rhodopsins, but into 7-cis in NeoR.

Stretching vibrational frequencies and pKa differences in H-bond networks of protein environments

The experimentally measured stretching vibrational frequencies of O-D [νO-D(donor)] and C=O [νC=O(donor)] H-bond donor groups can provide valuable information about the H-bonds in proteins. Here, using a quantum mechanical/molecular mechanical approach, the relationship between these vibrational frequencies and the difference in pKa values between H-bond donor and acceptor groups [ΔpKa(donor … acceptor)] in bacteriorhodopsin and photoactive yellow protein environments was investigated. The results show that νO-D(donor) is correlated with ΔpKa(donor … acceptor), regardless of the specific protein environment. νC=O(donor) is also correlated with ΔpKa(donor … acceptor), although the correlation is weak because the C=O bond does not have a proton. Importantly, the shifts in νO-D(donor) and νC=O(donor) are not caused by changes in pKa(donor) alone, but rather by changes in ΔpKa(donor … acceptor). Specifically, a decrease in ΔpKa(donor … acceptor) can lead to proton release from the H-bond donor group toward the acceptor group, resulting in shifts in the vibrational frequencies of the protein environment. These findings suggest that changes in the stretching vibrational frequencies, in particular νO-D(donor), can be used to monitor proton transfer in protein environments.

Counterion at an atypical position: Investigating the mechanism of photoisomerization in jellyfish rhodopsin

The position of the counterion in animal rhodopsins plays a crucial role in maintaining visible light sensitivity and facilitating the photoisomerization of their retinal chromophore. The counterion displacement is thought to be closely related to the evolution of rhodopsins, with different positions found in invertebrates and vertebrates. Interestingly, box jellyfish rhodopsin (JelRh) acquired the counterion in transmembrane 2 (TM2) independently. This is a unique feature, as in most animal rhodopsins, the counterion is found in a different location. In this study, we used Fourier Transform Infrared spectroscopy to examine the structural changes that occur in the early photointermediate state of JelRh. We aimed to determine whether the photochemistry of JelRh is similar to that of other animal rhodopsins by comparing its spectra to those of vertebrate bovine rhodopsin (BovRh) and invertebrate squid rhodopsin (SquRh). We observed that the N-D stretching band of the retinal Schiff base was similar to that of BovRh, indicating the interaction between the Schiff base and the counterion is similar in both rhodopsins, despite their different counterion positions. Furthermore, we found that the chemical structure of the retinal in JelRh is similar to that in BovRh, including the changes in the hydrogen-out-of-plane band that indicates a retinal distortion. Overall, the protein conformational changes induced by the photoisomerization of JelRh yielded spectra that resemble an intermediate between BovRh and SquRh, suggesting a unique spectral property of JelRh, and making it the only animal rhodopsin with a counterion in TM2 and an ability to activate G_s protein.

Difference FTIR Spectroscopy of Jumping Spider Rhodopsin-1 at 77 K

Animal visual rhodopsins can be classified into monostable and bistable rhodopsins, which are typically found in vertebrates and invertebrates, respectively. The former example is bovine rhodopsin (BovRh), whose structures and functions have been extensively studied. On the other hand, those of bistable rhodopsins are less known, despite their importance in optogenetics. Here, low-temperature Fourier-transform infrared (FTIR) spectroscopy was applied to jumping spider rhodopsin-1 (SpiRh1) at 77 K, and the obtained light-induced spectral changes were compared with those of squid rhodopsin (SquRh) and BovRh. Although chromophore distortion of the resting state monitored by HOOP vibrations is not distinctive between invertebrate and vertebrate rhodopsins, distortion of the all-trans chromophore after photoisomerization is unique for BovRh, and the distortion was localized at the center of the chromophore in SpiRh1 and SquRh. Highly conserved aspartate (D83 in BovRh) does not change the hydrogen-bonding environment in invertebrate rhodopsins. Thus, present FTIR analysis provides specific structural changes, leading to activation of invertebrate and vertebrate rhodopsins. On the other hand, the analysis of O-D stretching vibrations in D₂O revealed unique features of protein-bound water molecules. Numbers of water bands in SpiRh1 and SquRh were less and more than those in BovRh. The X-ray crystal structure of SpiRh1 observed a bridged water molecule between the protonated Schiff base and its counterion (E194), but strongly hydrogen-bonded water molecules were never detected in SpiRh1, as well as SquRh and BovRh. Thus, absence of strongly hydrogen-bonded water molecules is substantial for animal rhodopsins, which is distinctive from microbial rhodopsins.

Purification of the Na+-Driven PomAB Stator Complex and Its Analysis Using ATR-FTIR Spectroscopy

The flagellar motor of marine Vibrio is driven by the sodium-motive force across the inner membrane. The stator complex, consisting of two membrane proteins PomA and PomB, is responsible for energy conversion in the motor. To understand the coupling of the Na⁺ flux with torque generation, it is essential to clearly identify the Na⁺-binding sites and the Na⁺ flux pathway through the stator channel. Although residues essential for Na⁺ flux have been identified by using mutational analysis, it has been difficult to observe Na⁺ binding to the PomAB stator complex. Here we describe a method to monitor the binding of Na⁺ to purified PomAB stator complex using attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. This method demonstrates that Na⁺-binding sites are formed by critical aspartic acid and threonine residues located in the transmembrane segments of PomAB.

Specific zinc binding to heliorhodopsin

Heliorhodopsins (HeRs), a recently discovered family of rhodopsins, have an inverted membrane topology compared to animal and microbial rhodopsins. The slow photocycle of HeRs suggests a light-sensor function, although the actual function remains unknown. Although HeRs exhibit no specific binding of monovalent cations or anions, recent ATR-FTIR spectroscopy studies have demonstrated the binding of Zn²⁺ to HeR from Thermoplasmatales archaeon (TaHeR) and 48C12. Even though ion-specific FTIR spectra were observed for many divalent cations, only helical structural perturbations were observed for Zn²⁺-binding, suggesting a possible modification of the HeR function by Zn²⁺. The present study shows that Zn²⁺-binding lowers the thermal stability of TaHeR, and slows back proton transfer to the retinal Schiff base (M decay) during its photocycle. Zn²⁺-binding was similarly observed for a TaHeR opsin that lacks the retinal chromophore. We then studied the Zn²⁺-binding site by means of the ATR-FTIR spectroscopy of site-directed mutants. Among five and four mutants of His and Asp/Glu, respectively, only E150Q exhibited a completely different spectral feature of the α-helix (amide-I) in ATR-FTIR spectroscopy, suggesting that E150 is responsible for Zn²⁺-binding. Molecular dynamics (MD) simulations built a coordination structure of Zn²⁺-bound TaHeR, where E150 and protein bound water molecules participate in direct coordination. It was concluded that the specific binding site of Zn²⁺ is located at the cytoplasmic side of TaHeR, and that Zn²⁺-binding affects the structure and structural dynamics, possibly modifying the unknown function of TaHeR.

Unusual Photoisomerization Pathway in a Near-Infrared Light Absorbing Enzymerhodopsin

Microbial and animal rhodopsins possess retinal chromophores which capture light and normally photoisomerize from all-trans to 13-cis and from 11-cis to all-trans-retinal, respectively. Here, we show that a near-infrared light-absorbing enzymerhodopsin from Obelidium mucronatum (OmNeoR) contains the all-trans form in the dark but isomerizes into the 7-cis form upon illumination. The photoproduct (λ_max = 372 nm; P₃₇₂) possesses a deprotonated Schiff base, and the system exhibits a bistable nature. The photochemistry of OmNeoR was arrested at <270 K, indicating the presence of a potential barrier in the excited state. Formation of P₃₇₂ is accompanied by protonation changes of protonated carboxylic acids and peptide backbone changes of an α-helix. Photoisomerization from the all-trans to 7-cis retinal conformation rarely occurs in any solvent and protein environments; thus, the present study reports on a novel photochemistry mediated by a microbial rhodopsin, leading from the all-trans to 7-cis form selectively.

Proton-transporting heliorhodopsins from marine giant viruses

Rhodopsins convert light into signals and energy in animals and microbes. Heliorhodopsins (HeRs), a recently discovered new rhodopsin family, are widely present in archaea, bacteria, unicellular eukaryotes, and giant viruses, but their function remains unknown. Here, we report that a viral HeR from Emiliania huxleyi virus 202 (V2HeR3) is a light-activated proton transporter. V2HeR3 absorbs blue-green light, and the active intermediate contains the deprotonated retinal Schiff base. Site-directed mutagenesis study revealed that E191 in TM6 constitutes the gate together with the retinal Schiff base. E205 and E215 form a PAG of the Schiff base, and mutations at these positions converted the protein into an outward proton pump. Three environmental viral HeRs from the same group as well as a more distantly related HeR exhibited similar proton-transport activity, indicating that HeR functions might be diverse similarly to type-1 microbial rhodopsins. Some strains of E. huxleyi contain one HeR that is related to the viral HeRs, while its viruses EhV-201 and EhV-202 contain two and three HeRs, respectively. Except for V2HeR3 from EhV-202, none of these proteins exhibit ion transport activity. Thus, when expressed in the E. huxleyi cell membranes, only V2HeR3 has the potential to depolarize the host cells by light, possibly to overcome the host defense mechanisms or to prevent superinfection. The neuronal activity generated by V2HeR3 suggests that it can potentially be used as an optogenetic tool, similarly to type-1 microbial rhodopsins.

Molecule-to-Material-to-Bio Nanoarchitectonics with Biomedical Fullerene Nanoparticles

Nanoarchitectonics integrates nanotechnology with various other fields, with the goal of creating functional material systems from nanoscale units such as atoms, molecules, and nanomaterials. The concept bears strong similarities to the processes and functions seen in biological systems. Therefore, it is natural for materials designed through nanoarchitectonics to truly shine in bio-related applications. In this review, we present an overview of recent work exemplifying how nanoarchitectonics relates to biology and how it is being applied in biomedical research. First, we present nanoscale interactions being studied in basic biology and how they parallel nanoarchitectonics concepts. Then, we overview the state-of-the-art in biomedical applications pursuant to the nanoarchitectonics framework. On this basis, we take a deep dive into a particular building-block material frequently seen in nanoarchitectonics approaches: fullerene. We take a closer look at recent research on fullerene nanoparticles, paying special attention to biomedical applications in biosensing, gene delivery, and radical scavenging. With these subjects, we aim to illustrate the power of nanomaterials and biomimetic nanoarchitectonics when applied to bio-related applications, and we offer some considerations for future perspectives.

Biomimetic and Biological Nanoarchitectonics

A post-nanotechnology concept has been assigned to an emerging concept, nanoarchitectonics. Nanoarchitectonics aims to establish a discipline in which functional materials are fabricated from nano-scale components such as atoms, molecules, and nanomaterials using various techniques. Nanoarchitectonics opens ways to form a more unified paradigm by integrating nanotechnology with organic chemistry, supramolecular chemistry, material chemistry, microfabrication technology, and biotechnology. On the other hand, biological systems consist of rational organization of constituent molecules. Their structures have highly asymmetric and hierarchical features that allow for chained functional coordination, signal amplification, and vector-like energy and signal flow. The process of nanoarchitectonics is based on the premise of combining several different processes, which makes it easier to obtain a hierarchical structure. Therefore, nanoarchitectonics is a more suitable methodology for creating highly functional systems based on structural asymmetry and hierarchy like biosystems. The creation of functional materials by nanoarchitectonics is somewhat similar to the creation of functional systems in biological systems. It can be said that the goal of nanoarchitectonics is to create highly functional systems similar to those found in biological systems. This review article summarizes the synthesis of biomimetic and biological molecules and their functional structure formation from various viewpoints, from the molecular level to the cellular level. Several recent examples are arranged and categorized to illustrate such a trend with sections of (i) synthetic nanoarchitectonics for bio-related units, (ii) self-assembly nanoarchitectonics with bio-related units, (iii) nanoarchitectonics with nucleic acids, (iv) nanoarchitectonics with peptides, (v) nanoarchitectonics with proteins, and (vi) bio-related nanoarchitectonics in conjugation with materials.

Identification of metal-sensitive structural changes in the Ca2+-binding photocomplex from Thermochromatium tepidum by isotope-edited vibrational spectroscopy

Calcium ions play a dual role in expanding the spectral diversity and structural stability of photocomplexes from several Ca2+-requiring purple sulfur phototrophic bacteria. Here, metal-sensitive structural changes in the isotopically labeled light-harvesting 1 reaction center (LH1-RC) complexes from the thermophilic purple sulfur bacterium Thermochromatium ( Tch.) tepidum were investigated by perfusion-induced attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy. The ATR-FTIR difference spectra induced by exchanges between native Ca2+ and exogenous Ba2+ exhibited interconvertible structural and/or conformational changes in the metal binding sites at the LH1 C-terminal region. Most of the characteristic Ba2+/Ca2+ difference bands were detected even when only Ca ions were removed from the LH1-RC complexes, strongly indicating the pivotal roles of Ca2+ in maintaining the LH1-RC structure of Tch. tepidum. Upon 15N-, 13C- or 2H-labeling, the LH1-RC complexes exhibited characteristic 15N/14N-, 13C/12C-, or 2H/1H-isotopic shifts for the Ba2+/Ca2+ difference bands. Some of the 15N/14N or 13C/12C bands were also sensitive to further 2H-labelings. Given the band frequencies and their isotopic shifts along with the structural information of the Tch. tepidum LH1-RC complexes, metal-sensitive FTIR bands were tentatively identified to the vibrational modes of the polypeptide main chains and side chains comprising the metal binding sites. Furthermore, important new IR marker bands highly sensitive to the LH1 BChl a conformation in the Ca2+-bound states were revealed based on both ATR-FTIR and near-infrared Raman analyses. The present approach provides valuable insights concerning the dynamic equilibrium between the Ca2+- and Ba2+-bound states statically resolved by x-ray crystallography.

Structural characterization of proton-pumping rhodopsin lacking a cytoplasmic proton donor residue by X-ray crystallography

DTG/DTS rhodopsin, which was named based on a three-residue motif (DTG or DTS) that is important for its function, is a light-driven proton-pumping microbial rhodopsin using a retinal chromophore. In contrast to other light-driven ion-pumping rhodopsins, DTG/DTS rhodopsin does not have a cytoplasmic proton donor residue, such as Asp, Glu, or Lys. Because of the lack of cytoplasmic proton donor residue, proton directly binds to the retinal chromophore from the cytoplasmic solvent. However, mutational experiments that showed the complicated effects of mutations were not able to clarify the roles played by each residue, and the detail of proton uptake pathway is unclear because of the lack of structural information. To understand the proton transport mechanism of DTG/DTS rhodopsin, here we report the three-dimensional structure of one of the DTG/DTS rhodopsins, PspR from Pseudomonas putida, by X-ray crystallography. We show that the structure of the cytoplasmic side of the protein is significantly different from that of bacteriorhodopsin, the best-characterized proton-pumping rhodopsin, and large cytoplasmic cavities were observed. We propose that these hydrophilic cytoplasmic cavities enable direct proton uptake from the cytoplasmic solvent without the need for a specialized cytoplasmic donor residue. The introduction of carboxylic residues homologous to the cytoplasmic donors in other proton-pumping rhodopsins resulted in higher pumping activity with less pH dependence, suggesting that DTG/DTS rhodopsins are advantageous for producing energy and avoiding intracellular alkalization in soil and plant-associated bacteria.

Antibody‐invertase Cross‐linkage Nanoparticles: A New Signal Tag for Point‐of‐Care Immunoassay of Alpha‐fetoprotein for Hepatocellular Carcinoma with Personal Glucometer

Methods based on immunoassays have been developed for cancer biomarker alpha‐fetoprotein (AFP), but most involve complicated or stripping procedures and are unfavourable for routine use. Herein we report the proof‐of‐concept of simple and point‐of‐care (POC) immunoassay for AFP in hepatocellular carcinoma on a portable personal glucometer (PGM) by using antibody‐invertase cross‐linkage nanoparticles as the signal‐generation tags. Antibody‐invertase cross‐linkage nano tags were synthesized by using reverse micellar method with glutaraldehyde. The POC immunoassay was carried out on monoclonal anti‐AFP capture antibody‐coated microplate with a sandwich‐type reaction mode. Introduction of invertase nano labels accompanying target AFP could hydrolyse sucrose into glucose and fructose. The produced glucose molecules could be determined on a portable personal glucometer. Relative to unimolecular invertase labelling, improved analytical features were acquired with antibody‐invertase nano labelling. With the nano labels, PGM‐based immunoassay exhibited good electrochemical responses for the detection of AFP, and allowed detection of AFP at a concentration as low as 5.4 pg mL−1. Moreover, a good repeatability and intermediate precision could be found down to 12.68 %. Good well‐matched results were obtained for analysis of human serum specimens between POC immunoassay and commercial human AFP ELISA kit.

Retinal Vibrations in Bacteriorhodopsin are Mechanically Harmonic but Electrically Anharmonic: Evidence From Overtone and Combination Bands

Fundamental vibrations of the chromophore in the membrane protein bacteriorhodopsin (BR), a protonated Schiff base retinal, have been studied for decades, both by resonance Raman and by infrared (IR) difference spectroscopy. Such studies started comparing vibrational changes between the initial BR state (all-trans retinal) and the K intermediate (13-cis retinal), being later extended to the rest of intermediates. They contributed to our understanding of the proton-pumping mechanism of BR by exploiting the sensitivity of fundamental vibrational transitions of the retinal to its conformation. Here, we report on new bands in the 2,500 to 1,800 cm⁻¹ region of the K-BR difference FT-IR spectrum. We show that the bands between 2,500 and 2,300 cm⁻¹ originate from overtone and combination transitions from C-C stretches of the retinal. We assigned bands below 2,300 cm⁻¹ to the combination of retinal C-C stretches with methyl rocks and with hydrogen-out-of-plane vibrations. Remarkably, experimental C-C overtone bands appeared at roughly twice the wavenumber of their fundamentals, with anharmonic mechanical constants ≤3.5 cm⁻¹, and in some cases of ∼1 cm⁻¹. Comparison of combination and fundamental bands indicates that most of the mechanical coupling constants are also very small. Despite the mechanical quasi-harmonicity of the C-C stretches, the area of their overtone bands was only ∼50 to ∼100 times smaller than of their fundamental bands. We concluded that electrical anharmonicity, the second mechanism giving intensity to overtone bands, must be particularly high for the retinal C-C stretches. We corroborated the assignments of negative bands in the K-BR difference FT-IR spectrum by ab initio anharmonic vibrational calculations of all-trans retinal in BR using a quantum-mechanics/molecular mechanics approach, reproducing reasonably well the small experimental anharmonic and coupling mechanical constants. Yet, and in spite accounting for both mechanical and electrical anharmonicities, the intensity of overtone C-C transitions was underestimated by a factor of 4–20, indicating room for improvement in state-of-the-art anharmonic vibrational calculations. The relatively intense overtone and combination bands of the retinal might open the possibility to detect retinal conformational changes too subtle to significantly affect fundamental transitions but leaving a footprint in overtone and combination transitions.

FTIR and Raman Spectroscopy of Rhodopsins

Vibrational spectroscopy such as FTIR and Raman spectroscopy is a powerful, sensitive, and informative method for studying protein structural changes in rhodopsins during their functions. The usefulness has been historically proven for the study of bacteriorhodopsin and bovine rhodopsin before their structural determination of rhodopsins. We now have atomic structures of many animal and microbial rhodopsins, and it is now important to know the structural dynamics of rhodopsins for function. FTIR and Raman spectroscopy provides useful information for this aim. In this chapter, we introduce the methods of FTIR and resonance Raman spectroscopy applied to rhodopsins. These vibrational methods offer deeper understanding on the mechanism how rhodopsins change their structures for function.

Proton transfer pathway in anion channelrhodopsin-1

Anion channelrhodopsin from Guillardia theta (GtACR1) has Asp234 (3.2 Å) and Glu68 (5.3 Å) near the protonated Schiff base. Here, we investigate mutant GtACR1s (e.g., E68Q/D234N) expressed in HEK293 cells. The influence of the acidic residues on the absorption wavelengths was also analyzed using a quantum mechanical/molecular mechanical approach. The calculated protonation pattern indicates that Asp234 is deprotonated and Glu68 is protonated in the original crystal structures. The D234E mutation and the E68Q/D234N mutation shorten and lengthen the measured and calculated absorption wavelengths, respectively, which suggests that Asp234 is deprotonated in the wild-type GtACR1. Molecular dynamics simulations show that upon mutation of deprotonated Asp234 to asparagine, deprotonated Glu68 reorients toward the Schiff base and the calculated absorption wavelength remains unchanged. The formation of the proton transfer pathway via Asp234 toward Glu68 and the disconnection of the anion conducting channel are likely a basis of the gating mechanism.

Strongly Hydrogen-Bonded Schiff Base and Adjoining Polyene Twisting in the Retinal Chromophore of Schizorhodopsins

A transmembrane proton gradient is generated and maintained by proton pumps in a cell. Metagenomics studies have recently identified a new category of rhodopsin intermediates between type-1 rhodopsins and heliorhodopsins, named schizorhodopsins (SzRs). SzRs are light-driven inward proton pumps. Comprehensive resonance Raman measurements were conducted to characterize the structure of the retinal chromophore in the unphotolyzed state of four SzRs. The spectra of all four SzRs show that the retinal chromophore is in the all-trans and 15-anti configuration and that the Schiff base is protonated. The polyene chain is planar in the center of the retinal chromophore and is twisted in the vicinity of the protonated Schiff base. The protonated Schiff base in the SzRs forms a stronger hydrogen bond than that in outward proton-pumping rhodopsins. We determined that the hydrogen-bonding partner of the protonated Schiff base is not a water molecule but an amino acid residue, presumably an Asp residue in helix G. The present observations provide valuable insights into the inward proton-pumping mechanism of SzRs.

Nanoarchitectonics for Analytical Science at Interfaces and with Supramolecular Nanostructures

For materials development with high-level structural regulations, the emerging concept of nanoarchitectonics has been proposed. Analytical sciences, including sensing/detection, sensors, and related device construction, are active targets of the nanoarchitectonics approach. This review article focuses on the two features of interface and nanostructures are especially focused to discuss nanoarchitectonics for analytical science. Especially, two selected topics, (i) analyses on molecular sensing at interfaces and (ii) sensors using self-assembled supramolecular nanostructures, are exemplified in this review article. In addition to recent general examples, specific molecular recognition at the air-water interface and fabrication of sensing materials upon self-assembly of fullerene units are discussed. Descriptions of these examples indicate that nanoarchitectonics and analytical science share common benefits, and therefore, developments in both research fields should lead to synergies.

Excited State Resonance Raman of Flavin Mononucleotide: Comparison of Theory and Experiment

Blue light absorbing flavoproteins play important roles in a variety of photobiological processes. Consequently, there have been numerous investigations of their excited state structure and dynamics, in particular by time-resolved vibrational spectroscopy. The isoalloxazine chromophore of the flavoprotein cofactors has been studied in detail by time-resolved Raman, lending it a benchmark status for mode assignments in excited electronic states of large molecules. However, detailed comparisons of calculated and measured spectra have proven challenging, as there are many more modes calculated than are observed, and the role of resonance enhancement is difficult to characterize in excited electronic states. Here we employ a recently developed approach due to Elles and co-workers ( J. Phys. Chem. A 2018, 122, 8308-8319) for the calculation of resonance-enhanced Raman spectra of excited states and apply it to the lowest singlet and triplet excited states of the isoalloxazine chromophore. There is generally good agreement between calculated and observed enhancements, which allows assignment of vibrational bands of the flavoprotein cofactors to be refined. However, some prominently enhanced bands are found to be absent from the calculations, suggesting the need for further development of the theory.

Inverse Hydrogen-Bonding Change Between the Protonated Retinal Schiff Base and Water Molecules upon Photoisomerization in Heliorhodopsin 48C12

Heliorhodopsin (HeR) is a new class of the rhodopsin family discovered in 2018 through functional metagenomic analysis (named 48C12). Similar to typical microbial rhodopsins, HeR possesses seven transmembrane (TM) α-helices and an all-trans-retinal covalently bonded to the lysine residue on TM7 via a protonated Schiff base. Remarkably, the HeR membrane topology is inverted compared with that of typical microbial rhodopsins. The X-ray crystal structure of HeR 48C12 was elucidated after the first report on a HeR variant from Thermoplasmatales archaeon SG8-52-1, which revealed the water-mediated hydrogen-bonding network connected to the Schiff base region in the cytoplasmic side. Herein, low-temperature light-induced FTIR spectroscopic analyses of HeR 48C12 and ¹⁵N isotopically labeled proteins were used to elucidate the structural changes during retinal photoisomerization. N-D stretching vibrations of the protonated retinal Schiff base (PRSB) at 2286 and 2302 cm^-1 in the dark state, and 2239 and 2252 cm^-1 in the K intermediate were observed. The frequency changes indicated that the hydrogen bond of PRSB strengthens upon photoisomerization in HeR. Moreover, O-D stretching vibration frequencies of the internal water molecules indicate that the hydrogen-bonding strength decreases concomitantly. Therefore, the PRSB hydrogen bond responds to photoisomerization in an opposite way to the hydrogen-bonding network involving water molecules. No frequency changes of the indole N-H or N-D stretching vibrations of tryptophan residues were observed upon photoisomerization, suggesting that all tryptophan residues in the HeR 48C12 maintained the hydrogen-bonding strengths in the K intermediate. These results provide insights into the molecular mechanism of the energy storage and propagation upon retinal photoisomerization in HeR.

Nanoarchitectonics on living cells

In this review article, the recent examples of nanoarchitectonics on living cells are briefly explained. Not limited to conventional polymers, functional polymers, biomaterials, nanotubes, nanoparticles (conventional and magnetic ones), various inorganic substances, metal-organic frameworks (MOFs), and other advanced materials have been used as components for nanoarchitectonic decorations for living cells. Despite these artificial processes, the cells can remain active or remain in hibernation without being killed. In most cases, basic functions of the cells are preserved and their resistances against external assaults are much enhanced. The possibilities of nanoarchitectonics on living cells would be high, equal to functional modifications with conventional materials. Living cells can be regarded as highly functionalized objects and have indispensable contributions to future materials nanoarchitectonics.

Role of Thr82 for the unique photochemistry of TAT rhodopsin

Marine bacterial TAT rhodopsin possesses the pKa of the retinal Schiff base, the chromophore, at neutral pH, and photoexcitation of the visible protonated state forms the isomerized 13-cis state, but reverts to the original state within 10^–5 sec. To understand the origin of these unique molecular properties of TAT rhodopsin, we mutated Thr82 into Asp, because many microbial rhodopsins contain Asp at the corresponding position as the Schiff base counterion. A pH titration study revealed that the pKa of the Schiff base increased considerably in T82D (>10.5), and that the pKa of the counterion, which is likely to be D82, is 8.1. It was thus concluded that T82 is the origin of the neutral pKa of the Schiff base in TAT rhodopsin. The photocycle of T82D TAT rhodopsin exhibited strong pH dependence. When pH is lower than the pKa of the counterion (pH <8.1), formation of the primary K intermediate was observed by low-temperature UV-visible spectroscopy, but flash photolysis failed to monitor photointermdiates at >10^–5 sec. The results were identical for the wild-type TAT rhodopsin. In contrast, when pH was higher than the pKa of the counterion, we observed the formation of the M intermediate, which decayed with the time constants of 3.75 ms and 12.2 sec. It is likely that the protonation state of D82 dramatically switches the photoreaction dynamics of T82D, whose duration lies between <10^–5 sec and >10 sec. It was thus concluded that T82 is one of the determinants of the unique photochemistry of TAT rhodopsin.

Vibrational analysis of acetylcholine binding to the M2 receptor

The M₂ muscarinic acetylcholine receptor (M₂R) is a prototypical G protein-coupled receptor (GPCR) that responds to acetylcholine (ACh) and mediates various cellular responses in the nervous system. We recently established Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopy for ligand binding to M₂R reconstituted in lipid membranes, paving the way to understand the mechanism in atomic detail. However, the obtained difference FTIR spectra upon ligand binding contained ligand, protein, lipid, and water signals, so a vibrational assignment was needed for a thorough understanding. In the present study, we compared difference FTIR spectra between unlabeled and 2-¹³C labeled ACh, and assigned the bands at 1741 and 1246 cm⁻¹ as the C Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> O and C–O stretches of ACh, respectively. The CO stretch of ACh in M₂R is close to that in aqueous solution (1736 cm⁻¹), and much lower in frequency than the free CO stretch (1778–1794 cm⁻¹), indicating a strong hydrogen bond, which probably formed with N404^6.52. We propose that a water molecule bridges ACh and N404^6.52. The other ACh terminal is positively charged, and it interacts with negatively charged D103^3.32. The present study revealed that D103^3.32 is deprotonated (negatively charged) in both ACh-bound and free states, a suggested mechanism to stabilize the negative charge of D103^3.32 in the free M₂R.

We recently reported difference FTIR spectra upon binding of Ach to M₂R.

Unique Retinal Binding Pocket of Primate Blue-Sensitive Visual Pigment

The visual pigments of humans contain 11-cis retinal as the chromophore of light perception, and its photoisomerization to the all-trans form initiates visual excitation in our eyes. It is well-known that three isomeric states of retinal (11-cis, all-trans, and 9-cis) are in photoequilibrium at very low temperatures such as 77 K. Here we report the lack of formation of the 9-cis form in monkey blue (MB) at 77 K, as revealed by light-induced difference Fourier transform infrared spectroscopy. This indicates that the chromophore binding pocket of MB does not accommodate the 9-cis form, even though it accommodates the all-trans form by twisting the chromophore. Mutation of the blue-specific tyrosine at position 265 to tryptophan, which is highly conserved in other animal rhodopsins, led to formation of the 9-cis form in MB, suggesting that Y265 is one of the determinants of the unique photochemistry in blue pigments. We also found that 9-cis retinal does not bind to MB opsin, implying that the chromophore binding pocket does not accommodate the 9-cis form at physiological temperature. The unique property of MB is discussed on the basis of the results presented here.