Factors that differentiate the H-bond strengths of water near the Schiff bases in bacteriorhodopsin and Anabaena sensory rhodopsin

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.

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.

Mechanism of Absorption Wavelength Shift of Bacteriorhodopsin During Photocycle

Bacteriorhodopsin, a light-driven proton pump, alters the absorption wavelengths in the range of 410-617 nm during the photocycle. Here, we report the absorption wavelengths, calculated using 12 bacteriorhodopsin crystal structures (including the BR, BR_13-cis, J, K₀, K_E, K_L, L, M, N, and O state structures) and a combined quantum mechanical/molecular mechanical/polarizable continuum model (QM/MM/PCM) approach. The QM/MM/PCM calculations reproduced the experimentally measured absorption wavelengths with a standard deviation of 4 nm. The shifts in the absorption wavelengths can be explained mainly by the following four factors: (i) retinal Schiff base deformation/twist induced by the protein environment, leading to a decrease in the electrostatic interaction between the protein environment and the retinal Schiff base; (ii) changes in the protonation state of the protein environment, directly altering the electrostatic interaction between the protein environment and the retinal Schiff base; (iii) changes in the protonation state; or (iv) isomerization of the retinal Schiff base, where the absorption wavelengths of the isomers originally differ.

Correlation between C═O Stretching Vibrational Frequency and pKa Shift of Carboxylic Acids

Identifying the pK_a values of aspartic acid (Asp) and glutamic acid (Glu) in active sites is essential for understanding enzyme reaction mechanisms. In this study, we investigated the correlation between the C=O stretching vibrational frequency (ν_C=O) of protonated carboxylic acids and the pK_a values using density functional theory calculations. In unsaturated carboxylic acids (e.g., benzoic acid analogues), ν_C=O decreases as the pK_a increases (the negative correlation), whereas in saturated carboxylic acids (e.g., acetic acid analogues, Asp, and Glu), ν_C=O increases as the pK_a increases (the positive correlation) as long as the structure of the H-bond network around the acid is identical. The negative/positive correlation between ν_C=O and pK_a can be rationalized by the presence or absence of the C=C double bond. The pK_a shift was estimated from the ν_C=O shift of Asp and Glu in proteins on the basis of the negative correlation derived from benzoic acids. The previous estimations should be revisited by using the positive correlation derived in this study, as demonstrated by quantum mechanical/molecular mechanical calculations of ν_C=O and electrostatic calculations of pK_a on a key Asp85 in the proton-transfer pathway of bacteriorhodopsin.

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.

Discovery of a new light-driven Li+/Na+-pumping rhodopsin with DTG motif

Microbial pumping rhodopsin is a seven-transmembrane retinal binding protein, which is light-driven ion pump with a functional key motif. Ion-pumping with the key motif and charged amino acids in the rhodopsin is biochemically important. The rhodopsins with DTG motif have been discovered in various eubacteria, and they function as H⁺ pump. Especially, the DTG motif rhodopsins transported H⁺ despite the replacement of a proton donor by Gly. We investigated Methylobacterium populi rhodopsin (MpR) in one of the DTG motif rhodopsin clades. To determine which ions the MpR transport, we tested with various monovalent ion solutions and determined that MpR transports Li⁺/Na⁺. By replacing the three negatively charged residues residues which are located in helix B, Glu32, Glu33, and Asp35, we concluded that the residues play a critical role in the transport of Li⁺/Na⁺. The MpR E33Q transported H⁺ in place of Li⁺/Na⁺, suggesting that Glu33 is a Li⁺/Na⁺ binding site on the cytoplasmic side. Gly93 in MpR was replaced by Asp to convert from the Li⁺/Na⁺ pump to the H⁺ pump, resulting in MpR G93D transporting H⁺. Dissociation constant (K_d) values of Na⁺ for MpR WT and E33Q were determined to be 4.0 and 72.5 mM, respectively. These results indicated the mechanism by which MpR E33Q transports H⁺. Up to now, various ion-pumping rhodopsins have been discovered, and Li⁺/Na⁺-pumping rhodopsins were only found in the NDQ motif in NaR. Here, we report a new light-driven Na⁺ pump MpR and have determined the important residues required for Li⁺/Na⁺-pumping different from previously known NaR.

Mechanism of absorption wavelength shifts in anion channelrhodopsin-1 mutants

Using a quantum mechanical/molecular mechanical approach, we show the mechanisms of how the protein environment of Guillardia theta anion channelrhodopsin-1 (GtACR1) can shift the absorption wavelength. The calculated absorption wavelengths for GtACR1 mutants, M105A, C133A, and C237A are in agreement with experimentally measured wavelengths. Among 192 mutant structures investigated, mutations at Thr101, Cys133, Pro208, and Cys237 are likely to increase the absorption wavelength. In particular, T101A GtACR1 was expressed in HEK293T cells. The measured absorption wavelength is 10 nm higher than that of wild type, consistent with the calculated wavelength. (i) Removal of a polar residue from the Schiff base moiety, (ii) addition of a polar or acidic residue to the β-ionone ring moiety, and (iii) addition of a bulky residue to increase the planarity of the β-ionone and Schiff base moieties are the basis of increasing the absorption wavelength.

Insights into the Protein Functions and Absorption Wavelengths of Microbial Rhodopsins

Using a quantum mechanical/molecular mechanical approach, the absorption wavelength of the retinal Schiff base was calculated based on 13 microbial rhodopsin crystal structures. The results showed that the protein electrostatic environment decreases the absorption wavelength significantly in the cation-conducting rhodopsin but only slightly in the sensory rhodopsin. Among the microbial rhodopsins with different functions, the differences in the absorption wavelengths are caused by differences in the arrangement of the charged residues at the retinal Schiff base binding moiety, namely, one or two counterions at the three common positions. Among the microbial rhodopsins with similar functions, the differences in the polar residues at the retinal Schiff base binding site are responsible for the differences in the absorption wavelengths. Counterions contribute to an absorption wavelength shift of 50-120 nm, whereas polar groups contribute to a shift of up to ∼10 nm. It seems likely that protein function is directly associated with the absorption wavelength in microbial rhodopsins.

Vectorial Proton Transport Mechanism of RxR, a Phylogenetically Distinct and Thermally Stable Microbial Rhodopsin

Rubrobacter xylanophilus rhodopsin (RxR) is a phylogenetically distinct and thermally stable seven-transmembrane protein that functions as a light-driven proton (H⁺) pump with the chromophore retinal. To characterize its vectorial proton transport mechanism, mutational and theoretical investigations were performed for carboxylates in the transmembrane region of RxR and the sequential proton transport steps were revealed as follows: (i) a proton of the retinylidene Schiff base (Lys209) is transferred to the counterion Asp74 upon formation of the blue-shifted M-intermediate in collaboration with Asp205, and simultaneously, a respective proton is released from the proton releasing group (Glu187/Glu197) to the extracellular side, (ii) a proton of Asp85 is transferred to the Schiff base during M-decay, (iii) a proton is taken up from the intracellular side to Asp85 during decay of the red-shifted O-intermediate. This ion transport mechanism of RxR provides valuable information to understand other ion transporters since carboxylates are generally essential for their functions.

X-ray structure analysis of bacteriorhodopsin at 1.3 Å resolution

Bacteriorhodopsin (bR) of Halobacterium salinarum is a membrane protein that acts as a light-driven proton pump. bR and its homologues have recently been utilized in optogenetics and other applications. Although the structures of those have been reported so far, the resolutions are not sufficient for elucidation of the intrinsic structural features critical to the color tuning and ion pumping properties. Here we report the accurate crystallographic analysis of bR in the ground state. The influence of X-rays was suppressed by collecting the data under a low irradiation dose at 15 K. Consequently, individual atoms could be separately observed in the electron density map at better than 1.3 Å resolution. Residues from Thr5 to Ala233 were continuously constructed in the model. The twist of the retinal polyene was determined to be different from those in the previous models. Two conformations were observed for the proton release region. We discuss the meaning of these fine structural features.

Applications of deuterium oxide in human health

The main aim goal of this review was to gather information about recent publications related to deuterium oxide (D₂O), and its use as a scientific tool related to human health. Searches were made in electronic databases Pubmed, Scielo, Lilacs, Medline and Cochrane. Moreover, the following patent databases were consulted: EPO (Espacenet patent search), USPTO (United States Patent and Trademark Office) and Google Patents, which cover researches worldwide related to innovations using D₂O.

pH-Dependent absorption spectrum of a protein: a minimal electrostatic model of Anabaena sensory rhodopsin

A minimal electrostatic model is introduced which aims at reproducing and analyzing the visible-light absorption energy shift of a protein with pH.

A natural light-driven inward proton pump

Light-driven outward H+ pumps are widely distributed in nature, converting sunlight energy into proton motive force. Here we report the characterization of an oppositely directed H+ pump with a similar architecture to outward pumps. A deep-ocean marine bacterium, Parvularcula oceani, contains three rhodopsins, one of which functions as a light-driven inward H+ pump when expressed in Escherichia coli and mouse neural cells. Detailed mechanistic analyses of the purified proteins reveal that small differences in the interactions established at the active centre determine the direction of primary H+ transfer. Outward H+ pumps establish strong electrostatic interactions between the primary H+ donor and the extracellular acceptor. In the inward H+ pump these electrostatic interactions are weaker, inducing a more relaxed chromophore structure that leads to the long-distance transfer of H+ to the cytoplasmic side. These results demonstrate an elaborate molecular design to control the direction of H+ transfers in proteins.

Proton transfer reactions and hydrogen-bond networks in protein environments

In protein environments, proton transfer reactions occur along polar or charged residues and isolated water molecules. These species consist of H-bond networks that serve as proton transfer pathways; therefore, thorough understanding of H-bond energetics is essential when investigating proton transfer reactions in protein environments. When the pKa values (or proton affinity) of the H-bond donor and acceptor moieties are equal, significantly short, symmetric H-bonds can be formed between the two, and proton transfer reactions can occur in an efficient manner. However, such short, symmetric H-bonds are not necessarily stable when they are situated near the protein bulk surface, because the condition of matching pKa values is opposite to that required for the formation of strong salt bridges, which play a key role in protein-protein interactions. To satisfy the pKa matching condition and allow for proton transfer reactions, proteins often adjust the pKa via electron transfer reactions or H-bond pattern changes. In particular, when a symmetric H-bond is formed near the protein bulk surface as a result of one of these phenomena, its instability often results in breakage, leading to large changes in protein conformation.

The role of protein-bound water molecules in microbial rhodopsins

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.

Eubacterial rhodopsins - unique photosensors and diverse ion pumps

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.

Formation of an unusually short hydrogen bond in photoactive yellow protein

The photoactive chromophore of photoactive yellow protein (PYP) is p-coumaric acid (pCA). In the ground state, the pCA chromophore exists as a phenolate anion, which is H-bonded by protonated Glu46 (O(Glu46)-O(pCA)=~2.6Å) and protonated Tyr42. On the other hand, the O(Glu46)-O(pCA) H-bond was unusually short (O(Glu46)-O(pCA)=2.47Å) in the intermediate pR(CW) state observed in time-resolved Laue diffraction studies. To understand how the existence of the unusually short H-bond is energetically possible, we analyzed the H-bond energetics adopting a quantum mechanical/molecular mechanical (QM/MM) approach based on the atomic coordinates of the PYP crystal structures. In QM/MM calculations, the O(Glu46)-O(pCA) bond is 2.60Å in the ground state, where Tyr42 donates an H-bond to pCA. In contrast, when the hydroxyl group of Tyr42 is flipped away from pCA, the H-bond was significantly shortened to 2.49Å in the ground state. The same H-bond pattern reproduced the unusually short H-bond in the pR(CW) structure (O(Glu46)-O(pCA)=2.49Å). Intriguingly, the potential-energy profile resembles that of a single-well H-bond, suggesting that the pK(a) values of the donor (Glu46) and acceptor (pCA) moieties are nearly equal. The present results indicate that the "equal pK(a)" requirement for formation of single-well or low-barrier H-bond (LBHB) is satisfied only when Tyr42 does not donate an H-bond to pCA, and argue against the possibility that the O(Glu46)-O(pCA) bond is an LBHB in the ground state, where Tyr42 donates an H-bond to pCA.