Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy

Label-free vibrational imaging of different Aβ plaque types in Alzheimer's disease reveals sequential events in plaque development

The neuropathology of Alzheimer’s disease (AD) is characterized by hyperphosphorylated tau neurofibrillary tangles (NFTs) and amyloid-beta (Aβ) plaques. Aβ plaques are hypothesized to follow a development sequence starting with diffuse plaques, which evolve into more compact plaques and finally mature into the classic cored plaque type. A better molecular understanding of Aβ pathology is crucial, as the role of Aβ plaques in AD pathogenesis is under debate. Here, we studied the deposition and fibrillation of Aβ in different plaque types with label-free infrared and Raman imaging. Fourier-transform infrared (FTIR) and Raman imaging was performed on native snap-frozen brain tissue sections from AD cases and non-demented control cases. Subsequently, the scanned tissue was stained against Aβ and annotated for the different plaque types by an AD neuropathology expert. In total, 160 plaques (68 diffuse, 32 compact, and 60 classic cored plaques) were imaged with FTIR and the results of selected plaques were verified with Raman imaging. In diffuse plaques, we detect evidence of short antiparallel β-sheets, suggesting the presence of Aβ oligomers. Aβ fibrillation significantly increases alongside the proposed plaque development sequence. In classic cored plaques, we spatially resolve cores containing predominantly large parallel β-sheets, indicating Aβ fibrils. Combining label-free vibrational imaging and immunohistochemistry on brain tissue samples of AD and non-demented cases provides novel insight into the spatial distribution of the Aβ conformations in different plaque types. This way, we reconstruct the development process of Aβ plaques in human brain tissue, provide insight into Aβ fibrillation in the brain, and support the plaque development hypothesis.

A quantum cascade laser setup for studying irreversible photoreactions in H2O with nanosecond resolution and microlitre consumption

Time-resolved infrared spectroscopy on irreversible reactions requires in general an exchange of sample for thousands of acquisitions leading to high sample consumption. Here, we present a setup employing a modern quantum cascade laser (QCL) as a probe light source to record time-resolved difference spectra of irreversible photoreactions in H2O. The combination of the focused QCL with a pressure-tolerant flow cell and a micrometre stage orthogonal to the flow allowed us to drastically reduce the sample consumption. We investigated the irreversible photoreduction of the cofactor flavin mononucleotide (FMN) in H2O, which is a common reaction taking place in biological photoreceptors. A broad time range from 20 nanoseconds to 1 second was accessible, because the approach minimized any signal drift by the flow. Kinetics were recorded at 46 selected wavenumbers consuming 12 microlitres for a complete dataset. The tuning range of 1490-1740 cm-1 included relevant carbonyl vibrations and the region of strong water absorption at around 1650 cm-1. A continuous dataset in the spectral dimension was generated by applying a fit with a sum of Lorentzians. Subsequent global analysis allowed us to resolve reference spectra and kinetics of the photoreaction proceeding from the triplet excited state via the intermediate flavin anion radical to the product, the fully reduced state of FMN. Accordingly, the neutral radical state is not populated in the disproportionation. The approach strongly facilitates the spectroscopic access to irreversible reactions of flavin-containing photoreceptors and photoenzymes with high time resolution and small sample consumption.

pH-Dependent Water Clusters in Photoacid Solution: Real-Time Observation by ToF-SIMS at a Submicropore Confined Liquid-Vacuum Interface

Water clusters are ubiquitously formed in aqueous solutions by hydrogen bonding, which is quite sensitive to various environment factors such as temperature, pressure, electrolytes, and pH. Investigation of how the environment has impact on water structure is important for further understanding of the nature of water and the interactions between water and solutes. In this work, pH-dependent water structure changes were studied by monitoring the changes for the size distribution of protonated water clusters by in-situ liquid ToF-SIMS. In combination with a light illumination system, in-situ liquid ToF-SIMS was used to real-time measure the changes of a light-activated organic photoacid under different light illumination conditions. Thus, the proton transfer and pH-mediated water cluster changes were analyzed in real-time. It was found that higher concentration of free protons could lead to a strengthened local hydrogen bonding network as well as relatively larger protonated water clusters in both organic acid and inorganic acid. Besides, the accumulation of protons at the liquid-vacuum interface under light illumination was observed owing to the affinity of organic molecules to the low-pressure gas phase. The application of in-situ liquid ToF-SIMS analysis in combination with in-situ light illumination system opened up an avenue to real-time investigate light-activated reactions. Besides, the results regarding water structure changes in acidic solutions showed important insights in related atmospheric and physiochemical processes.

Structure-Based Functional Modification Study of a Cyanobacterial Chloride Pump for Transporting Multiple Anions

Understanding the structure and functional mechanisms of cyanobacterial halorhodopsin has become increasingly important, given the report that Synechocystis halorhodopsin (SyHR), a homolog of the cyanobacterial halorhodopsin from Mastigocladopsis repens (MrHR), can take up divalent ions, such as SO₄^2-, as well as chloride ions. Here, the crystal structure of MrHR, containing a unique "TSD" chloride ion conduction motif, was determined as a homotrimer at a resolution of 1.9 Å. The detailed structure of MrHR revealed a unique trimeric topology of the light-driven chloride pump, with peculiar coordination of two water molecules and hydrogen-mediated bonds near the TSD motif, as well as a short B-C loop. Structural and functional analyses of MrHR revealed key residues responsible for the anion selectivity of cyanobacterial halorhodopsin and the involvement of two chloride ion-binding sites in the ion conduction pathway. Alanine mutant of Asn63, Pro118, and Glu182 locating in the anion inlet induce multifunctional uptake of chloride, nitrate, and sulfate ions. Moreover, the structure of N63A/P118A provides information on how SyHR promotes divalent ion transport. Our findings significantly advance the structural understanding of microbial rhodopsins with different motifs. They also provide insight into the general structural framework underlying the molecular mechanisms of the cyanobacterial chloride pump containing SyHR, the only molecule known to transport both sulfate and chloride ions.

Photoisomerization of azobenzene units drives the photochemical reaction cycles of proteorhodopsin and bacteriorhodopsin analogues

In this study we substituted the retinal units in proteorhodopsin (PR) and bacteriorhodopsin (BR) with azo chromophores to investigate the mechanism of photoinduced proton pumping in rhodopsins and potentially develop new artificial molecular pumps. We used an indium tin oxide electrode to investigate the photoinduced proton transfer of the azo analogues of PR and BR. We also employed flash photolysis to determine the characteristic photocycles, comprising multiple transient intermediates, of the azo chromophore-bound PR and BR. Moreover, our studies of the photoinduced proton pumping functions of azo-proteoopsin and azo-bacterioopsin complexes revealed that they did not pump protons upon illumination, even though they underwent photoinduced proton transfer and the characteristic photocycle. Mutational analysis suggested that the proton pumping malfunction of the azo analogues of PR and BR resulted from the absence of proton transfer reactions through cytoplasmic channels, even though these reactions were evoked in extracellular channels. Based on our experimental findings, we propose herein a putative model of the proton transfer reaction mechanism for the azo analogues of PR and BR.

Deprotonation of Guanine Radical Cation G•+ Mediated by the Protonated Water Cluster

Proton transfer is regarded as a fundamental process in chemical reactions of DNA molecules and continues to be an active research theme due to the connection with charge transport and oxidation damage of DNA. For the guanine radical cation (G^•+) derived from one-electron oxidation, experiments suggest a facile proton transfer within the G^•+:C base pair, and a rapid deprotonation from N1 in free base or single-strand DNA. To address the deprotonation mechanism, we perform a thorough investigation on deprotonation of G^•+ in free G base by combining density functional theory (DFT) and laser flash photolysis spectroscopy. Experimentally, kinetics of deprotonation is monitored at temperatures varying from 280 to 298 K, from which the activation energy of 15.1 ± 1.5 kJ/mol is determined for the first time. Theoretically, four solvation models incorporating explicit waters and the polarized continuum model (PCM), i.e., 3H₂O-PCM, 4H₂O-PCM, 5H₂O-PCM, and 7H₂O-PCM models are used to calculate deprotonation potential energy profile, and the barriers of 5.5, 13.4, 14.4, and 13.7 kJ/mol are obtained, respectively. It is shown that at least four explicit waters are required for properly simulating the deprotonation reaction, where the participation of protonated water cluster plays key roles in facilitating the proton release from G^•+.

Protein Conformational Changes in Breast Cancer Sera Using Infrared Spectroscopic Analysis

Protein structural alterations, including misfolding and aggregation, are a hallmark of several diseases, including cancer. However, the possible clinical application of protein conformational analysis using infrared spectroscopy to detect cancer-associated structural changes in proteins has not been established yet. The present study investigates the applicability of Fourier transform infrared spectroscopy in distinguishing the sera of healthy individuals and breast cancer patients. The cancer-associated alterations in the protein structure were analyzed by fitting the amide I (1600-1700 cm-1) band of experimental curves, as well as by comparing the ratio of the absorbance values at the amide II and amide III bands, assigning those as the infrared spectral signatures. The snapshot of the breast cancer-associated alteration in circulating DNA and RNA was also evaluated by extending the spectral fitting protocol to the complex region of carbohydrates and nucleic acids, 1140-1000 cm-1. The sensitivity and specificity of these signatures, representing the ratio of the α-helix and β-pleated sheet in proteins, were both 90%. Likewise, the ratio of amides II and amide III (I1556/I1295) had a sensitivity and specificity of 100% and 80%, respectively. Thus, infrared spectroscopy can serve as a powerful tool to understand the protein structural alterations besides distinguishing breast cancer and healthy serum samples.

Peptide Side-COOH Groups Have Two Distinct Conformations under Biorelevant Conditions

The carboxyl (COOH) side chain groups of amino acids, such as aspartic acid, play an important role in biochemical processes, including enzymatic proton transport. In many theoretical studies, it was found that the (bio)chemical reactivity of the carboxyl group strongly depends on the conformation of this group. Interestingly, up to now there has been no experimental investigation of the geometry and the stability of different COOH conformers under biorelevant conditions. Here, we investigate the conformational isomerism of the side chain COOH group of N-acetyl aspartic acid amide using polarization-resolved two-dimensional infrared spectroscopy. We find that the carboxyl group shows two distinct near-planar conformers (syn and anti) when dissolved in water at room temperature. Both conformers are significantly populated in aqueous solution (75 ± 10% and 25 ± 10% for syn and anti, respectively). Molecular dynamics simulations show that the anti conformer interacts more strongly with water molecules than the syn conformer, explaining why this conformer is significantly present in aqueous solution.

Schizorhodopsins: A family of rhodopsins from Asgard archaea that function as light-driven inward H+ pumps

Schizorhodopsins (SzRs), a rhodopsin family first identified in Asgard archaea, the archaeal group closest to eukaryotes, are present at a phylogenetically intermediate position between typical microbial rhodopsins and heliorhodopsins. However, the biological function and molecular properties of SzRs have not been reported. Here, SzRs from Asgardarchaeota and from a yet unknown microorganism are expressed in Escherichia coli and mammalian cells, and ion transport assays and patch clamp analyses are used to demonstrate SzR as a novel type of light-driven inward H⁺ pump. The mutation of a cytoplasmic glutamate inhibited inward H⁺ transport, suggesting that it functions as a cytoplasmic H⁺ acceptor. The function, trimeric structure, and H⁺ transport mechanism of SzR are similar to that of xenorhodopsin (XeR), a light-driven inward H⁺ pumping microbial rhodopsins, implying that they evolved convergently. The inward H⁺ pump function of SzR provides new insight into the photobiological life cycle of the Asgardarchaeota.

Light-induced effects in glycine aqueous solution studied by Fourier transform infrared-emission spectroscopy and ultraviolet-visible spectroscopy

Although amino acids are insensitive to visible light, as is generally accepted, we show that particular light-matter interaction can break this obviousness. Using sensitive (FT-IR)-technique in a combination of a broadband visible light source, we registered emission spectra of glycine in the range 2500-500 cm^-1. Sensitivity of the infrared emission spectrum to the exciting power -induced changes in the glycine structure was demonstrated experimentally.Vibrational spectra of glycine displayed the prominent spectral features of CH₂, COO-, COOH, NH⁺₃ groups in the "fingerprint region". Simultaneous appearance of ionised COO- and unionised COOH forms of glycine in solution at neutral pH clearly indicated that visible light induces the partial protonation of COO- groups; if so, visible light irradiation should lead to occurrence of dimers or dimeric hydrogen - bonded structures. Spectroscopic and microscopic evidence of visible light-mediated formation of aggregates and nucleus in aqueous solution was presented.Electronic absorption/emission spectra of glycine in aqueous solution were primarily characterized in the near ultraviolet-visible region (240-600 nm). Negligible absorption near 270 nm was observed for a 1.0 M solution and dramatically enhanced with its "aging". Moreover, an extension of the absorption edge into the region above 400 nm could be seen. Due to the visible light irradiation, we observed modification of electronic structure or occurrence of additional species causing changes in absorption of glycine amino acid. For "aged" solution, it was shown that excitation spectra corresponding to the different emission wavelengths were entirely different, at that each excitation-spectral band had a characteristic emission band.Communicated by Ramaswamy H. Sarma.

Time-resolved mid-infrared dual-comb spectroscopy

Dual-comb spectroscopy can provide broad spectral bandwidth and high spectral resolution in a short acquisition time, enabling time-resolved measurements. Specifically, spectroscopy in the mid-infrared wavelength range is of particular interest, since most of the molecules have their strongest rotational-vibrational transitions in this "fingerprint" region. Here we report time-resolved mid-infrared dual-comb spectroscopy, covering ~300 nm bandwidth around 3.3 μm with 6 GHz spectral resolution and 20 μs temporal resolution. As a demonstration, we study a CH₄/He gas mixture in an electric discharge, while the discharge is modulated between dark and glow regimes. We simultaneously monitor the production of C₂H₆ and the vibrational excitation of CH₄ molecules, observing the dynamics of both processes. This approach to broadband, high-resolution, and time-resolved mid-infrared spectroscopy provides a new tool for monitoring the kinetics of fast chemical reactions, with potential applications in various fields such as physical chemistry and plasma/combustion analysis.

How [FeFe]-Hydrogenase Facilitates Bidirectional Proton Transfer

Hydrogenases are metalloenzymes that catalyze the conversion of protons and molecular hydrogen, H₂. [FeFe]-hydrogenases show particularly high rates of hydrogen turnover and have inspired numerous compounds for biomimetic H₂ production. Two decades of research on the active site cofactor of [FeFe]-hydrogenases have put forward multiple models of the catalytic proceedings. In comparison, our understanding of proton transfer is poor. Previously, residues were identified forming a hydrogen-bonding network between active site cofactor and bulk solvent; however, the exact mechanism of catalytic proton transfer remained inconclusive. Here, we employ in situ infrared difference spectroscopy on the [FeFe]-hydrogenase from Chlamydomonas reinhardtii evaluating dynamic changes in the hydrogen-bonding network upon photoreduction. While proton transfer appears to be impaired in the oxidized state (Hox), the presented data support continuous proton transfer in the reduced state (Hred). Our analysis allows for a direct, molecular unique assignment to individual amino acid residues. We found that transient protonation changes of glutamic acid residue E141 and, most notably, arginine R148 facilitate bidirectional proton transfer in [FeFe]-hydrogenases.

Evolution of aqSOA from the Air-Liquid Interfacial Photochemistry of Glyoxal and Hydroxyl Radicals

The effect of photochemical reaction time on glyoxal and hydrogen peroxide at the air-liquid (a-l) interface is investigated using in situ time-of-flight secondary ion mass spectrometry (ToF-SIMS) enabled by a system for analysis at the liquid vacuum interface (SALVI) microreactor. Carboxylic acids are formed mainly by reaction with hydroxyl radicals in the initial reactions. Oligomers, cluster ions, and water clusters formed due to longer photochemistry. Our results provide direct molecular evidence that water clusters are associated with proton transfer and the formation of oligomers and cluster ions at the a-l interface. The oligomer formation is facilitated by water cluster and cluster ion formation over time. Formation of higher m/z oligomers and cluster ions indicates the possibility of highly oxygenated organic components formation at the a-l interface. Furthermore, new chemical reaction pathways, such as surface organic cluster, hydration shell, and water cluster formation, are proposed based on SIMS spectral observations, and the existing understanding of glyoxal photochemistry is expanded. Our in situ findings verify that the a-l interfacial reactions are important pathways for aqueous secondary organic aerosol (aqSOA) formation.

Vibrational Relaxation Dynamics of the Core and Outer Part of Proton-Hydration Clusters

We study the ultrafast relaxation dynamics of hydrated proton clusters in acetonitrile using femtosecond mid-infrared pump-probe spectroscopy. We observe a strong dependence of transient absorption dynamics on the frequency of excitation. When we excite the OH vibrations with frequencies ≤3100 cm^–1, we observe an ultrafast energy relaxation that leads to the heating of the local environment of the proton. This response is assigned to the OH vibrations of the water molecules in the core of the hydrated proton cluster. When we excite with frequencies ≥3200 cm^–1, we observe a relatively slow vibrational relaxation with a T₁ time constant ranging from 0.22 ± 0.04 ps at ν_ex = 3200 cm^–1 to 0.37 ± 0.02 ps at ν_ex = 3520 cm^–1. We assign this response to water molecules in the outer part of the hydrated proton cluster.

Proton-Conducting Poly-γ-glutamic Acid Nanofiber Embedded Sulfonated Poly(ether sulfone) for Proton Exchange Membranes

Development and fabrication of novel proton exchange membranes (PEMs) with excellent performance have a great significance to the commercial application of PEM fuel cell. Inspired from the proton-conducting mechanism, γ-poly(glutamic acid) (γ-PGA) nanofibers (NFs) are first fabricated by solution blowing with the help of polylactic acid (PLA) and designed to form amino acid arrays as efficient proton channels for PEMs. The NFs with 50% γ-PGA exhibit a high proton conductivity of 0.572 S cm^-1 at 80 °C/50% relative humidity (RH), and 1.28 S cm^-1 at 40 °C/90% RH. Density functional theory is carried out to explain the mechanisms of proton hopping in γ-PGA, and the activation energy barriers from NH to COO^- for trans and cis conformations under anhydrous conditions are only 0.64 and 0.62 eV, respectively. Then the γ-PGA/PLA NFs are incorporated into sulfonated poly(ether sulfone) to prepare PEMs, which show remarkable performance compared with the Nafion membrane. The composite membrane with 30 wt % NFs exhibits the highest proton conductivity (0.261 S cm^-1 at 80 °C/100% RH). The direct methanol fuel cells with this membrane show a maximum power density (202.3 mW cm^-2) among all of the PEMs, showing great application potential in the field of PEMs.

Dynamics of proteins in solution

The dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.

Unifying photocycle model for light adaptation and temporal evolution of cation conductance in channelrhodopsin-2

Although channelrhodopsin (ChR) is a widely applied light-activated ion channel, important properties such as light adaptation, photocurrent inactivation, and alteration of the ion selectivity during continuous illumination are not well understood from a molecular perspective. Herein, we address these open questions using single-turnover electrophysiology, time-resolved step-scan FTIR, and Raman spectroscopy of fully dark-adapted ChR2. This yields a unifying parallel photocycle model integrating now all so far controversial discussed data. In dark-adapted ChR2, the protonated retinal Schiff base chromophore (RSBH⁺) adopts an all-trans,C=N-anti conformation only. Upon light activation, a branching reaction into either a 13-cis,C=N-anti or a 13-cis,C=N-syn retinal conformation occurs. The anti-cycle features sequential H⁺ and Na⁺ conductance in a late M-like state and an N-like open-channel state. In contrast, the 13-cis,C=N-syn isomer represents a second closed-channel state identical to the long-lived P₄₈₀ state, which has been previously assigned to a late intermediate in a single-photocycle model. Light excitation of P₄₈₀ induces a parallel syn-photocycle with an open-channel state of small conductance and high proton selectivity. E90 becomes deprotonated in P₄₈₀ and stays deprotonated in the C=N-syn cycle. Deprotonation of E90 and successive pore hydration are crucial for late proton conductance following light adaptation. Parallel anti- and syn-photocycles now explain inactivation and ion selectivity changes of ChR2 during continuous illumination, fostering the future rational design of optogenetic tools.

Amyloid blood biomarker detects Alzheimer's disease

Alzheimer's disease (AD) is currently incurable, but there is general agreement that a minimally invasive blood biomarker for screening in preclinical stages would be crucial for future therapy. Diagnostic tools for detection of AD are either invasive like cerebrospinal fluid (CSF) biomarkers or expensive such as positron emission tomography (PET) scanning. Here, we determine the secondary structure change of amyloid‐β (Aβ) in human blood. This change used as blood amyloid biomarker indicates prodromal AD and correlates with CSF AD biomarkers and amyloid PET imaging in the cross‐sectional BioFINDER cohort. In a further population‐based longitudinal cohort (ESTHER), the blood biomarker detected AD several years before clinical diagnosis in baseline samples with a positive likelihood ratio of 7.9; that is, those who were diagnosed with AD over the years were 7.9 times more likely to test positive. This assay may open avenues for blood screening of early AD stages as a funnel for further more invasive and expensive tests.

Intracluster proton transfer in protonated benzonitrile–(H2O)n≤6 nanoclusters: hydrated hydronium core for n ≥ 2

Infrared spectroscopy and density functional theory calculations of protonated benzonitrile–(H₂O)_n clusters reveal proton transfer to solvent for n ≥ 2 and the drastic effects of the aromatic dopant molecule on the network of H⁺(H₂O)_n+1.

Kinetic and experimental study on the reaction of 3,7-dinitro-1,3,5,7-tetraazabicyclo[3.3.1]nonane in nitric acid

A comprehensive experimental and kinetic study on the reaction of DPT in nitric acid has been performed. The overall yield of the stepwise method for preparing HMX was up to 82.7%, which is a landmark breakthrough for the preparation of HMX from DPT.

Water assisted biomimetic synergistic process and its application in water-jet rewritable paper

The colour of water-jet rewritable paper (WJRP) is difficult to be expanded via single hydrochromic molecule, especially black. Here, inspired by the amazing phenomenon of bound-water in cells enabling various biological transformations via facilitating synergistic inter-/intra-molecular proton transfer, we present a simple strategy toward WJRP based on binary systems containing less-sensitive acidochromic dyes and mild proton donors (or developers). With such a binary system containing commercial black dye as the colouring agent, benzyl 4-hydroxybenzoate as the developer, and biomimetic bound-water as proton-transferring medium, we successfully achieve the long-awaited black WJRP. Printed images on such WJRP have excellent performances and long retaining time (>1 month). In addition, the robustness, durability and reversibility of WJRP could be increased distinctly by using polyethylene terephthalate as substrate. This strategy significantly expands hydrochromic colours to entire visible range in an eco-friendly way, which opens an avenue of smart materials for practical needs and industrialization.

Water based inks used for water-jet rewritable paper (WJRP) are an environmental friendly alternative to conventional printing, but black colour in WJRP could not be realized so far. Here the authors demonstrate black as well as other colour WJRP based on binary systems containing less-sensitive acidochromic dyes and mild proton donors.

Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases

The unmatched catalytic turnover rates of [FeFe]-hydrogenases require an exceptionally efficient proton-transfer (PT) pathway to shuttle protons as substrates or products between bulk water and catalytic center. For clostridial [FeFe]-hydrogenase CpI such a pathway has been proposed and analyzed, but mainly on a theoretical basis. Here, eleven enzyme variants of two different [FeFe]-hydrogenases (CpI and HydA1) with substitutions in the presumptive PT-pathway are examined kinetically, spectroscopically, and crystallographically to provide solid experimental proof for its role in hydrogen-turnover. Targeting key residues of the PT-pathway by site directed mutagenesis significantly alters the pH-activity profile of these variants and in presence of H₂ their cofactor is trapped in an intermediate state indicative of precluded proton-transfer. Furthermore, crystal structures coherently explain the individual levels of residual activity, demonstrating e.g. how trapped H₂O molecules rescue the interrupted PT-pathway. These features provide conclusive evidence that the targeted positions are indeed vital for catalytic proton-transfer.

[FeFe]-hydrogenases catalyze H₂-evolution and -oxidation at very high turnover-rates. Here the authors provide experimental evidence for the proposed proton-transfer (PT) pathway by kinetically, spectroscopically, and crystallographically characterizing eleven mutants from the two [FeFe]-hydrogenases CpI and HydA1.

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.

Proton Transfer at the Interaction Interface of Graphene Oxide

Proton transfer plays a crucial role in a variety of biological phenomena. The transformation of nanomaterials in the environment and biology makes probing the potential proton transfer between nanomaterials and biomolecules a crucial issue, but it still remains a significant challenge. Here, we report proton transfer at the interface of graphene oxide (GO) by studying the GO-induced vibrational changes of interfacial water and carboxyl-terminated self-assembled monolayer (SAM) with surface-enhanced infrared absorption spectroscopy. In addition to simply acting as a macromolecular buffer in solution, the GO sheet behaves as a two-dimensional hydrogen-bonded exchangeable proton pool to dissociate and transfer protons at the interface with a suitable Brønsted base pair, which may bear a significant potential toxic origin for biological systems with proton-coupled reactions.

Dewetting transitions coupled to K-channel activation in cytochrome c oxidase

Cytochrome c oxidase (CcO) drives aerobic respiratory chains in all organisms by transducing the free energy from oxygen reduction into an electrochemical proton gradient across a biological membrane.

Cytochrome c oxidase (CcO) drives aerobic respiratory chains in all organisms by transducing the free energy from oxygen reduction into an electrochemical proton gradient across a biological membrane. CcO employs the so-called D- and K-channels for proton uptake, but the molecular mechanism for activation of the K-channel has remained elusive for decades. We show here by combining large-scale atomistic molecular simulations with graph-theoretical water network analysis, and hybrid quantum/classical (QM/MM) free energy calculations, that the K-channel is activated by formation of a reactive oxidized intermediate in the binuclear heme a₃/Cu_B active site. This state induces electrostatic, hydration, and conformational changes that lower the barrier for proton transfer along the K-channel by dewetting pathways that connect the D-channel with the active site. Our combined results reconcile previous experimental findings and indicate that water dynamics plays a decisive role in the proton pumping machinery in CcO.

Negative influence of pKa on activation energy barrier: A case study for double proton transfer reaction in inorganic acid dimers

Strength of acid can be determined by means of pK_a value. Attempts have been made to find a relationship between pK_a and activation energy barrier for a double proton transfer (DPT) reaction in inorganic acid dimers. Negative influence of pK_a is observed on activation energy (E_a ) which is contrary to the general convention of pK_a . Four different levels of theories with two different basis sets have been used to calculate the activation energy barrier of the DPT reaction in inorganic acid dimers. A model based on first and second order polynomial has been created to find the relationship between activation energy for DPT reaction. © 2018 Wiley Periodicals, Inc.

Perfect-absorption graphene metamaterials for surface-enhanced molecular fingerprint spectroscopy

Graphene plasmon with extremely strong light confinement and tunable resonance frequency represents a promising surface-enhanced infrared absorption (SEIRA) sensing platform. However, plasmonic absorption is relatively weak (approximately 1%-9%) in monolayer graphene nanostructures, which would limit its sensitivity. Here, we theoretically propose a hybrid plasmon-metamaterial structure that can realize perfect absorption in graphene with a low carrier mobility of 1000 cm² V^-1 s^-1. This structure combines a gold reflector and a gold grating to the graphene plasmon structures, which introduce interference effect and the lightning-rod effect, respectively, and largely enhance the coupling of light to graphene. The vibration signal of trace molecules can be enhanced up to 2000-fold at the hotspot of the perfect-absorption structure, enabling the SEIRA sensing to reach the molecular level. This hybrid metal-graphene structure provides a novel path to generate high sensitivity in nanoscale molecular recognition for numerous applications.

Nanomaterial-Based Plasmon-Enhanced Infrared Spectroscopy

Surface-enhanced infrared absorption (SEIRA) has attracted increasing attention due to the potential of infrared spectroscopy in applications such as molecular trace sensing of solids, polymers, and proteins, specifically fueled by recent substantial developments in infrared plasmonic materials and engineered nanostructures. Here, the significant progress achieved in the past decades is reviewed, along with the current state of the art of SEIRA. In particular, the plasmonic properties of a variety of nanomaterials are discussed (e.g., metals, semiconductors, and graphene) along with their use in the design of efficient SEIRA configurations. To conclude, perspectives on potential applications, including single-molecule detection and in vivo bioassays, are presented.

Induction of long-lived room temperature phosphorescence of carbon dots by water in hydrogen-bonded matrices

Phosphorescence shows great potential for application in bioimaging and ion detection because of its long-lived luminescence and high signal-to-noise ratio, but establishing phosphorescence emission in aqueous environments remains a challenge. Herein, we present a general design strategy that effectively promotes phosphorescence by utilising water molecules to construct hydrogen-bonded networks between carbon dots (CDs) and cyanuric acid (CA). Interestingly, water molecules not only cause no phosphorescence quenching but also greatly enhance the phosphorescence emission. This enhancement behaviour can be explained by the fact that the highly ordered bound water on the CA particle surface can construct robust bridge-like hydrogen-bonded networks between the CDs and CA, which not only effectively rigidifies the C=O bonds of the CDs but also greatly enhances the rigidity of the entire system. In addition, the CD-CA suspension exhibits a high phosphorescence lifetime (687 ms) and is successfully applied in ion detection based on its visible phosphorescence.