Substitution of both histidines in the active site of yeast alcohol dehydrogenase 1 exposes underlying pH dependencies

Histidine residues 44 and 48 in yeast alcohol dehydrogenase (ADH) bind to the coenzymes NAD(H) and contribute to catalysis. The individual H44R and H48Q substitutions alter the kinetics and pH dependencies, and now the roles of other ionizable groups in the enzyme were studied in the doubly substituted H44R/H48Q ADH. The substitutions make the enzyme more resistant to inactivation by diethyl pyrocarbonate, modestly improve affinity for coenzymes, and substantially decrease catalytic efficiencies for ethanol oxidation and acetaldehyde reduction. The pH dependencies for several kinetic parameters are shifted from pK values for wild-type ADH of 7.3-8.1 to values for H44R/H48Q ADH of 8.0-9.6, and are assigned to the water or alcohol bound to the catalytic zinc. It appears that the rate of binding of NAD+ is electrostatically favored with zinc-hydroxide whereas binding of NADH is faster with neutral zinc-water. The pH dependencies of catalytic efficiencies (V/EtKm) for ethanol oxidation and acetaldehyde reduction are similarly controlled by deprotonation and protonation, respectively. The substitutions make an enzyme that resembles the homologous horse liver H51Q ADH, which has Arg-47 and Gln-51 and exhibits similar pK values. In the wild-type ADHs, it appears that His-48 (or His-51) in the proton relay systems linked to the catalytic zinc ligands modulate catalytic efficiencies.

Characterizing Hydroxyl Radical Formation from the Light-Driven Fe(II)-Peracetic Acid Reaction, a Key Process for Aerosol-Cloud Chemistry

The reaction of peracetic acid (PAA) and Fe(II) has recently gained attention due to its utility in wastewater treatment and its role in cloud chemistry. Aerosol-cloud interactions, partly mediated by aqueous hydroxyl radical (OH) chemistry, represent one of the largest uncertainties in the climate system. Ambiguities remain regarding the sources of OH in the cloud droplets. Our research group recently proposed that the dark and light-driven reaction of Fe(II) with peracids may be a key contributor to OH formation, producing a large burst of OH when aerosol particles take up water as they grow to become cloud droplets, in which reactants are consumed within 2 min. In this work, we quantify the OH production from the reaction of Fe(II) and PAA across a range of physical and chemical conditions. We show a strong dependence of OH formation on ultraviolet (UV) wavelength, with maximum OH formation at λ = 304 ± 5 nm, and demonstrate that the OH burst phenomenon is unique to Fe(II) and peracids. Using kinetics modeling and density functional theory calculations, we suggest the reaction proceeds through the formation of an [Fe(II)-(PAA)2(H2O)2] complex, followed by the formation of a Fe(IV) complex, which can also be photoactivated to produce additional OH. Determining the characteristics of OH production from this reaction advances our knowledge of the sources of OH in cloudwater and provides a framework to optimize this reaction for OH output for wastewater treatment purposes.

Modeling the Role in pH on Contaminant Sequestration by Zerovalent Metals: Chromate Reduction by Zerovalent Magnesium

The role of pH in sequestration of Cr(VI) by zerovalent magnesium (ZVMg) was characterized by global fitting of a kinetic model to time-series data from unbuffered batch experiments with varying initial pH values. At initial pH values ranging from 2.0 to 6.8, ZVMg (0.5 g/L) completely reduced Cr(VI) (18.1 μM) within 24 h, during which time pH rapidly increased to a plateau value of ∼10. Time-series correlation analysis of the pH and aqueous Cr(VI), Cr(III), and Mg(II) concentration data suggested that these conditions are controlled by combinations of reactions (involving Mg0 oxidative dissolution and Cr(VI) sequestration) that evolve over the time course of each experiment. Since this is also likely to occur during any engineering applications of ZVMg for remediation, we developed a kinetic model for dynamic pH changes coupled with ZVMg corrosion processes. Using this model, the synchronous changes in Cr(VI) and Mg(II) concentrations were fully predicted based on the Langmuir-Hinshelwood kinetics and transition-state theory, respectively. The reactivity of ZVMg was different in two pH regimes that were pH-dependent at pH < 4 and pH-independent at the higher pH. This contrasting pH effect could be ascribed to the shift of the primary oxidant of ZVMg from H+ to H2O at the lower and higher pH regimes, respectively.

pH-Dependent Adsorption of Human Serum Albumin Protein on a Polystyrene-Block-Poly(acrylic acid)-Coated PVDF Membrane

This study reports the investigation of human serum albumin (HSA) adsorption on a poy-styrene-block-poly(acrylic acid) (PS-b-PAA)-coated PVDF membrane, which is a potential smart material for biomedical applications. First, copolymer coating on the membrane surface was successfully performed, due to the hydrophobic interaction of the PS anchoring group with the PVDF membrane. This was confirmed by Fourier transform infrared spectroscopy (FTIR) characterization of the membrane. Then, HSA adsorption onto the coated membrane was assessed and was proved to be strongly dependent on the pH of the protein solution. Indeed, both FTIR mapping and mass balance calculation using UV-visible spectroscopy displayed a greater HSA adsorption on the membrane at pH 5, even though it still took place at higher pH, but to a lower extent. Afterwards, an ionic strength influence study evinced the role of electrostatic interactions between HSA and the PAA layer on HSA adsorption. Dead-end filtration of HSA through the coated membrane confirmed the pH dependence of HSA adsorption on the coated membrane.

Computational Investigation of Mechanisms for pH Modulation of Human Chloride Channels

Many transmembrane proteins are modulated by intracellular or extracellular pH. Investigation of pH dependence generally proceeds by mutagenesis of a wide set of amino acids, guided by properties such as amino-acid conservation and structure. Prediction of pKas can streamline this process, allowing rapid and effective identification of amino acids of interest with respect to pH dependence. Commencing with the calcium-activated chloride channel bestrophin 1, the carboxylate ligand structure around calcium sites relaxes in the absence of calcium, consistent with a measured lack of pH dependence. By contrast, less relaxation in the absence of calcium in TMEM16A, and maintenance of elevated carboxylate sidechain pKas, is suggested to give rise to pH-dependent chloride channel activity. This hypothesis, modulation of calcium/proton coupling and pH-dependent activity through the extent of structural relaxation, is shown to apply to the well-characterised cytosolic proteins calmodulin (pH-independent) and calbindin D9k (pH-dependent). Further application of destabilised, ionisable charge sites, or electrostatic frustration, is made to other human chloride channels (that are not calcium-activated), ClC-2, GABAA, and GlyR. Experimentally determined sites of pH modulation are readily identified. Structure-based tools for pKa prediction are freely available, allowing users to focus on mutagenesis studies, construct hypothetical proton pathways, and derive hypotheses such as the model for control of pH-dependent calcium activation through structural flexibility. Predicting altered pH dependence for mutations in ion channel disorders can support experimentation and, ultimately, clinical intervention.

Excited State Dynamics of Alizarin Red S Nanoparticles in Solution

Alizarin red S is a sulfonated, water-soluble derivative of alizarin. This work presents femtosecond studies of alizarin red S (ARS) nanoparticles in comparison to ARS in aqueous solution and to alizarin in DMSO. The femtosecond studies cover a probing spectral range of 350-750 nm using different excitation wavelengths, taking into account the variation of the absorption spectra with the pH values of the solvent. Stationary absorption spectra show slight differences between solution and nanoparticles. Excitation at 530 nm results in low and noisy responses, therefore, we additionally recorded transient spectra of the nanoparticles at λex = 267 nm. While the results in DMSO are comparable to previous studies in non-aqueous solvents, we report a relatively fast relaxation of 14 ps in [La(OH)2][ARS] nanoparticles in aqueous solution after excitation at 530 nm, which is similar to Na(ARS) solution (19 ps). The dynamics changed with lower pH, but still without significant differences between nanoparticles and solution. We propose [La(OH)2][ARS] nanoparticles as a suitable alternative to dissolved molecules with similar spectroscopic properties, for example, with regard to biomarker applications.

Selection of an Amino Acid Site with One of the Fastest Cleavage Kinetics by the Endosomal Protease Cathepsin B for Potential Use in Drug Delivery Systems

On the basis of known published data, six peptide sequences were selected that are potentially capable of being rapidly cleaved by the endosomal protease cathepsin B. For comparison, the cleavage of common linker sequences, polyglycine and polyglycine-serine, by cathepsin B was also studied. Different ends of these peptides were labeled with sulfoCyanine3 and sulfoCyanine5 fluorescent dyes, between which Förster resonant energy transfer (FRET) is possible. The kinetics of cleavage of peptides by cathepsin B was studied on a multimodal plate reader by FRET signal reduction. FKFL and FRRG cleavage sites have been shown to be the most suitable for potential use in various drug delivery systems. These sites are much more efficiently cleaved under slightly acidic conditions of endosomes than at neutral extracellular pH.

pH- and Facet-Dependent Surface Chemistry of TiO2 in Aqueous Environment from First Principles

TiO₂ is a relevant catalytic material, and its chemistry in aqueous environment is a challenging aspect to address. Also, the morphology of TiO₂ particles at the nanoscale is often complex, spanning from faceted to spherical. In this work, we study the pH- and facet-dependent surface chemistry of TiO₂/water interfaces by performing ab initio molecular dynamics simulations with the grand canonical formulation of species in solution. We first determined the acid-base equilibrium constants at the interface, which allows us to estimate the pH at the point of zero charge, an important experimental observable. Then, based on simulated equilibrium constants, we predict the amount of H⁺, OH^-, and adsorbed H₂O species present on the surfaces as a function of the pH, a relevant aspect for water splitting semi-reactions. We approximated the complex morphology of TiO₂ particles by considering the rutile (110) and (011), and anatase (101), (001), and (100) surfaces.

Modulation of Slow Desensitization (Tachyphylaxis) of Acid-Sensing Ion Channel (ASIC)1a

Among the proton-activated channels of the ASIC family, ASIC1a exhibits a specific tachyphylaxis phenomenon in the form of a progressive decrease in the response amplitude during a series of activations. This process is well known, but its mechanism is poorly understood. Here, we demonstrated a partial reversibility of this effect using long-term whole-cell recording of CHO cells transfected with rASIC1a cDNA. Thus, tachyphylaxis represents a slow desensitization of ASIC1a. Prolonged acidifications provided the same recovery from slow desensitization as short acidifications of the same frequency. Slow desensitization and steady-state desensitization are independent processes although the latter attenuates the development of the former. We found that drugs which facilitate ASIC1a activation (e.g., amitriptyline) cause an enhancement of slow desensitization, while inhibition of ASIC1a by 9-aminoacridine attenuates this process. Overall, for a broad variety of exposures, including increased calcium concentration, different pH conditions, and modulating drugs, we found a correlation between their effects on ASIC1a response amplitude and the development of slow desensitization. Thus, our results demonstrate that slow desensitization occurs only when ASIC1a is in the open state.

[A Study on Mechanisms Underlying Proton Transport in Proton Pump-type Microbial Rhodopsins]

Microbial rhodopsins are photoreceptive membrane proteins composed of seven transmembrane α-helical apoproteins (opsin) and a covalently bound retinal chromophore. Microbial rhodopsins exhibit a cyclic photochemical reaction referred to as photocycle when illuminated. During their photocycles, these proteins perform various functions such as ions transport and photosensing. Among the various functional types of rhodopsins found to date, we have focused on the utility of proton pump-type microbial rhodopsins as optogenetic tools for optical pH control in cells or organelles. To develop effective toolkits for this purpose, a deeper understanding of the proton-pumping mechanism in these rhodopsins may be required. In this review, we first introduce a useful experimental method for measuring rapid transient pH changes with photoinduced proton uptake/release using transparent tin oxide (SnO₂) or indium-tin oxide (ITO) electrodes. In addition, we describe the unique pH-dependent behavior of the photoinduced proton transfer sequence as well as the vectoriality of proton transportation in proteorhodopsin (PR) from marine eubacteria. Through intensive ITO experiments over wide pH range, including extremely high or low pH values, in combination with photoelectric measurements using Xenopus oocytes or a thin polymer film "Lumirror," we encountered several interesting observations on photoinduced proton transfer in PR:1) proton uptake/release sequence reversal and potential proton translocation direction reversal under alkali conditions, and 2) fast proton release from D227, a secondary counterion of the protonated retinal Schiff base at acidic pH values.

Investigation of the Effect of pH on the Adsorption-Desorption of Doxycycline in Feed for Small Ruminants

Orally administered tetracycline antibiotics interact with feed, which may impact their bioavailability and efficacy. Therefore, the pH-dependent adsorption of doxycycline and its interaction with feed for ruminants was studied in vitro. Adsorption experiments on animal feed (135 and 270 mg) with initial doxycycline concentrations of 35, 75, and 150 µg/mL were performed. Desorption experiments were conducted by agitation of a predetermined mass of doxycycline-loaded animal feed in PBS, at pH = 3.0, 6.0, and 7.4, to simulate changes in the gastrointestinal tract. Antibiotic concentrations were determined by LC-MS/MS analysis. The adsorption/desorption of doxycycline was described by mathematical models. Chemisorption with strong intermolecular interactions between the active functional groups of doxycycline and the organic biomass was found. The experimental release curve comprised three sections: initial prolonged 27-30% release (pH = 6.0), followed by moderate 56-59% release (pH = 3.0), and final 63-74% release (pH = 7.4). The sigmoidal model showed a considerable role of diffusion with an initial prevalence of desorption and a decreased desorption rate thereafter. The Weibull equation revealed an initial release stage followed by a lag time section and sustained release. The study of doxycycline adsorption by the animal feed proved a maximum 80% encapsulation efficiency and revealed initial diffusion followed by chemisorption. The highest release efficiency of 74% suggests high bioavailability of doxycycline after oral administration in ruminants.

A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution

Introduction: Peptides carry out diverse biological functions and the knowledge of the conformational ensemble of polypeptides in various experimental conditions is important for biological applications. All fast dedicated softwares perform well in aqueous solution at neutral pH. Methods: In this study, we go one step beyond by combining the Debye-Hückel formalism for charged-charged amino acid interactions and a coarse-grained potential of the amino acids to treat pH and salt variations. Results: Using the PEP-FOLD framework, we show that our approach performs as well as the machine-leaning AlphaFold2 and TrRosetta methods for 15 well-structured sequences, but shows significant improvement in structure prediction of six poly-charged amino acids and two sequences that have no homologous in the Protein Data Bank, expanding the range of possibilities for the understanding of peptide biological roles and the design of candidate therapeutic peptides.

Insight on the heterogeneously activated H2O2 with goethite under visible light for cefradine degradation: pH dependence and photoassisted effect

The iron mineral-catalyzed degradation of cephalosporin antibiotics with H₂O₂ occurs ubiquitously in nature. Despite numerous studies, the effects of environmental conditions on reactive species production and degradation processes of cephalosporins remain unclear. Here, we report the iron mineral of goethite as the efficient and heterogenous catalyst for the degradation of cefradine (CRD) via H₂O₂ activation under different conditions involving pH and visible light irradiation. Results show that the CRD removal rate is highly dependent on pH and visible light irradiation. Interestingly, when the pH ranges from 4.0 to 7.0, the degradation intermediates of CRD under dark are the same as under visible light conditions in the goethite/H₂O₂ system. And, the ratio of CRD degradation rate constant (k_Light/k_Dark) reaches a maximum at pH 5.0, suggesting that CRD existing as zwitterion species is preferable for its removal with photoassistance. The mechanism investigation reveals that both •OH and ≡[Fe^IVO]²⁺ oxidants are generated during the reaction process, and •OH is the major oxidant at acidic pH, while ≡[Fe^IVO]²⁺ is more likely to be formed with photoassistance at near-neutral pH. According to UPLC-MS/MS analysis, CRD degradation likely happens via hydrogen atom abstraction from cyclohexadienyl by •OH, thioether and olefin oxidation by ≡[Fe^IVO]²⁺, and Fe^III-catalyzed hydrolytic cleavage of β-lactam ring. These findings highlight the vital roles of pH and photoassistance in the heterogeneously activated H₂O₂ with goethite for CRD degradation.

pH-Dependent Release of Vancomycin from Modularly Assembled Collagen Laminates

To prevent surgical site infections, antibiotics can be released from carriers made of biomaterials, such as collagen, that support the healing process and are slowly degraded in the body. In our labs we have developed collagen laminates that can be easily assembled and bonded on-site, according to medical needs. As shown previously, the asymmetric assembly leads to different release rates at the major faces of the laminate. Since the pH changes during the wound healing and infection, we further examined the effect of an acidic and alkaline pH, in comparison to pH 7.4 on the release of vancomycin from different collagen samples. For this purpose, we used an additively manufactured sample holder and quantified the release by HPLC. Our results show that the pH value does not have any influence on the total amount of released vancomycin (atelocollagen sponge pH 5.5: 71 ± 2%, pH 7.4: 68 ± 8%, pH 8.5: 74 ± 3%, bilayer laminate pH 5.5: 61 ± 6%, pH 7.4: 69 ± 4% and pH 8.5: 67 ± 3%) but on the time for half-maximal release. At an acidic pH of 5.5, the swelling of the atelocollagen sponge is largely increased, leading to a 2-3 h retarded release, compared to the physiological pH. No changes in swelling were observed at the basic pH and the compound release was 1-2 h delayed. These effects need to be considered when choosing the materials for the laminate assembly.

Calcium regulates acid-sensing ion channel 3 activation by competing with protons in the channel pore and at an allosteric binding site

The extracellular Ca²⁺ concentration changes locally under certain physiological and pathological conditions. Such variations affect the function of ion channels of the nervous system and consequently also neuronal signalling. We investigated here the mechanisms by which Ca²⁺ controls the activity of acid-sensing ion channel (ASIC) 3. ASICs are neuronal, H⁺-gated Na⁺ channels involved in several physiological and pathological processes, including the expression of fear, learning, pain sensation and neurodegeneration after ischaemic stroke. It was previously shown that Ca²⁺ negatively modulates the ASIC pH dependence. While protons are default activators of ASIC3, this channel can also be activated at pH7.4 by the removal of the extracellular Ca²⁺. Two previous studies concluded that low pH opens ASIC3 by displacing Ca²⁺ ions that block the channel pore at physiological pH. We show here that an acidic residue, distant from the pore, together with pore residues, controls the modulation of ASIC3 by Ca²⁺. Our study identifies a new regulatory site in ASIC3 and demonstrates that ASIC3 activation involves an allosteric mechanism together with Ca²⁺ unbinding from the channel pore. We provide a molecular analysis of a regulatory mechanism found in many ion channels.

Preparation and Characterization of Pazopanib Hydrochloride-Loaded Four-Component Self-Nanoemulsifying Drug Delivery Systems Preconcentrate for Enhanced Solubility and Dissolution

The aim of this study was to develop a four-component self-nanoemulsifying drug delivery system (FCS) to enhance the solubility and dissolution of pazopanib hydrochloride (PZH). In the solubility test, PZH showed a highly pH-dependent solubility (pH 1.2 > water >> pH 4.0 and pH 6.8) and was solubilized at 70 °C in the order Kollisolv PG (5.38%, w/w) > Kolliphor RH40 (0.49%) > Capmul MCM C10 (0.21%) and Capmul MCM C8 (0.19%), selected as the solubilizer, the surfactant, and the oils, respectively. In the characterization of the three-component SNEDDS (TCS) containing Kolliphor RH40/Capmul MCM C10, the particle size of dispersion was very small (<50 nm) and the PZH loading was 0.5% at the weight ratio of 9/1. In the characterization of FCS containing additional Kollisolv PG to TCS, PZH loading was increased to 5.30% without any PZH precipitation, which was 10-fold higher compared to the TCS. The optimized FCS prepared with the selected formulation (Kolliphor RH40/Capmul MCM C10/Kollisolv PG) showed a consistently complete and high dissolution rate (>95% at 120 min) at four different pHs with 1% polysorbate 80, whereas the raw PZH and Kollisolv PG solution showed a pH-dependent poor dissolution rate (about 40% at 120 min), specifically at pH 6.8 with 1% polysorbate 80. In conclusion, PZH-loaded FCS in this work demonstrated enhanced solubility and a consistent dissolution rate regardless of medium pH.

A pathway of the generation of acid mine drainage and release of arsenic in the bioleaching of orpiment

Arsenic in acid mine drainage (AMD) is commonly associated with the bioleaching of arsenic sulfide minerals. Orpiment is iron free and one of the most common arsenic sulfide minerals, but no studies are involved with the relationship between the iron free bioleaching of orpiment and the generation of arsenic-containing AMD. In this study, the iron free bioleaching experiments with Acidithiobacillus thiooxidans (T.t) or Acidithiobacillus caldus (A.c) were carried out. In the experiments with T.t, the pH value decreased with time, and the leached arsenic increased significantly. Meanwhile, the density of planktonic bacteria increased gradually, suggesting that T.t survived in the orpiment pulp. However, in the experiments with initial pH of 1, pH changed little and arsenic was nearly not leached, implying that the bioleaching of orpiment can be inhibited when the initial pH was too low. The XRD patterns and the TFESEM-EDS analyses showed that no elemental sulfur was detected on the orpiment surface. It was supposed that the sulfur was converted to sulfuric acid in the bioleaching process. The CFESEM images showed that no corrosion pits were formed though a few cells adhered to the orpiment surface, and the TEM images showed that no extracellular polymeric substances (EPS) were excreted by the attached cells on the orpiment particles. In the experiments with A.c, similar results were obtained. It is inferred that the bioleaching of orpiment under iron deficient conditions in mining areas generates arsenic-containing AMD, but can be inhibited when the initial pH is too low.

A fine balance of hydrophobic-electrostatic communication pathways in a pH-switching protein

Allostery is the phenomenon of coupling between distal binding sites in a protein. Such coupling is at the crux of protein function and regulation in a myriad of scenarios, yet determining the molecular mechanisms of coupling networks in proteins remains a major challenge. Here, we report mechanisms governing pH-dependent myristoyl switching in monomeric hisactophilin, whereby the myristoyl moves between a sequestered state, i.e., buried within the core of the protein, to an accessible state, in which the myristoyl has increased accessibility for membrane binding. Measurements of the pH and temperature dependence of amide chemical shifts reveal protein local structural stability and conformational heterogeneity that accompany switching. An analysis of these measurements using a thermodynamic cycle framework shows that myristoyl-proton coupling at the single-residue level exists in a fine balance and extends throughout the protein. Strikingly, small changes in the stereochemistry or size of core and surface hydrophobic residues by point mutations readily break, restore, or tune myristoyl switch energetics. Synthesizing the experimental results with those of molecular dynamics simulations illuminates atomistic details of coupling throughout the protein, featuring a large network of hydrophobic interactions that work in concert with key electrostatic interactions. The simulations were critical for discerning which of the many ionizable residues in hisactophilin are important for switching and identifying the contributions of nonnative interactions in switching. The strategy of using temperature-dependent NMR presented here offers a powerful, widely applicable way to elucidate the molecular mechanisms of allostery in proteins at high resolution.

EPR Evidence for Mechanistic Diversity of Cu(II)/Peroxygen Oxidation Systems by Tracing the Origin of DMPO Spin Adducts

Electron paramagnetic resonance (EPR) has been extensively used for the identification of free radicals that are generated from advanced oxidation processes (AOPs) so as to establish the reaction mechanism. However, some misinterpretations or controversies on the identity of detected EPR signals remain in the literature. This study, with Cu(II)-based AOPs as examples, comprehensively investigated the origin of 5,5-dimethyl-l-pyrroline N-oxide (DMPO) adducts in Cu(II) alone, Cu(II)/H₂O₂, Cu(II)/peroxymonosulfate (PMS), and Cu(II)/peroxydisulfate (PDS) systems. In most Cu(II) systems, DMPO-OH signals can be detected even without any peroxygens, indicating the presence of other origins of this adduct in addition to the genuine spin trapping of ^•OH by DMPO. According to the formed secondary radical adducts (DMPO-OCH₃ from a nonradical process or DMPO-CH₂OH from a radical oxidation) derived from methanol quenching, we propose that CuO⁺, instead of free radicals, is involved in the Cu(II)/PMS system, while ^•OH is indeed generated in the Cu(II)/H₂O₂ and Cu(II)/PDS systems under neutral conditions. Notably, ¹⁷O-incorporation experiments demonstrate that -OH in the detected DMPO-OH adduct originates 100% from water in the Cu(II) alone system but the amount of -OH is over 99.8% from the oxidant while peroxygens are added. In addition, DMPO-O₂^- appears only in the Cu(II)/PDS system under highly alkaline conditions and H₂O is not involved in superoxide formation.

Determination of the pH dependence, substrate specificity, and turnovers of alternative substrates for human ornithine aminotransferase

Hepatocellular carcinoma (HCC) is the most common primary cancer of the liver and occurs predominantly in patients with underlying chronic liver diseases. Over the past decade, human ornithine aminotransferase (hOAT), which is an enzyme that catalyzes the metabolic conversion of ornithine into an intermediate for proline or glutamate synthesis, has been found to be overexpressed in HCC cells. hOAT has since emerged as a promising target for novel anticancer therapies, especially for the ongoing rational design effort to discover mechanism-based inactivators (MBIs). Despite the significance of hOAT in human metabolism and its clinical potential as a drug target against HCC, there are significant knowledge deficits with regard to its catalytic mechanism and structural characteristics. Ongoing MBI design efforts require in-depth knowledge of the enzyme active site, in particular, pKa values of potential nucleophiles and residues necessary for the molecular recognition of ligands. Here, we conducted a study detailing the fundamental active-site properties of hOAT using stopped-flow spectrophotometry and X-ray crystallography. Our results quantitatively revealed the pH dependence of the multistep reaction mechanism and illuminated the roles of ornithine α-amino and δ-amino groups in substrate recognition and in facilitating catalytic turnover. These findings provided insights of the catalytic mechanism that could benefit the rational design of MBIs against hOAT. In addition, substrate recognition and turnover of several fragment-sized alternative substrates of hOATs, which could serve as structural templates for MBI design, were also elucidated.

Applications of triplex DNA nanostructures in sensor development

Triplex DNA nanostructures are one of the most emerging and fascinating self-assembled nanostructures due to their unique nanoparticle-like organization and inherit characteristics. They have attracted numerous interests recently because of their versatile and powerful utility in diverse areas of science and technology, such as clinical or disease diagnosis and stimuli-based drug delivery. This review addresses particularly the utilization of DNA triplexes in the development of biosensors for detecting nucleic acid; strategies in sensing pH, protein activity, ions, or molecules. Finally, an outlook for potential applications of triplex DNA nanoswitches is provided.

Role of Histidine 78 of leaf ferredoxin in the interaction with ferredoxin-NADP+ reductase: regulation of pH dependency and negative cooperativity with NADP(H)

In chloroplast stroma, dynamic pH change occurs in response to fluctuating light conditions. We investigated the pH-dependent electron transfer activity between ferredoxin-NADP+ reductase (FNR) and ferredoxin (Fd) isoproteins from maize leaves. By increasing pH (from 5.5 to 8.5), the electron transfer activity from FNR to photosynthetic-type Fd (Fd1) significantly increased while the activity to nonphotosynthetic type Fd (Fd3) decreased, which was mainly due to their differences in the pH dependency of Km for Fd. Mutation of His78 of Fd1 to Val, corresponding amino acid residue in Fd3, lost the pH dependency, indicating a regulatory role of the His78 in the interaction with FNR. We previously showed that the interaction between FNR and Fd was weakened by the allosteric binding of NADP(H) on FNR. His78Val Fd1 mutant largely suppressed this negative cooperativity. These results indicate the involvement of Fd1 His78 in pH dependency and negative cooperativity in the interaction with FNR.

The Physical Basis for pH Sensitivity in Biomolecular Structure and Function, With Application to the Spike Protein of SARS-CoV-2

Since pH sensitivity has a fundamental role in biology, much effort has been committed to establishing physical models to rationalize and predict pH dependence from molecular structures. Two of the key challenges are to accurately calculate ionizable group solvation and hydration and then to apply this modeling to all conformations relevant to the process in question. Explicit solvent methods coupled to molecular dynamics simulation are increasingly complementing lower resolution implicit solvent techniques, but equally, the scale of biological data acquisition leaves a role for high-throughput modeling. Additionally, determination of ranges of structures for a system allows sampling of key stages in solvation. In a review of the area, it is emphasized that pH sensors in biology beyond the most obvious candidate (histidine side chain, with an unshifted pK a near neutral pH) should be considered; that modeling can benefit from other concepts in bioinformatics, in particular modulation of interactions and function in families of homologs; and that it can also be beneficial to incorporate as many experimental structures as possible, to mitigate against small variations in conformation and to analyze larger, functional, conformational changes. These aspects are then demonstrated with new work on the spike protein of SARS-CoV-2, looking at the pH dependence of variants, including prediction of a change in the balance of locked, closed, and open forms at neutral pH for the Omicron variant spike protein.

The pH Effects on SARS-CoV and SARS-CoV-2 Spike Proteins in the Process of Binding to hACE2

COVID-19 has been threatening human health since the late 2019, and has a significant impact on human health and economy. Understanding SARS-CoV-2 and other coronaviruses is important to develop effective treatments for COVID-19 and other coronavirus-caused diseases. In this work, we applied multi-scale computational approaches to study the electrostatic features of spike (S) proteins for SARS-CoV and SARS-CoV-2. From our results, we found that SARS-CoV and SARS-CoV-2 have similar charge distributions and electrostatic features when binding with the human angiotensin-converting enzyme 2 (hACE2). Energy pH-dependence calculations revealed that the complex structures of hACE2 and the S proteins of SARS-CoV/SARS-CoV-2 are stable at pH values ranging from 7.5 to 9. Three independent 100 ns molecular dynamics (MD) simulations were performed using NAMD to investigate the hydrogen bonds between S proteins RBD and hACE2 RBD. From MD simulations, we found that SARS-CoV-2 forms 19 pairs (average of three simulations) of hydrogen bonds with high occupancy (>50%) to hACE2, compared to 16 pairs between SARS-CoV and hACE2. Additionally, SARS-CoV viruses prefer sticking to the same hydrogen bond pairs, while SARS-CoV-2 tends to have a larger range of selections on hydrogen bonds acceptors. We also labelled key residues involved in forming the top five hydrogen bonds that were found in all three independent 100 ns simulations. This identification is important to potential drug designs for COVID-19 treatments. Our work will shed the light on current and future coronavirus-caused diseases.

pH Dependence of Hydroxyl Radical, Ferryl, and/or Ferric Peroxo Species Generation in the Heterogeneous Fenton Process

The heterogeneous Fenton process in the presence of Fe-containing minerals is ubiquitous in nature and widely deployed in wastewater treatment. While there have been extensive relevant studies, the dependence on pH of the nature and extent of oxidant generation and key reaction pathways remain unclear. Herein, the adsorption and decomposition of formate and H₂O₂ were quantified in the presence of ferrihydrite within the pH range of 3.0-6.0, and experiments with methyl phenyl sulfoxide were conducted to distinguish between HO^• and weaker oxidant(s) which react via oxygen atom transfer including ferryl ion ([Fe^IVO]²⁺) and/or ferric hydroperoxo intermediates (≡Fe^III(O₂H)). Both HO^• and [Fe^IVO]²⁺/≡Fe^III(O₂H) are concurrently produced on the surface over the acidic to near-neutral pH range. Despite the simultaneous formation of both oxidants, HO^• is the major oxidant responsible for substrate oxidation in the interfacial boundary layer with [Fe^IVO]²⁺/≡Fe^III(O₂H) exhibiting limited exposure to substrates. With an increase of pH, the yield of both oxidants is inhibited by the decreasing availability of surface sites due to ferrihydrite particle aggregation. Increasing pH also favors the nonradical decay of H₂O₂ as evident from the consistent oxidant production rate relative to the surface area (SSA) despite an accelerated H₂O₂ decay rate relative to SSA with pH increase.

Optimal pH 8.5 to 9 for the Hydrolysis of Vixotrigine and Other Basic Substrates of Carboxylesterase-1 in Human Liver Microsomes

Vixotrigine is a voltage- and use-dependent sodium channel blocker under investigation for the potential treatment of neuropathic pain. One of the major in vivo metabolic pathways of vixotrigine in humans is the hydrolysis of the carboxamide to form the carboxylic acid metabolite M14.The in vitro formation of M14 in human hepatocytes was inhibited by the carboxylesterase (CES) inhibitor Bis(4-nitrophenyl) phosphate in a concentration-dependent manner. The hydrolysis reaction was identified to be catalyzed by recombinant human CES1b.Initial observation of only trace level formation of M14 in human liver microsomes at pH 7.4 caused us to doubt the involvement of CES1, an enzyme localized at the endoplasmic reticulum and the dominant carboxylesterase in human liver. Further investigation has revealed that optimal pH for the hydrolysis of vixotrigine and two other basic substrates of CES1, methylphenidate and oseltamivir, in human liver microsomes was pH 8.5 to 9 which is higher than their respective pK_a(base), suggesting that neutral form of basic substrates is probably preferred for CES1 catalysis in liver microsomes.

Cytokinin Perception in Ancient Plants beyond Angiospermae

Cytokinins (CKs) control many plant developmental processes and responses to environmental cues. Although the CK signaling is well understood, we are only beginning to decipher its evolution. Here, we investigated the CK perception apparatus in early-divergent plant species such as bryophyte Physcomitrium patens, lycophyte Selaginella moellendorffii, and gymnosperm Picea abies. Of the eight CHASE-domain containing histidine kinases (CHKs) examined, two CHKs, PpCHK3 and PpCHK4, did not bind CKs. All other CHK receptors showed high-affinity CK binding (K_D of nM range), with a strong preference for isopentenyladenine over other CK nucleobases in the moss and for trans-zeatin over cis-zeatin in the gymnosperm. The pH dependences of CK binding for these six CHKs showed a wide range, which may indicate different subcellular localization of these receptors at either the plasma- or endoplasmic reticulum membrane. Thus, the properties of the whole CK perception apparatuses in early-divergent lineages were demonstrated. Data show that during land plant evolution there was a diversification of the ligand specificity of various CHKs, in particular, the rise in preference for trans-zeatin over cis-zeatin, which indicates a steadily increasing specialization of receptors to various CKs. Finally, this distinct preference of individual receptors to different CK versions culminated in vascular plants, especially angiosperms.

NMR characterization of H2O2 hydrogen exchange

Quantification of H2O2 concentration in aqueous solutions is of interest in many fields. It usually is based on indirect methods that rely on oxidation reactions that turn on/off fluorescent probes. Such methods can suffer from reaction incompleteness and interfering chemical species. We describe optimization of NMR detection that enables direct quantification of H2O2 down to the nanomolar range. Taking advantage of fast hydrogen exchange (HX) between H2O2 and water permits the use of very short interscan delays, greatly increasing sensitivity. The specific acid-, base- and water-catalyzed HX rates at 2 °C were measured to be 2.1 × 107, 6.1 × 109, and 1.4 × 10-1 M-1s-1, respectively, which result in a minimum HX rate at pH 6.2. Furthermore, the exchange is accelerated by general acid/base catalysis. MES and phosphate buffers catalyze HX strongest in their unprotonated forms. For imidazole, only the unprotonated form catalyzes HX, which contrasts with acetic acid where only the protonated state catalyzes exchange. Inorganic salts such as sodium chloride and azide have negligible effect on HX. We present optimal conditions for accurate measurement of H2O2 concentrations as low as 40 nM in aqueous samples in a few hours.

The Relationship between Antibiotic Susceptibility and pH in the Case of Uropathogenic Bacteria

Urinary tract infections (UTIs) are common bacterial infections caused mainly by enteric bacteria. Numerous virulence factors assist bacteria in the colonization of the bladder. Bacterial efflux pumps also contribute to bacterial communication and to biofilm formation. In this study, the phenotypic and genetic antibiotic resistance of clinical UTI pathogens such as Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis were determined by disk diffusion method and polymerase chain reaction (PCR). Following this, different classes of antibiotics were evaluated for their antibacterial activity at pH 5, 6, 7 and 8 by a microdilution method. Gentamicin (GEN) was the most potent antibacterial agent against E. coli strains. The effect of GEN on the relative expression of marR and sdiA genes was evaluated by quantitative PCR. The slightly acidic pH (pH 6) and GEN treatment induced the upregulation of marR antibiotic resistance and sdiA QS activator genes in both E. coli strains. Consequently, bacteria had become more susceptible to GEN. It can be concluded that antibiotic activity is pH dependent and so the artificial manipulation of urinary pH can contribute to a more effective therapy of multidrug resistant bacterial infections.

Key Considerations When Assessing Novel Fenton Catalysts: Iron Oxychloride (FeOCl) as a Case Study

Iron oxychloride (FeOCl) has been reported to be a highly efficient heterogeneous Fenton catalyst over a wide pH range. In order to determine the true catalytic performance of FeOCl, we simultaneously quantified the adsorptive and oxidative removal of formate, oxalate, and rhodamine-B (RhB) and the formation of RhB oxidation products at both pH 4.0 and 7.0. FeOCl was found to be a poor Fenton catalyst at either pH, as gauged by the oxidation of formate, oxalate, and rhodamine B and the decomposition of H₂O₂, in comparison with ferrihydrite (Fhy), one of the most common Fe-containing Fenton catalysts. The adsorption of target contaminants to FeOCl and homogeneous Fenton processes, induced by dissolved iron, resulted in overevaluation of the catalytic performance of FeOCl, especially for (i) the use of strongly adsorbing target compounds, without consideration of the role of adsorption in their removal and (ii) exceedingly high concentrations of H₂O₂ to remove trace quantities of target contaminants. Overall, this study highlights that the systematic quantification of H₂O₂ decomposition, target compound adsorption, and oxidation as well as the concentrations of oxidized products formed are prerequisites for unequivocal elucidation of the catalytic nature and reaction mechanism of solid Fenton catalysts.

Predicting the potential of capacitive deionization for the separation of pH-dependent organic molecules

One of the main steps in the biotechnological production of chemical building blocks, such as, e.g. bio-based succinic acid which is used for lubricants, cosmetics, food, and pharmaceuticals, is the isolation and purification of the target molecule. A new approach to isolate charged, bio-based chemicals is by electrosorption onto carbon surfaces. In contrast to ion exchange, electrosorption does not require additional chemicals for elution and regeneration. However, while the electrosorption of inorganic salts is well understood and in commercial use, the knowledge about electrosorption of weak organic acids including the strong implications of the pH-dependent dissociation and their affinity towards physical adsorption must be expanded. Here, we show a detailed discussion of the main pH-dependent effects determining the achievable charge efficiencies and capacities. An explicit set of equations allows the fast prediction of the named key figures for constant voltage and constant current operation. The calculated and experimental results obtained for the electrosorption of maleic acid show that the potential-free adsorption of differently protonated forms of the organic acid play a dominating role in the process. At pH 8 and a voltage threshold of 1.3 V, charge efficiencies of 25% and capacities around 40 mmol/kg could be reached for a constant current experiment. While this capacity is clearly below that of ion exchange resins, the required carbon materials are inexpensive and energy costs are only about 0.013 €/mol. Therefore, we anticipate that electrosorption has the potential to become an interesting alternative to conventional unit operations for the isolation of charged target molecules.

Proton-modulated interactions of ions with transport sites of prokaryotic and eukaryotic NCX prototypes

The cytosolic pH decline from 7.2 to 6.9 results in 90% inactivation of mammalian Na⁺/Ca²⁺ exchangers (NCXs) due to protons interactions with regulatory and transport domains ("proton block"). Remarkably, the pH titration curves of mammalian and prokaryotic NCXs significantly differ, even after excluding the allosteric effects through regulatory domains. This is fascinating since "only" three (out of twelve) ion-coordinating residues (T50S, E213D, and D240N) differ between the archaeal NCX_Mj and mammalian NCXs although they contain either three or two carboxylates, respectively. To resolve the underlying mechanisms of pH-dependent regulation, the ion-coordinating residues of NCX_Mj were mutated to imitate the ion ligation arrays of mammalian NCXs; the mutational effects were tested on the ion binding/transport by using ion-flux assays and two-dimensional infrared (2D IR) spectroscopy. Our analyses revealed that two deprotonated carboxylates ligate 3Na⁺ or 1Ca²⁺ in NCX prototypes with three or two carboxylates. The Na⁺/Ca²⁺ exchange rates of NCX_Mj reach saturation at pH 5.0, whereas the Na⁺/Ca²⁺ exchange rates of the cardiac NCX1.1 gradually increase even at alkaline pHs. The T50S replacement in NCX_Mj "recapitulates" the pH titration curves of mammalian NCX by instigating an alkaline shift. Proteolytic shaving of regulatory CBD domains activates NCX1.1, although the normalized pH-titration curves are comparable in trypsin treated and untreated NCX1.1. Thus, the T50S-dependent alkaline shift sets a dynamic range for "proton block" function at physiological pH, whereas the CBDs (and other regulatory modes) modulate incremental changes in the transport rates rather than affect the shape of pH dependent curves.

pH-Dependent Flavin Adenine Dinucleotide and Nicotinamide Adenine Dinucleotide Ultraviolet Resonance Raman (UVRR) Spectra at Intracellular Concentration

The ultraviolet resonance Raman spectra of the adenine-containing enzymatic redox cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide in aqueous solution of physiological concentration are compared with the aim of distinguishing between them and their building block adenine in potential co-occurrence in biological materials. At an excitation wavelength of 266 nm, the spectra are dominated by the strong resonant contribution from adenine; nevertheless, bands assigned to vibrational modes of the nicotinamide and the flavin unit are found to appear at similar signal strength. Comparison of spectra measured at pH 7 with data obtained pH 10 and pH 3 shows characteristic changes when pH is increased or lowered, mainly due to deprotonation of the flavin and nicotinamide moieties, and protonation of the adenine, respectively.

Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease

Intravesicular pH plays a crucial role in melanosome maturation and function. Melanosomal pH changes during maturation from very acidic in the early stages to neutral in late stages. Neutral pH is critical for providing optimal conditions for the rate-limiting, pH-sensitive melanin-synthesizing enzyme tyrosinase (TYR). This dramatic change in pH is thought to result from the activity of several proteins that control melanosomal pH. Here, we computationally investigated the pH-dependent stability of several melanosomal membrane proteins and compared them to the pH dependence of the stability of TYR. We confirmed that the pH optimum of TYR is neutral, and we also found that proteins that are negative regulators of melanosomal pH are predicted to function optimally at neutral pH. In contrast, positive pH regulators were predicted to have an acidic pH optimum. We propose a competitive mechanism among positive and negative regulators that results in pH equilibrium. Our findings are consistent with previous work that demonstrated a correlation between the pH optima of stability and activity, and they are consistent with the expected activity of positive and negative regulators of melanosomal pH. Furthermore, our data suggest that disease-causing variants impact the pH dependence of melanosomal proteins; this is particularly prominent for the OCA2 protein. In conclusion, melanosomal pH appears to affect the activity of multiple melanosomal proteins.

Physicochemical and Electrochemical Characterization of Electropolymerized Polydopamine Films: Influence of the Deposition Process

Polydopamine (PDA) is a synthetic eumelanin polymer which is, to date, mostly obtained by dip coating processes. In this contribution, we evaluate the physical and electrochemical properties of electrochemically deposited PDA films obtained by cyclic voltammetry or pulsed deposition. The obtained PDA thin films are investigated with respect to their electrochemical properties, i.e., electron transfer (ET) kinetics and charge transfer resistance using scanning electrochemical microscopy and electrochemical impedance spectroscopy, and their nanomechanical properties, i.e., Young’s modulus and adhesion forces at varying experimental conditions, such as applied potential or pH value of the medium using atomic force microscopy. In particular, the ET behavior at different pH values has not to date been investigated in detail for electrodeposited PDA thin films, which is of particular interest for a multitude of applications. Adhesion forces strongly depend on applied potential and surrounding pH value. Moreover, force spectroscopic measurements reveal a significantly higher percentage of polymeric character compared to films obtained by dip coating. Additionally, distinct differences between the two depositions methods are observed, which indicate that the pulse deposition process leads to denser, more cross-linked films.

Effect of pH on the phase behavior of DMPC bilayers

We have studied the effect of acidic pH on the phase behavior of the zwitterionic lipid 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) using differential scanning calorimetry and x-ray scattering. Dispersions of DMPC in HCl solutions of pH = 4 and 3 behave identical to dispersions in water. The main transition temperature increases sharply and the pre-transition disappears at lower pH. An untilted gel phase is observed at pH = 2 and 1, in contrast to the tilted gel phase found at higher pH. The relatively large periodicity of the untilted gel phase, in comparison to that of the tilted gel phase occurring near neutral pH, clearly demonstrates the simultaneous charging and dehydration of the headgroups as the pH approaches the pK of the phosphate group. Headgroup dehydration at low pH also leads to the formation of DMPC crystallites and the inverted hexagonal phase at low and high temperatures, respectively, after a few days of incubation. These results show the significant effect of acidic pH on the phase behavior of zwitterionic lipids.

Bioconcentration of Several Series of Cationic Surfactants in Rainbow Trout

Cationic surfactants have a strong affinity to sorb to phospholipid membranes and thus possess an inherent potential to bioaccumulate, but there are few measurements of bioconcentration in fish. We measured the bioconcentration of 10 alkylamines plus two quaternary ammonium compounds in juvenile rainbow trout at pH 7.6, and repeated the measurements at pH 6.2 for 6 of these surfactants. The BCF of the amines with chain lengths ≤ C14 was positively correlated with chain length, increasing ∼0.5 log units per carbon. Their BCF was also pH dependent and approximately proportional to the neutral fraction of the amine in the water. The BCFs of the quaternary ammonium compounds showed no pH dependence and were >2 orders of magnitude less than for amines of the same chain length at pH 7.6. This indicates that systemic uptake of permanently charged cationic surfactants is limited. The behavior of the quaternary ammonium compounds and the two C16 amines studied was consistent with previous observations that these surfactants accumulate primarily to the gills and external surfaces of the fish. At pH 7.6 the BCF exceeded 2000 L kg-1 for 4 amines with chains ≥ C13, showing that bioconcentration can be considerable for some longer chained cationic surfactants.

pH-Dependent Photoinduced Interconversion of Furocoumaric and Furocoumarinic Acids

Photo-controlled or photo-regulated molecules, especially biologically active and operating in physiological conditions, are in steady demand. Herein, furocoumaric and furocoumarinic acids being (Z/E)-isomers relative to each other were obtained in two stages starting from psoralen: the alkaline solvolysis of psoralen led to furocoumaric acid, which was further Z → E photoisomerized (365 nm) to furocoumarinic acid. The kinetics of Z → E photoisomerization was monitored by HPLC and UV-vis spectrophotometry. Photophysical characteristics in the aqueous phase for both acids, as well as the reversibility of (Z/E) photoisomerization process, were also assessed. Furocoumarinic acid was found to be visibly fluorescent at pH 2.0-12.0, with the maxima of fluorescence emission spectra being pH-dependent. The reverse E → Z photoisomerization predicted by quantum chemistry calculations as energetically favorable for the monoanionic form of furocoumarinic acid was proved in the experiment while being complicated by pyrone ring closure back to psoralen in acidic and neutral conditions. The preparative synthesis of furocoumarinic acid outlined in this work is particularly valuable in view of a wide range of pharmacological effects previously predicted for this compound.

The voltage sensor is responsible for ΔpH dependence in Hv1 channels

The dissipation of acute acid loads by the voltage-gated proton channel (H_v1) relies on regulating the channel's open probability by the voltage and the ΔpH across the membrane (ΔpH = pH_ex - pH_in). Using monomeric Ciona-H_v1, we asked whether ΔpH-dependent gating is produced during the voltage sensor activation or permeation pathway opening. A leftward shift of the conductance-voltage (G-V) curve was produced at higher ΔpH values in the monomeric channel. Next, we measured the voltage sensor pH dependence in the absence of a functional permeation pathway by recording gating currents in the monomeric nonconducting D160N mutant. Increasing the ΔpH leftward shifted the gating charge-voltage (Q-V) curve, demonstrating that the ΔpH-dependent gating in H_v1 arises by modulating its voltage sensor. We fitted our data to a model that explicitly supposes the H_v1 voltage sensor free energy is a function of both the proton chemical and the electrical potential. The parameters obtained showed that around 60% of the free energy stored in the ΔpH is coupled to the H_v1 voltage sensor activation. Our results suggest that the molecular mechanism underlying the H_v1 ΔpH dependence is produced by protons, which alter the free-energy landscape around the voltage sensor domain. We propose that this alteration is produced by accessibility changes of the protons in the H_v1 voltage sensor during activation.

The molecular mechanisms of listeriolysin O-induced lipid membrane damage

Listeria monocytogenes is an intracellular food-borne pathogen that causes listeriosis, a severe and potentially life-threatening disease. Listeria uses a number of virulence factors to proliferate and spread to various cells and tissues. In this process, three bacterial virulence factors, the pore-forming protein listeriolysin O and phospholipases PlcA and PlcB, play a crucial role. Listeriolysin O belongs to a family of cholesterol-dependent cytolysins that are mostly expressed by gram-positive bacteria. Its unique structural features in an otherwise conserved three-dimensional fold, such as the acidic triad and proline-glutamate-serine-threonine-like sequence, enable the regulation of its intracellular activity as well as distinct extracellular functions. The stability of listeriolysin O is pH- and temperature-dependent, and this provides another layer of control of its activity in cells. Moreover, many recent studies have demonstrated a unique mechanism of pore formation by listeriolysin O, i.e., the formation of arc-shaped oligomers that can subsequently fuse to form membrane defects of various shapes and sizes. During listerial invasion of host cells, these membrane defects can disrupt phagosome membranes, allowing bacteria to escape into the cytosol and rapidly multiply. The activity of listeriolysin O is profoundly dependent on the amount and accessibility of cholesterol in the lipid membrane, which can be modulated by the phospholipase PlcB. All these prominent features of listeriolysin O play a role during different stages of the L. monocytogenes life cycle by promoting the proliferation of the pathogen while mitigating excessive damage to its replicative niche in the cytosol of the host cell.

Quantum mechanical reference spectrum simulation for precursors and degradation products of chemicals relevant to the Chemical Weapons Convention

A selection of acidic, alkaline and neutral degradation products relevant to the Chemical Weapons Convention was studied in wide range of pH conditions to determine their spin systems as well as spectral parameters. The pH dependence of chemical shifts and J couplings was parameterized using Henderson-Hasselbalch-based functions using dichloromethane as additional shift reference in TSP-d₄ referenced spectra. The resulting parameters allowed calculation of precise chemical shifts and J coupling constants in arbitrary pH conditions. The validity of the obtained spin system definitions and parameters as a source of quantum mechanically simulated reference data in chemical verification analysis is demonstrated.

A new cyanine from oxidative coupling of chlorogenic acid with tryptophan: Assessment of the potential as red dye for food coloring

A red pigment was prepared by reaction of chlorogenic acid (CGA) with tryptophan (TRP) in air at pH 9 (37% w/w yield) and evaluated as food dye. The main component of pigment was formulated as an unusual benzochromeno[2,3-b]indole linked to a TRP unit, featuring a cyanine type chromophore (λ_max 542, 546 nm, 1% extinction coefficient of the sodium salt = 244 ± 2). The chromophore showed a minimal pH dependence and proved stable for at least 3 h at 90 °C, both at pH 3.6 or 7.0, whereas red wine anthocyanins showed a substantial (30%) and betanin a complete abatement after 1 h at the acidic pHs. An intense coloring of different food matrices was obtained with the pigment at 0.01 % w/w. No toxicity was observed up to 0.2 mg/mL on hepatic and colonic cell lines. These data make this dye a promising alternative for red coloring of food.

Alcohol metabolite acetic acid activates BK channels in a pH-dependent manner and decreases calcium oscillations and exocytosis of secretory granules in rat pituitary GH3 cells

Acetaldehyde and acetic acid/acetate, the active metabolites of alcohol (ethanol, EtOH), generate actions of their own ranging from behavioral, physiological, to pathological/cancerogenic effects. EtOH and acetaldehyde have been studied to some depth, whereas the effects of acetic acid have been less well explored. In this study, we investigated the effect of acetic acid on big conductance calcium-activated potassium (BK) channels present in GH3 rat pituitary tumor cells in more detail. In whole cell voltage clamp recordings, extracellular application of acetic acid increased total outward currents in a dose-dependent manner. This effect was prevented after the application of the specific BK channel blocker paxilline. Acetic acid action was pH-dependent-in whole cell current and single BK channel recordings, open probability (Po) was significantly increased by extracellular pH reduction and decreased by neutral or base pH. Acetic acid hyperpolarized the membrane potential, whereas acidic physiological solution had a depolarizing effect. Moreover, acetic acid reduced calcium (Ca2+) oscillations and exocytosis of growth hormone contained secretory granules from GH3 cells. These effects were partially prevented by BK inhibitors-tetraethylammonium or paxillin. In conclusion, our experiments indicate that acetic acid activates BK channels in GH3 cells which eventually contribute to acetic acid-induced membrane hyperpolarization, cessation of Ca2+ oscillations, and decrease of growth hormone release.

A Picosecond Time-Resolved Spectroscopic Investigation of the Effect of pH on Morin Fluorescence

In this work, we investigated for the first time morin in MeOH at different pH values by picosecond time-resolved fluorescence. We identified the two species responsible for the fluorescence at low and high pH. The solvated morin-solvent hydrogen-bonded complex has been experimentally observed for the first time. We give also the typical fluorescence spectra as well as the fluorescence lifetimes of the probable emitting species. In this work we put forward new insights concerning the contribution of free morin to the fluorescence. We hope that these new data improve the accuracy of the interpretation of the cation:morin complexes titration using fluorescence signal.

Degradation Kinetics and Shelf Life of N-acetylneuraminic Acid at Different pH Values

The objective of this study was to investigate the stability and degradation kinetics of N-acetylneuraminic acid (Neu5Ac). The pH of the solution strongly influenced the stability of Neu5Ac, which was more stable at neutral pH and low temperatures. Here, we provide detailed information on the degradation kinetics of Neu5Ac at different pH values (1.0, 2.0, 11.0 and 12.0) and temperatures (60, 70, 80 and 90 °C). The study of the degradation of Neu5Ac under strongly acidic conditions (pH 1.0–2.0) is highly pertinent for the hydrolysis of polysialic acid. The degradation kinetics of alkaline deacetylation were also studied. Neu5Ac was highly stable at pH 3.0–10.0, even at high temperature, but the addition of H₂O₂ greatly reduced its stability at pH 5.0, 7.0 and 9.0. Although Neu5Ac has a number of applications in products of everyday life, there are no reports of rigorous shelf-life studies. This research provides kinetic data that can be used to predict product shelf lives at different temperatures and pH values.

A Single Second Shell Amino Acid Determines Affinity and Kinetics of Linagliptin Binding to Type 4 Dipeptidyl Peptidase and Fibroblast Activation Protein

Drugs targeting type 4 dipeptidyl peptidase (DPP‐4) are beneficial for glycemic control, whereas fibroblast activation protein alpha (FAP‐α) is a potential target for cancer therapies. Unlike other gliptins, linagliptin displays FAP inhibition. We compared biophysical and structural characteristics of linagliptin binding to DPP‐4 and FAP to better understand what differentiates linagliptin from other gliptins. Linagliptin exhibited high binding affinity (K_D) and a slow off‐rate (k_off) when dissociating from DPP‐4 (K_D 6.6 pM; k_off 5.1×10⁻⁵ s⁻¹), and weaker inhibitory potency to FAP (K_D 301 nM; k_off>1 s⁻¹). Co‐structures of linagliptin with DPP‐4 or FAP were similar except for one second shell amino acid difference: Asp663 (DPP‐4) and Ala657 (FAP). pH dependence of enzymatic activities and binding of linagliptin for DPP‐4 and FAP are dependent on this single amino acid difference. While linagliptin may not display any anticancer activity at therapeutic doses, our findings may guide future studies for the development of optimized inhibitors.

Carbon Dots Derived from the Maillard Reaction for pH Sensors and Cr (VI) Detection

The Maillard reaction involves a series of complex reactions; fluorescent compounds have been considered as vital intermediate products of the reaction. In this article, carbon dots (CDs) based on the Maillard reaction (MR-CDs) were prepared with L-tryptophan and D-glucose, and they had excellent photoluminescence stability. MR-CDs showed stable pH-dependence behavior and exhibited an excellent linear response to pH in the range of 4.0–7.5 and 7.5–13.0, respectively. Under the masking effect of sodium fluoride for Fe(III), MR-CDs showed excellent selectivity and sensitivity for Cr (VI). The linear range of Cr(VI) was 0.2–50 μM and the limit of detection was 20 nM. (S/N ≥ 3). Furthermore, MR-CDs were used to detect Cr(VI) in tap water samples. The recoveries were between 95.8% and 98.94%, and RSDs were less than 3.17%.

Interplay between Carbonic Anhydrases and Metallothioneins: Structural Control of Metalation

Carbonic anhydrases (CAs) and metallothioneins (MTs) are both families of zinc metalloproteins central to life, however, they coordinate and interact with their Zn2+ ion cofactors in completely different ways. CAs and MTs are highly sensitive to the cellular environment and play key roles in maintaining cellular homeostasis. In addition, CAs and MTs have multiple isoforms with differentiated regulation. This review discusses current literature regarding these two families of metalloproteins in carcinogenesis, with a dialogue on the association of these two ubiquitous proteins in vitro in the context of metalation. Metalation of CA by Zn-MT and Cd-MT is described. Evidence for protein-protein interactions is introduced from changes in metalation profiles of MT from electrospray ionization mass spectrometry and the metalation rate from stopped-flow kinetics. The implications on cellular control of pH and metal donation is also discussed in the context of diseased states.

Modulation of the electron-proton coupling at cytochrome a by the ligation of the oxidized catalytic center in bovine cytochrome c oxidase

Cytochrome a was suggested as the key redox center in the proton pumping process of bovine cytochrome c oxidase (CcO). Recent studies showed that both the structure of heme a and its immediate vicinity are sensitive to the ligation and the redox state of the distant catalytic center composed of iron of cytochrome a₃ (Fe_a3) and copper (Cu_B). Here, the influence of the ligation at the oxidized Fe_a3³⁺-Cu_B²⁺ center on the electron-proton coupling at heme a was examined in the wide pH range (6.5-11). The strength of the coupling was evaluated by the determination of pH dependence of the midpoint potential of heme a (E_m(a)) for the cyanide (the low-spin Fe_a3³⁺) and the formate-ligated CcO (the high-spin Fe_a3³⁺). The measurements were performed under experimental conditions when other three redox centers of CcO are oxidized. Two slightly differing linear pH dependencies of E_m(a) were found for the CN- and the formate-ligated CcO with slopes of -13 mV/pH unit and -23 mV/pH unit, respectively. These linear dependencies indicate only a weak and unspecific electron-proton coupling at cytochrome a in both forms of CcO. The lack of the strong electron-proton coupling at the physiological pH values is also substantiated by the UV-Vis absorption and electron-paramagnetic resonance spectroscopy investigations of the cyanide-ligated oxidized CcO. It is shown that the ligand exchange at Fe_a³⁺ between His-Fe_a³⁺-His and His-Fe_a³⁺-OH^- occurs only at pH above 9.5 with the estimated pK >11.0.

Undesired Bulk Oxidation of LiMn2 O4 Increases Overpotential of Electrocatalytic Water Oxidation in Lithium Hydroxide Electrolytes

Chemical and structural changes preceding electrocatalysis obfuscate the nature of the active state of electrocatalysts for the oxygen evolution reaction (OER), which calls for model systems to gain systematic insight. We investigated the effect of bulk oxidation on the overpotential of ink-casted LiMn2 O4 electrodes by a rotating ring-disk electrode (RRDE) setup and X-ray absorption spectroscopy (XAS) at the K shell core level of manganese ions (Mn-K edge). The cyclic voltammogram of the RRDE disk shows pronounced redox peaks in lithium hydroxide electrolytes with pH between 12 and 13.5, which we assign to bulk manganese redox based on XAS. The onset of the OER is pH-dependent on the scale of the reversible hydrogen electrode (RHE) with a Nernst slope of -40(4) mV/pH at -5 μA monitored at the RRDE ring. To connect this trend to catalyst changes, we develop a simple model for delithiation of LiMn2 O4 in LiOH electrolytes, which gives the same Nernst slope of delithiation as our experimental data, i. e., 116(25) mV/pH. From this data, we construct an ERHE -pH diagram that illustrates robustness of LiMn2 O4 against oxidation above pH 13.5 as also verified by XAS. We conclude that manganese oxidation is the origin of the increase of the OER overpotential at pH lower than 14 and also of the pH dependence on the RHE scale. Our work highlights that vulnerability to transition metal redox may lead to increased overpotentials, which is important for the design of stable electrocatalysts.