A Tin Oxide Transparent Electrode Provides the Means for Rapid Time‐resolved pH Measurements: Application to Photoinduced Proton Transfer of Bacteriorhodopsin and Proteorhodopsin†

An electrochemical cell was previously reported in which bacteriorhodopsin (BR, purple membrane) was adsorbed on the surface of a transparent SnO₂ electrode, and illumination resulted in potential or current changes (Koyama et al., Science 265:762–765, 1994; Robertson and Lukashev, Biophys. J. 68:1507–1517, 1995; Koyama et al., Photochem. Photobiol. 68:400–406, 1998). In this paper, we concluded that pH changes caused by proton transfer by the deposited BR or proteorhodopsin (PR) films lead to the flash‐induced potential change in the SnO₂ electrode. Thus, the signals originate from BR and PR acting as light‐driven proton pumps. This conclusion was drawn from the following observations. (1) The relation between the potential of a bare electrode and pH is linear for a wide pH range. (2) The flash‐induced potential changes decrease with an increase in the buffer concentration. (3) The action spectrum of PR agrees well with the absorption spectrum. (4) The present electrode can monitor the pH change in the time range from 10 ms to several hundred milliseconds, as deduced by comparing the SnO₂ signal with the signals of pH‐sensitive dyes. Using this electrode system, flash‐induced proton transfer by BR was measured for a wide pH range from 2 to 10. From these data, we reconfirmed various pK_a values reported previously, indicating that the present method can give the correct pK_a values. This is the first report to estimate these pK_a values directly from the proton transfer. We then applied this method to flash‐induced proton transfer of PR. We observed proton uptake followed by release for the pH range from 4 to 9.5, and in other pH ranges, proton release followed by uptake was observed.     

Photoisomerization in proteorhodopsin mutant D97N

The first steps of the photocycle of the D97N mutant of proteorhodopsin (PR) have been investigated by means of ultrafast transient absorption spectroscopy. A comparison with the primary dynamics of native PR and D85N mutant of bacteriorhodopsin is given. Upon photoexcitation of the covalently bound all-trans retinal the excited state decays biexponentially with time constants of 1.4 and 20 ps via a conical intersection, resulting in a 13-cis isomerized retinal. Neither of the two-deactivation channels is significantly preferred. The dynamics is slowed down in comparison with native PR at pH 9 and reaction rates are even lower than for native PR at pH 6, where the primary proton acceptor (Asp97) is protonated. Therefore, the ultrafast isomerization is not only controlled by the charge distribution within the retinal binding pocket. This study shows that in addition to direct electrostatics other effects have to be taken into account to explain the catalytic function of Asp97 in PR on the ultrafast isomerization reaction. This may include sterical interactions and/or bound water molecules within the retinal binding pocket.     

MCCE2: Improving protein pKa calculations with extensive side chain rotamer sampling

Multiconformation continuum electrostatics (MCCE) explores different conformational degrees of freedom in Monte Carlo calculations of protein residue and ligand pK_as. Explicit changes in side chain conformations throughout a titration create a position dependent, heterogeneous dielectric response giving a more accurate picture of coupled ionization and position changes. The MCCE2 methods for choosing a group of input heavy atom and proton positions are described. The pK_as calculated with different isosteric conformers, heavy atom rotamers and proton positions, with different degrees of optimization are tested against a curated group of 305 experimental pK_as in 33 proteins. QUICK calculations, with rotation around Asn and Gln termini, sampling His tautomers and torsion minimum hydroxyls yield an RMSD of 1.34 with 84% of the errors being <1.5 pH units. FULL calculations adding heavy atom rotamers and side chain optimization yield an RMSD of 0.90 with 90% of the errors <1.5 pH unit. Good results are also found for pK_as in the membrane protein bacteriorhodopsin. The inclusion of extra side chain positions distorts the dielectric boundary and also biases the calculated pK_as by creating more neutral than ionized conformers. Methods for correcting these errors are introduced. Calculations are compared with multiple X‐ray and NMR derived structures in 36 soluble proteins. Calculations with X‐ray structures give significantly better pK_as. Results with the default protein dielectric constant of 4 are as good as those using a value of 8. The MCCE2 program can be downloaded from http://www.sci.ccny.cuny.edu/～mcce . © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

The influence of water on the photochemical reaction cycle of proteorhodopsin at low and high pH

Dried samples were prepared from suspension of proteorhodopsin. With HCl and NaOH the pH of the samples was adjusted below and above the pKa of the proton acceptor Asp-97, which was established earlier to be 7.1. Both types of samples were photoactive, and exhibited a truncated photocycle, compared to that measured in suspension. The photocycle of the low pH sample had a K like red shifted intermediate, decaying through an energized PR' intermediate to the ground state protein. The high pH sample had a more complex photocycle in which beside of the red shifted intermediate an M like intermediate could be identified, having a deprotonated Schiff-base. This blue shifted intermediate decays through an intermediate we designated PR', which is spectrally identical to the unphotolysed ground state. The humidity and temperature dependence of the photocycle in both cases was studied to understand the role of water in the function of the proteorhodopsin. The effects measured on proteorhodopsin were very similar to that measured earlier on bacteriorhodopsin.     

Modulation of Excited‐State Proton Transfer of 2‐(2′‐Hydroxyphenyl)benzimidazole in a Macrocyclic Cucurbit[7]uril Host Cavity: Dual Emission Behavior and pKa Shift

The effect of the macrocyclic host, cucurbit[7]uril (CB7), on the photophysical properties of the 2‐(2′‐hydroxyphenyl)benzimidazole (HPBI) dye have been investigated in aqueous solution by using ground‐state absorption and steady‐state and time‐resolved fluorescence measurements. All three prototropic forms of the dye (cationic, neutral, and anionic) form inclusion complexes with CB7, with the largest binding constant found for the cationic form (K≈2.4×10⁶ M ^?1). At pH≈4, the appearance of a blue emission band upon excitation of the HPBI cation in the presence of CB7 indicates that encapsulation into the CB7 cavity retards the deprotonation process of the excited cation, and hence reduces its subsequent conversion to the keto form. Excitation of the neutral form (pH≈8.5), however, leads to an increase in the keto form fluorescence, indicating an enhanced excited‐state intramolecular proton‐transfer process for the encapsulated dye. In both the ground and excited states, the two pK_a values of the HPBI dye show upward shifts in the presence of CB7. The prototropic equilibrium of the CB7‐complexed dye is represented by a six‐state model, and the pH‐dependent changes in the binding constants have been analyzed accordingly. It has been observed that the calculated pK_a values using this six‐state model match well with the values obtained experimentally. The changes in the pK_a values in the presence of CB7 have been corroborated with the modulation of the proton‐transfer process of the dye within the host cavity.     

Factors driving the protonation of poly(N-vinylimidazole) hydrogels

Poly(N-vinylimidazole) hydrogels immersed in aqueous acid solutions produce an increment in the pH of the bath because of proton uptake by basic imidazole moieties, leading to hydrogel protonation. Both kinetic and equilibrium measurements of the pH of the bath have been performed under a variety of conditions and with different hydrogel samples. The kinetics of the xerogel protonation process (which includes solvent and titrant diffusion, the true protonation reaction or ion–dipole association, and the polymer relaxation to a new conformation) are mostly driven by the size of the hydrogel sample, whereas other magnitudes, such as the initial pH, the effective polymer concentration, and the network structure, governed by the crosslinker ratio and total comonomer concentration in the feeding, have a minor influence. pK_a changes with the degree of protonation (α), delimitating two different regions: (1) a broad α range in which pK_a decreases with increasing α but less pronouncedly with increasing ionic strength and (2) an α range close to α = 1 in which pK_a decreases abruptly, more markedly with sulfate than with chloride counteranions and with larger ionic strengths. In the first region, pK_a is determined by repulsive electrostatic interactions and so is larger for titration with H₂SO₄ than with HCl and increases as the effective polymer concentration and ionic strength increase. Two steps (i.e., two protonation sites) can be observed in the titration curves, the second one corresponding to abrupt changes in the basicity of the second pK_a-versus-α region. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 2294–2307, 2004     

Oil-Water Partitioning of a Synthetic Tetracarboxylic Acid as a Function of pH

The oil-water partitioning of a synthetic tetraacid acting as a model compound for indigenous C₈₀-C₈₂ ARN acids has been studied as a function of pH, ionic strength and type of monovalent counterion. Experimental data obtained with ultraviolet-visible and HPLC/UV analyses have been fitted to thermodynamic models based on one, two or four dissociation steps to obtain o/w partition coefficients (K _wo ) of the fully protonated acid between chloroform and aqueous solutions, and its apparent acidity constant(s), pK _a. As the study is conducted above the CMC of the tetraacid, in general high apparent acidity constants were obtained in the range from 6 to 8 resulting from micellization equilibria. K _wo values were obtained in the range from 10^?3 to 10^?4, and decreasing with increasing salinity. At 50 mM K⁺, no conclusions could be made regarding the number of distinguishable dissociation steps, while at higher ionic strength (184 mM and 452 mM K⁺) and at 184 mM Na⁺ a model with two dissociation steps provided good fits to the experimental data. The first step was found to be given by a pK _a ≈ 6.6–6.8 and the second dissociation step at pK _a values ≈ 7.8–8.3. The two-step mechanism supports previous results obtained by potentiometric titrations. No significant difference in the o/w behavior was observed when changing the counterion from potassium to sodium. The main partitioning of the tetraacid in the aqueous phase occurred above pH 8, where the fully deprotonated acid was formed.     

Influence of the membrane potential on the protonation of bacteriorhodopsin: insights from electrostatic calculations into the regulation of proton pumping

Proton binding and release are elementary steps for the transfer of protons within proteins, which is a process that is crucial in biochemical catalysis and biological energy transduction. Local electric fields in proteins affect the proton binding energy compared to aqueous solution. In membrane proteins, also the membrane potential affects the local electrostatics and can thus be crucial for protein function. In this paper, we introduce a procedure to calculate the protonation probability of titratable sites of a membrane protein in the presence of a membrane potential. In the framework of continuum electrostatics, we use a modified Poisson-Boltzmann equation to include the influence of the membrane potential. Our method considers that in a transmembrane protein each titratable site is accessible for protons from only one side of the membrane depending on the hydrogen bond pattern of the protein. We show that the protonation of sites receiving their protons from different sides of the membrane is differently influenced by the membrane potential. In addition, the effect of the membrane potential is combined with the effect of the pH gradient resulting from proton pumping. Our method is applied to bacteriorhodopsin, a light-activated proton pump. We find that the proton pumping of this protein might be regulated by Asp115, a conserved residue for which no function has been identified yet. According to our calculations, the interaction of Asp115 with Asp85 leads to the protonation of the latter if the pH gradient or the membrane potential becomes too large. Since Asp85 is the primary proton acceptor in the photocycle, bacteriorhodopsin molecules in which Asp85 is protonated cannot pump protons. Furthermore, we estimate how the membrane potential affects the energetics of the individual proton-transfer reactions of the photocycle. Most reactions, except the initial proton transfer from the Schiff base to Asp85, are influenced. Our calculations give new insights into the mechanism with which bacteriorhodopsin senses the membrane potential and the pH gradient and how the proton pumping is regulated by these parameters.     

Poly(L‐lysine)‐Induced Aggregation of Single‐Strand Oligo‐DNA‐Modified Gold Nanoparticles

Single‐strand oligo‐DNA‐modified Au nanoparticles (AuNPs) undergo aggregation in the presence of poly(L ‐lysine) (PLL), which is attributed to the interactions between the oligo‐DNA and PLL. These interactions between the oligo‐DNA and PLL were identified to be electrostatic when the lysine residues of PLL were positively charged and to be hydrogen bonding when the residues were deprotonated. The aggregation was promoted with an increase in the pH value at a pH level lower than the pK_a value of PLL (pK_a≈10.0) due to the gradual deprotonation of the lysine residues and thus suppressed electrostatic interactions between the positively charged lysine residues of PLL and the negatively charged backbone phosphate groups of the oligo‐DNA. At pH levels higher than the pK_a value of PLL, the aggregation was identified to be dominated by the hydrogen bonds between the bases of the oligo‐DNA and the deprotonated lysine residues of PLL. This study prompts the possibility that the spectral, and thus color, change of AuNPs upon aggregation can be used as a probe to follow the interactions between oligo‐DNA and polypeptides.     

2‐Nitro‐1,4‐diaminobenzene‐Functionalized Poly(vinyl amine)s as Water‐Soluble UV‐Vis‐Sensitive pH Sensors

Summary: Nucleophilic aromatic substitution of 2,6‐O‐dimethyl‐β‐cyclodextrin (β‐DMCD)‐complexed 4‐fluoro‐3‐nitroaniline derivatives with poly(vinyl amine) (PVAm) in water results in 2‐nitro‐1,4‐benzenediamine‐functionalized water‐soluble PVAms in one step. The 2‐nitro‐1,4‐benzenediamine moiety linked to the polymer is solvatochromic and undergoes protonation and deprotonation as function of pH as shown by UV‐Vis spectroscopy. The occurrence of an isosbestic point in the UV‐Vis spectrum is suitable to directly determine the pK_a value using the Henderson‐Hasselbalch equation. The influence of the methyl group substitution of the polymer and the 2‐nitro‐1,4‐benzenediamine moiety on the pK_a is discussed.

Structure of the 4‐N,N‐dimethyl‐2‐nitro‐1,4‐benzenediamine‐functionalized PVAm and its solution in water at varying pH.     

Chemically Triggered C–ON Bond Homolysis in Alkoxyamines. Part 2: DFT Investigation and Application of the pH Effect on NMP

In recent work, a 15‐fold increase in the C–ON bond homolysis rate constant k_d of 4‐pyridylethyl‐SG1‐based alkoxyamine was observed upon protonation of the pyridyl moiety in organic solvent. In this report, the pH dependence of k_d (pK_a = 4.7) is investigated in D₂O/CD₃OD (v/v 1:1). A 64‐fold increase in k_d is observed at acidic pH. Calculations show that the increase in k_d upon protonation is due to both an increase in the stabilization of the protonated 4‐pyridylethyl radical and an increase of the destabilization of the starting materials through an increase in the polarity of the alkyl fragment. This new alkoxyamine is applied to NMP of styrene and sodium styrene sulfonate.     

Fragment Binding to Kinase Hinge: If Charge Distribution and Local pKa Shifts Mislead Popular Bioisosterism Concepts

Medicinal‐chemistry optimization follows strategies replacing functional groups and attaching larger substituents at a promising lead scaffold. Well‐established bioisosterism rules are considered, however, it is difficult to estimate whether the introduced modifications really match the required properties at a binding site. The electron density distribution and pK_a values are modulated influencing protonation states and bioavailability. Considering the adjacent H‐bond donor/acceptor pattern of the hinge binding motif in a kinase, we studied by crystallography a set of fragments to map the required interaction pattern. Unexpectedly, benzoic acid and benzamidine, decorated with the correct substituents, are totally bioisosteric just as carboxamide and phenolic OH. A mono‐dentate pyridine nitrogen out‐performs bi‐dentate functionalities. The importance of correctly designing pK_a values of attached functional groups by additional substituents at the parent scaffold is rendered prominent.     

CE determination of the thermodynamic pKa values and limiting ionic mobilities of 14 low molecular mass UV absorbing ampholytes for accurate characterization of the pH gradient in carrier ampholytes-based IEF and its numeric simulation

Fourteen low molecular mass UV absorbing ampholytes containing 1 or 2 weakly acidic and 1 or 2 weakly basic functional groups that best satisfy Rilbe's requirement for being good carrier ampholytes (ΔpK_a = pKa_monoanion ‒ pKa_monocation < 2) were selected from a large group of commercially readily available ampholytes in a computational study using two software packages (ChemSketch and SPARC). Their electrophoretic mobilities were measured in 10 mM ionic strength BGEs covering the 2 < pH < 12 range. Using our Debye-Hückel and Onsager-Fuoss laws-based new software, AnglerFish (freeware, https://echmet.natur.cuni.cz/software/download ), the effective mobilities were recalculated to zero ionic strength from which the thermodynamic pK_a values and limiting ionic mobilities of the ampholytes were directly calculated by Henderson-Hasselbalch equation-type nonlinear regression. The tabulated thermodynamic pK_a values and limiting ionic mobilities of these ampholytes (pI markers) facilitate both the overall and the narrow-segment characterization of the pH gradients obtained in IEF in order to mitigate the errors of analyte ampholyte pI assignments caused by the usual (but rarely proven) assumption of pH gradient linearity. These thermodynamic pK_a and limiting mobility values also enable the reality-based numeric simulation of the IEF process using, for example, Simul (freeware, https://echmet.natur.cuni.cz/software/download ).     

Effect of the acidity and chemical nature of the protonating agent on the rate of acetylene reduction catalyzed by the nitrogenase active site isolated from the enzyme

The effect of the acidity (pK _a) of the source of protons on the rate and selectivity of acetylene reduction has been investigated in order to elucidate the mechanism of protonation of substrate molecules coordinated to the reduced FeMoco cluster. A number of compounds whose pK _a in DMF varies between 6 and 20 have been examined as protonating agents. The rate of the reaction is almost independent of the acidity of the proton donor in a wide pK _a range. This can be explained in terms of the specific features of substrate protonation catalyzed by iron-sulfur clusters. Active protonating agents in the system are those which react with the catalyst to form hydrogen-bonded association species or those which are ligands reversibly binding to the cluster and are capable of donating protons, likely with simultaneous electron transfer.     

蒽与苯甲酸及其衍生物之间的作用机理研究

用紫外差光谱、红外光谱法和荧光猝灭法研究了典型多环芳烃蒽与苯甲酸及其羟基取代衍生物邻羟基苯甲酸和对羟基苯甲酸之间的作用机理。实验结果表明,在此芳香羧酸与蒽之间存在定向的、特异性的作用,其作用方式受到反应物结构和环境酸度的影响。对苯甲酸和邻羟基苯甲酸而言,当pH<pKa时,二者之间以蒽离域大π电子与羧基质子之间的π-H氢键作用为主,pH>pKa时,π-π电子给体受体作用逐渐成为主要结合方式。邻位羟基的存在使得苯甲酸与蒽的作用强度明显降低。对羟基苯甲酸特殊的D-π-A型分子结构使得它在溶液中形成平面多分子聚集体,这种多分子聚集体的生成使得对羟基苯甲酸与蒽的结合方式不随酸度变化,在pH2.0~10.0的范围内均以π-π电子给体受体作用相结合,且结合强度大于苯甲酸和邻羟基苯甲酸。     

UV‐Vis Spectroscopy Reveals a Correlation Between Y263 and BV Protonation States in Bacteriophytochromes

Red‐light photosensory proteins, phytochromes, link light activation to biological functions by interconverting between two conformational states. For this, they undergo large‐scale secondary and tertiary changes which follow small‐scale Z to E bond photoisomerization of the covalently bound bilin chromophore. The complex network of amino acid interactions in the chromophore‐binding pocket plays a central role in this process. Highly conserved Y263 and H290 have been found to be important for the photoconversion yield, while H260 has been identified as important for bilin protonation and proton transfer steps. Here, we focus on the roles these amino acids are playing in preserving the chemical properties of bilin in the resting Pr state of the photosensory unit of a bacteriophytochrome from Deinococcus radiodurans. By using pH‐dependent UV‐Vis spectroscopy and spectral decomposition modeling, we confirm the importance of H260 for biliverdin protonation. Further, we demonstrate that in the canonical bacteriophytochromes, the pK_a value of the phenol group of the Y263 is uncommonly low. This directly influences the protonation of the bilin molecule and likely the functional properties of the protein. Our study expands the understanding of the tight interplay between the nearby amino acids and bilin in the phytochrome family.     

Potentiometric and Voltammetric Study of 6‐Benzylaminopurine and Its Derivatives

The protonation‐deprotonation equilibrium of 6‐benzylaminopurine (6‐BAP) and its derivatives was studied by potentiometry and voltammetry. The effect of Cl‐ or OCH₃‐group in position 2′, 3′ and 4′ of the benzene ring of 6‐BAP on both pK_a values was investigated. To determine the enthalpy and entropy, the temperature dependence of pK_a was employed. It was found that with increasing temperature the pK_a decreased. In comparison with 6‐BAP the chloro‐ or methoxy‐ group resulted in pK_a increase. The first pK_a values were also determined by linear sweep (LSV) and elimination voltammetry with linear scan (EVLS). New approaches were shown not only for the determination of pK_a from voltammetric titration curves but also for the evaluation of the reduction processes of benzylaminopurines.     

Capillary electrokinetic fractionation mass spectrometry (CEkF/MS): Technology setup and application to metabolite fractionation from complex samples coupled at‐line with ultrahigh‐resolution mass spectrometry

Capillary electrokinetic fractionation (CEkF) is investigated as a new, simple, and robust approach for semipreparative and analytical sample analysis based on pK_a‐dependant pH‐driven electrophoretic mobility. CEkF was optimized with contactless conductivity detection and conducted with 10 kV reverse voltage for 10 min, then coupled on/at‐line to ESI/MS. We propose a semi‐empirical model with 14 representative compounds based on the correlation between sample/medium pH regulating the partial charge, the electrokinetic loading of the capillary and intensity (I) of analytes. According to the model, an empirical function (I = f (pH)) could be derived to calculate the acid dissociation constant (pK_a) of various model compounds based on their pH‐dependant MS intensity profiles with the RSD < 4.05. Using the ultrahigh‐resolution of ion cyclotron resonance Fourier transform MS, the pK_a model was further illustrated in real samples into the structure prediction of important compounds in wine over two vintages. The established CEkF was successfully used to selectively fractionate sulfur compounds from the complex wine samples at pH 1.66. The proposed CEkF approach should allow in the future the simultaneous pK_a evaluation of multiple constituents without complicated separation out of a complex mixture in metabolomics or environmental chemistry.     

Inverse opal pH sensors with various protic monomers copolymerized with polyhydroxyethylmethacrylate hydrogel

pH sensitive inverse opal sensors were synthesized using various vinyl monomers containing acidic or basic substituents. Acrylic acid (AA), vinylphosphonic acid (VPA), vinylimidazole (VI), and dimethylaminoethylmethacrylic acid (DMAEMA) were respectively copolymerized with hydroxyethylmethacrylate (HEMA), the building block monomer of the hydrogel via UV-initiated photopolymerization. Opal templating and subsequent template removal enabled the fabrication of four inverse opal (IO) hydrogel colorimetric sensors, which responded to pH in different fashions. pH-dependent swelling of the IO hydrogel induced the red-shift of the diffracted color. The sensors containing AA or VPA, the proton donating monomers showed the color shifts from green to red with pH increase due to the increased concentration of carboxylate anions bound to the hydrogel. Diprotic VPA sensor exhibited two-step increases of diffracted wavelengths at its pK_a1 and pK_a2 respectively. The sensors containing proton acceptors, VI and DMAEMA showed the pH-dependent color changes in an opposite way to the AA sensor and the VPA sensor since their ionizations take place by lowering pH due to the protonation at the amino groups. The shapes of pH response curves of VI and DMAEMA sensors were similar but pK_bs were different from each other. Optical diffraction responses of four sensors were compared with the calculated concentration ratios of the ionized species to the total monomer with pH variation, and a deswelling effect in the vicinities of pK_as of phosphate buffer on the swelling response could be explained by shrinkage of PHEMA hydrogel under high ionic environment. In addition, copolymerization of AA, VPA and HEMA was carried out which resulted in a pH sensor exhibiting a wider range of pH for color change.