IONIZATION OF INDIVIDUAL GROUPS IN DIBASIC ACIDS, WITH APPLICATION TO THE AMINO AND HYDROXYL GROUPS OF TYROSINE

Resolving coupled pH titrations using alchemical free energy calculations

In a protein, nearby titratable sites can be coupled: the (de)protonation of one may affect the other. The degree of this interaction depends on several factors and can influence the measured p K a . Here, we derive a formalism based on double free energy differences ( Δ Δ G ) for quantifying the individual site p K a values of coupled residues. As Δ Δ G values can be obtained by means of alchemical free energy calculations, the presented approach allows for a convenient estimation of coupled residue p K a s in practice. We demonstrate that our approach and a previously proposed microscopic p K a formalism, can be combined with alchemical free energy calculations to resolve pH-dependent protein p K a values. Toy models and both, regular and constant-pH molecular dynamics simulations, alongside experimental data, are used to validate this approach. Our results highlight the insights gleaned when coupling and microstate probabilities are analyzed and suggest extensions to more complex enzymatic contexts. Furthermore, we find that naïvely computed p K a values that ignore coupling, can be significantly improved when coupling is accounted for, in some cases reducing the error by half. In short, alchemical free energy methods can resolve the p K a values of both uncoupled and coupled residues.

2-Fluorotyrosine is a valuable but understudied amino acid for protein-observed 19F NMR

Incorporation of ¹⁹F into proteins allows for the study of their molecular interactions via NMR. The study of ¹⁹F labeled aromatic amino acids has largely focused on 4-,5-, or 6-fluorotryptophan, 4-fluorophenylalanine, (4,5, or 6FW) or 3-fluorotyrosine (3FY), whereas 2-fluorotyrosine (2FY) has remained largely understudied. Here we report a comparative analysis with different fluorinated amino acids. We first report the NMR chemical shift responsiveness of five aromatic amino acid mimics to changes in solvent polarity and find that the most responsive, a mimic of 3FY, has a 2.9-fold greater change in chemical shift compared to the other amino acid mimics in aprotic solvents including the 2FY mimic. We also probed the utility of 2FY for ¹⁹F NMR by measuring its NMR relaxation properties in solution and the chemical shift anisotropy (CSA) of a polycrystalline sample of the amino acid by magic angle spinning. Using protein-observed fluorine NMR (PrOF NMR), we compared the influence of 2FY and 3FY incorporation on stability and pK_a perturbation when incorporated into the KIX domain of CBP/p300. Lastly, we investigated the ¹⁹F NMR response of both 2FY and 3FY-labeled proteins to a protein-protein interaction partner, MLL, and discovered that 2FY can report on allosteric interactions that are not observed with 3FY-labeling in this protein complex. The reduced perturbation to pK_a and similar but reduced CSA of 2FY to 3FY supports 2FY as a suitable alternative amino acid for incorporation into large proteins for ¹⁹F NMR analysis.

Proton-Coupled Electron Transfer and a Tyrosine-Histidine Pair in a Photosystem II-Inspired β-Hairpin Maquette: Kinetics on the Picosecond Time Scale

Photosystem II (PSII) and ribonucleotide reductase employ oxidation and reduction of the tyrosine aromatic ring in radical transport pathways. Tyrosine-based reactions involve either proton-coupled electron transfer (PCET) or electron transfer (ET) alone, depending on the pH and the pKa of tyrosine's phenolic oxygen. In PSII, a subset of the PCET reactions are mediated by a tyrosine-histidine redox-driven proton relay, YD-His189. Peptide A is a PSII-inspired β-hairpin, which contains a single tyrosine (Y5) and histidine (H14). Previous electrochemical characterization indicated that Peptide A conducts a net PCET reaction between Y5 and H14, which have a cross-strand π-π interaction. The kinetic impact of H14 has not yet been explored. Here, we address this question through time-resolved absorption spectroscopy and 280-nm photolysis, which generates a neutral tyrosyl radical. The formation and decay of the neutral tyrosyl radical at 410 nm were monitored in Peptide A and its variant, Peptide C, in which H14 is replaced by cyclohexylalanine (Cha14). Significantly, both electron transfer (ET, pL 11, L = lyonium) and PCET (pL 9) were accelerated in Peptide A and C, compared to model tyrosinate or tyrosine at the same pL. Increased electronic coupling, mediated by the peptide backbone, can account for this rate acceleration. Deuterium exchange gave no significant solvent isotope effect in the peptides. At pL 9, but not at pL 11, the reaction rate decreased when H14 was mutated to Cha14. This decrease in rate is attributed to an increase in reorganization energy in the Cha14 mutant. The Y5-H14 mechanism in Peptide A is reminiscent of proton- and electron-transfer events involving YD-H189 in PSII. These results document a mechanism by which proton donors and acceptors can regulate the rate of PCET reactions.

A Thioester Substrate Binds to the Enzyme Arthrobacter Thioesterase in Two Ionization States; Evidence from Raman Difference Spectroscopy

4-Hydroxybenzoyl-CoA (4-HB-CoA) thioesterase from Arthrobacter is the final enzyme catalyzing the hydrolysis of 4-HB-CoA to produce coenzyme A and 4-hydroxybenzoic acid in the bacterial 4-chlorobenzoate dehalogenation pathway. Using a mutation E73A that blocks catalysis, stable complexes of the enzyme and its substrate can be analyzed by Raman difference spectroscopy. Here we have used Raman difference spectroscopy, in the non-resonance regime, to characterize 4-HB-CoA bound in the active site of the E73A thioesterase. In addition we have characterized complexes of the wild-type enzyme complexed with the unreactive substrate analog 4-hydroxyphenacyl-CoA (4-HP-CoA). Both sets of complexes show evidence for two forms of the ligand in the active site, one population has the 4-hydroxy group protonated, 4-OH, while the second has the group as the hydroxide, 4-O(-). For bound 4-HP-CoA X-ray data show that glutamate 78 is close to the 4-OH in the complex and it is likely that this is the proton acceptor for the 4-OH proton. Although the pK(a) of the 4-OH group on the free substrate in aqueous solution is 8.6, the relative populations of ionized and neutral 4-HB-CoA bound to E73A remain invariant between pH 7.3 and pH 9.8. The invariance with pH suggests that the 4-OH and the -COO(-) of E78 constitute a tightly coupled pair where their separate pK(a)s lose their individual qualities. Narrow band profiles are seen in the C=O double bond and C-S regions suggesting that the hydrolyzable thioester group is rigidly bound in the active site in a syn gauche conformation.

Deuterated Water Effects on Acid Ionization Constants

Linear relations of the form DeltapK = pK(D) - pK(H) = a + b pK(H) relating ionization constants of acids in light and heavy water must have the same slope b for any kind of acid unless the previously unconsidered charge type is important or this equation is not valid.

Identification of free radical species derived from caffeic acid and related polyphenols

Polyphenols are widely distributed in various fruits, vegetables and seasonings. It is well known that they have several physiological effects due to their antioxidative activities. Their activities depend on structural characteristics that favour the formation of their corresponding stable radicals. During the examination at which pH values, the polyphenol radicals are stabilized, we confirmed that polyphenol radicals were stabilized in NaHCO3/Na2CO3 buffer (pH 10) rather than in physiological pH region. Then, we measured electron spin resonance (ESR) spectra at pH 10 to examine the characteristics of free radical species derived from caffeic acid (CA) with an unsaturated side chain, dihydrocaffeic acid (DCA) with a saturated side chain, chlorogenic acid (ChA) and rosmarinic acid (RA). In analyzing the radical structures, ESR simulation, determinations of macroscopic and microscopic acid dissociation constants and molecular orbital (MO) calculation were performed. In CA, the monophenolate forms were assumed to participate in the formation of free radical species, while in DCA, the diphenol form and the monophenolate forms were presumed to contribute to the formation of free radical species. On the basis of the results, we propose the possible structures of the free radical species formed from polyphenols under alkaline conditions.

Electrostatic stabilization and general base catalysis in the active site of the human protein disulfide isomerase a domain monitored by hydrogen exchange

The nucleophilic Cys36 thiol of the human protein disulfide isomerase a domain is positioned over the N terminus of the alpha(2) helix. Amides in the active site exhibit diffusion-limited, hydroxide-catalyzed exchange, indicating that the local positive electrostatic potential decreases the pK value for peptide anion formation by at least 2 units so as to equal or exceed the acidity of water. In stark contrast to the pH dependence of exchange for simple peptides, the His38 amide in the reduced enzyme exhibits a maximum rate of exchange at pH 5 due to efficient general base catalysis by the neutral imidazole of its own side chain and suppression of its exchange by the ionization of the Cys36 thiol. Ionization of this thiol and deprotonation of the His38 side chain suppress the Cys39 amide hydroxide-catalyzed exchange by a million-fold. The electrostatic potential within the active site monitored by these exchange experiments provides a means of stabilizing the two distinct transition states that lead to substrate reduction and oxidation. Molecular modeling offers a role for the conserved Arg103 in coordinating the oxidative transition-state complex, thus providing further support for mechanisms of disulfide isomerization that utilize enzymatic catalysis at each step of the overall reaction.

Structure-function relationships in glutathione and its analogues

The results are presented of measurements of protonation constants (potentiometry and NMR), UV spectroscopic properties and redox potentials of GSH and its five analogues, which are modified at the C-terminal glycine residue (gammaGlu-Cys-X, X = Gly, Gly-NH2, Gly-OEt, Ala, Glu, Ser). Strong linear correlations were found between various properties of the thiol and other functions of these peptides. These results allow discussion of the relationships between the structures and properties in glutathione and its analogues, and provide a novel chemical background for the issue of control of GSH reactivity.

Protonation equilibrium and lipophilicity of olamufloxacin (HSR-903), a newly synthesized fluoroquinolone antibacterial

This study was performed to characterize the protonation equilibrium at the molecular level and pH-dependent lipophilicity of olamufloxacin. The deprotonation fraction of the carboxyl group as a function of pH was specifically calculated at the critical wavelength 294 nm, where UV pH-dependent absorbance of olamufloxacin was independent of the ionized state of the aminopyrrolidinyl amino group but heavily depended on that of the carboxyl moiety. Accordingly, micro-protonation equilibrium could be described using a nonlinear least-squares regression program MULTI. In contrast, macro-protonation equilibrium was depicted at most wavelengths where olamufloxacin absorbance was influenced by ionized states of both proton-binding groups, results coinciding with the former. Furthermore, distribution features of four microspecies in aqueous phase were assessed. The apparent partition coefficient versus pH profile of olamufloxacin showed a parabolic curve in n-octanol/buffer system which reached peak near pH 8, agreeing with the above determined isoelectric point (pI). Ion-pair effect was observed for olamufloxacin under an acidic condition, eliciting experimental values higher than those theoretically calculated, which was similar to ciprofloxacin but not levofloxacin due to amino group type. Moreover, olamufloxacin was moderately lipophilic in comparison with other quinolones, with an apparent partition coefficient of 1.95 at pH 7.4.

Microionization constants: novel approach for the determination of the zwitterionic equilibrium of hydroxyphenylalkylamines by photometric titration

The record of the formation of the phenolate and the zwitterionic form in the course of titration by photometry makes it possible to estimate the tautomeric equilibrium, K(Z), between the zwitterionic and the uncharged form of an ampholyte, provided that (1) the absorptivity of the phenolate and the zwitterionic form are identical and (2) the absorptivities of both forms are distinct from the absorptivities of the protonated and the uncharged form. The relation between the absorbance and K(Z), the degree of titration and the degree of overlapping of the basic and the acid ionization constant is given.

A cluster expansion method for the complete resolution of microscopic ionization equilibria from NMR titrations

The NMR chemical shift of spin 1/2 nuclei in a polyprotic molecule represents a sensitive probe of microscopic protonation equilibria. However, these equilibria are commonly parametrized in terms of microscopic equilibrium constants, whose number increases very rapidly with the number of ionizable groups. For that reason their determination was considered to be basically impossible except for the cases of the simplest molecules. On the basis of a cluster expansion of the free energy of a microstate, we propose a novel parametrization of this problem that drastically reduces the number of necessary parameters needed to specify the microscopic equilibria. Such cluster parameters can be extracted from NMR titration data in a straightforward way. Once these parameters are known, all microscopic equilibrium constants can be obtained.

Physicochemical properties of A-75998, an antagonist of luteinizing hormone releasing hormone

The physicochemical properties of A-75998, a synthetic antagonist of luteinizing hormone releasing hormone with potential for treatment of hormone-sensitive cancers and endometriosis, are described. An accelerated solution stability study indicated that the compound is relatively stable and showed a U-shaped pH-rate profile, with maximum stability between pH 4.5 and 6.5. The acid dissociation behavior of A-75998 was examined by UV-visible spectrophotometry at 25 degrees C in a series of buffers ranging from pH 1 to 13. The data were fit to a model in which the dissociations of all four ionizable groups contributed to changes in the absorbance. The estimated macroscopic acid dissociation constants were p beta 1 = 3.230 +/- 0.022, p beta 2 = 4.885 +/- 0.030, p beta 3 = 9.871 +/- 0.022, and p beta 4 = 11.026 +/- 0.157. The corresponding microscopic dissociation constants were pk1 = 3.24 (nicotinyl), pk2 = 4.88 (pyridyl), pk5 = 9.91 (tyrosyl), and pk6 = 10.99 (isopropyllysyl). The apparent n-octanol/water partition coefficients were measured from pH 2 to 13, and the profile was consistent with the expected acid-dissociation behavior. While appearing fairly water-soluble at pH < 5, dynamic light scattering of A-75998 in pH 4.5 buffer indicated the formation of aggregates of nonuniform size distribution. A-75998 exhibited reverse or thermal gelation; sodium chloride exacerbates this gel formation and self-association. Surface activity was pH-dependent, but no evidence was found for micelle formation. Based on the results, development of a parenteral formulation of A-75998 appears feasible, provided that aggregation can be minimized.

Transition metal complexes of L-cysteine containing di- and tripeptides

Nickel(II), cobalt(II), zinc(II), and cadmium(II) complexes of Ala-Cys, Phe-Cys, and Ala-Ala-Cys were studied by potentiometric and spectroscopic methods. Ni(II) induces deprotonation and coordination of the amide nitrogens, and the stable monomeric or oligomeric complexes are formed, depending on the metal to ligand molar ratios. Formation of the stable bis-complexes with [S,O] coordination mode is characteristic for cobalt(II), zinc(II), and cadmium(II) ions.

Distribution coefficients of atenolol and sotalol

Our original publication (Taylor & Cruickshank 1984) was addressed to one simple specific point: the confusion that has been caused by apparently contradictory data for the same two compounds. It is now criticised on two counts (Day & Parr 1984): that we used a confusing nomenclature; and that our treatment of the data was technically incorrect.

Determination of dissociation constants of 5-[1-hydroxy-2-[(1-methylethyl)amino]ethyl]-1-3-benzenediol

The microdissociation constants of 5-[1-hydroxy-2-[ (methylethyl)amino]ethyl]-1-3-benzenediol have been determined by means of spectrophotometric and spectrofluorometric techniques. Experimental data were analyzed using the linear regression method. Values of 8.90, 10.0, 10.25, 9.15, and 12.5 have been found for the microdissociation constants.

The interactions between nucleic acids and polyamines

Changes in the NMR chemical shifts of protons adjacent to the nitrogen atoms of Spermidine which are undergoing protonation have been measured by two-dimensional heteronuclear coupled NMR. Data thus obtained measure the dependence of the state of protonation of individual nitrogens on the pH, and permit calculation of the microprotonation constants of Spermidine and the concentrations of all of the variously protonated Spermidine species present at any pH.

Ionization constants of catechols and catecholamines

Catecholamines can appear in different charged states: as positive, negative and zwitterion and as zero-charged molecule. The microscopic ionization constants of ten catecholamines were determined spectrophotometrically. For each charged state the fraction of total catecholamine at pH = 7.85 was calculated from the microscopic ionization constants. Some attention is given to the interpretation of the differences between the fractions of corresponding charged states.

Enzymatic O-methylation of catechols and catecholamines

The reactivity of a number of catechols and catecholamines with regard to the enzymatic O-methylation by catechol-O-methyltransferase (COMT) was studied. The reaction was carried out in a vial at a temperature of 37 degrees C, the vial contained a certain concentration of one catechol(amine), catechol-O-methyltransferase (the enzyme), S-adenosylmethionine (the methyldonor), MgCl2 (a cofactor) and buffer pH = 7.85. After certain time intervals samples were taken, the reaction was stopped in acid. The catechol(amine) concentration decrease and the product concentration increase were determined by injecting the samples directly into an HPLC connected with a fluorimeter, giving the opportunity of estimating the mass balance. Vmax, Km, C3/C4 ratio (= ratio of 3-O- and 4-O-methylated product formed) and the reaction rate at low substrate (catecholamine) concentration (= Vmax. [S]/Km)-which appears to be related to log P - are given. It is conjectured that V at low substrate concentration is especially determined by the polarity of the catechol(amine) while Vmax is primarily determined by other physico-chemical properties like steric conformation (L-dopa vs DL-dopa; L-adrenaline vs DL-adrenaline).

The ionization of morphine, hydroxyamphetamine and (+)-tubocurarine chloride and a new method for calculating zwitterion constants

1 An improved method for estimating the zwitterion constants of phenolic amines is described which involves the exploratory least-squares fit of absorbance (at a suitable wavelength) to pH, starting with estimates of pK1 and pK2 obtained electrometrically. 2 With the method it is possible to see that hydroxyamphetamine (alpha-methyltyramine) has a higher zwitterion constant than tyramine and the zwitterion constants of both compounds are lower at 37 degree C than at 25 degree C. 3 The zwitterion constant of morphine is not reduced by raising the temperature from 25 degree to 37 degree C and the effect of temperature is much greater in compounds with a primary or secondary amino group than with those containing a tertiary amino group. Some zwitterions may be stabilized by hydration and their formation will be reduced by a rise in temperature which will break up water structure. 4 From electrometric titrations with (+)-tubocurarine chloride in 0.1 M NaCl estimates of pK1, pK2 and pK3 were 7.6, 8.65 and 9.65 at 25 degree C and 7.4, 8.6 and 9.7 at 37 degree C, compared with 7.8, 8.85 and 9.75 given by Perrin (1980). However, the effects of pH on absorbance show that the phenolic groups lose a proton before the ammonium group so there is extensive zwitterion formation which is probably greater at 25 degree than at 37 degree C. the p-phenolic group (position 13) probably ionizes first with the phenate form stabilized by hydration involving water molecules and the protonated form of the (1-) ammonium group.

Degradation of chlorambucil in aqueous solution

The stability of chlorambucil and its degradation product 4-[p-(2-chloroethyl-2-hydroxyethylamino)phenyl]butyric acid (I) was studied using reversed-phase high-pressure liquid chromatography. The degradation rate of chlorambucil was unaffected by pH between pH 5 and 10 but decreased at lower pH. The degradation rates of chlorambucil and I differed only slightly (pH < 6). The proteolytic properties of the compounds were studied using spectrophotometric and partition techniques.

Neoprontosil binding to carbonic anhydrase. Reasonance Raman and other studies on the ionization behavior of the sulfonamide

Alkalimetric, spectrophotometric, NMR, and resonance Raman titrations are reported for the sulfonamide Neoprontosil in aqueous solution. An assignment of the magnetic resonance peaks for each of the Neoprontosil protons has been made. Neoprontosil is shown to have two "coupled" iity of the microscopic pKs for these two groups precludes spectroscopic characterization of the separate -SO2NH2, -O- or -SO2NH-, -OH species. For this reason, no conclusion can be drawn on the ionization state of the drug when bound to carbonic anhydrase. The resonance Raman spectrum of Neoprontosil bound to human carbonic anhydrase B at pH 9.5 shows a shift in the intense -N=N- stretching mode from 1414 (free) to 1407 cm- (bound), suggesting that a slight conformational change about the -N=N- single bond linkages occurs upon binding.

Extraction of daunorubicin and doxorubicin and their hydroxyl metabolites: self-association in aqueous solution

The extraction of daunorubicin and doxorubicin and their hydroxyl metabolites daunorubicinol and doxorubicinol was studied using chloroform-1-pentanol (9:1) as the organic phase. Because of differences in acid dissociation constants, the pH for optimum extraction varied from 8.0 to 8.6 for the different compounds. Self-association in the aqueous phase significantly influenced the distribution ratio. Constants for the formation of dimers and tetramers in aqueous solutions were about 10(4.5) and 10(12), respectively.

Spectroscopic approach to estimation of microequilibrium constants of prototropic reactions of aminobenzoic acids

The microequilibrium constants of protolytic dissociation of diprotic acids, dihydric bases, or ampholytes such as the aminobenzoic acids, with dissimilar ionizing groups, can be estimated by spectrophotometric titration and measurement of the molar absorptivity at the long wavelength absorption maximum of simple alkylated derivatives. The method is applicable when the long wavelength absorption spectral bands of the tautomeric species are well resolved. Compared to the traditional method of estimating microequilibrium constants using the dissociation constants of alkylated derivatives, the proposed method is simpler, faster, and more accurate.

General method for determining macrodissociation constants of polyprotic, amphoteric compounds from solubility measurements

Equilibrium solubility and pH measurements can be used to determine macrodissociation constants of weak acids and bases of some highly insoluble substances. Equations are derived extending solubility, pH, and pKa (macroscopic) relationships to polyprotic, amphoteric substances. A general method for estimating pKa values, given a set of solubility and pH measurements, is presented. Included in the estimation procedure is a subroutine for approximating thermodynamic pKa values. The method was tested on two data sets (tyrosine and 2,3-dihydroxyadenine) and rendered pKa (thermodynamic) estimates in close agreement with those using other methods.

Electronic absorption spectra and protolytic equilibria of doxorubicin: direct spectrophotometric determination of microconstants

The ground- and excited-state dissociation constants and the electronic absorption and fluorescence spectra of doxorubicin were investigated by spectrophotometry. A general method for the direct calculation of individual microscopic dissociation constants was derived using the spectrophotometric data obtained. It was concluded that the protonated amino sugar group is slightly more acidic than the phenolic group. The spectrophotometric data were analyzed, and the macro- and microconstants for the various equilibria was reported.