The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK a

Several small ribozymes employ general acid–base catalysis as a mechanism to enhance site-specific RNA cleavage, even though the functional groups on the ribonucleoside building blocks of RNA have pK_a values far removed from physiological pH. The rate of the cleavage reaction is strongly affected by the identity of the metal cation present in the reaction solution; however, the mechanism(s) by which different cations contribute to rate enhancement has not been determined. Using the Neurospora VS ribozyme, we provide evidence that different cations confer particular shifts in the apparent pK_a values of the catalytic nucleobases, which in turn determines the fraction of RNA in the protonation state competent for general acid–base catalysis at a given pH, which determines the observed rate of the cleavage reaction. Despite large differences in observed rates of cleavage in different cations, mathematical models of general acid–base catalysis indicate that k₁, the intrinsic rate of the bond-breaking step, is essentially constant irrespective of the identity of the cation(s) in the reaction solution. Thus, in contrast to models that invoke unique roles for metal ions in ribozyme chemical mechanisms, we find that most, and possibly all, of the ion-specific rate enhancement in the VS ribozyme can be explained solely by the effect of the ions on nucleobase pK_a. The inference that k₁ is essentially constant suggests a resolution of the problem of kinetic ambiguity in favor of a model in which the lower pK_a is that of the general acid and the higher pK_a is that of the general base.     

Antibody binding of cartilage-specific proteoglycans

The spectroscopically observable acid dissociation constant of aspartate aminotransferase (EC 2.6.1.1) varies to different degrees upon the addition of different monovalent anions. These interactions may be described by the minimal scheme

where XEH and XE represent anion complexes with the acidic (EH) and basic (E) forms of the enzyme, respectively. Both graphical and computer procedures were used to determine the three equilibrium constants which describe such a system. The analysis was based upon the effects of salt concentration (X) upon the apparent pK′_a of the enzyme determined spectrophotometrically. The affinities for anions of the basic enyzme are less than those of the acidic form of the enzyme so that the apparent pK′_a rises with anion concentration to a limiting value; pK₄ of the enzyme anion complex. That different anion-enzyme complexes have different pK₄'s reflects the fact that the interaction specificities of the basic and acidic enzymes differ. Cacodylate did not appear either to cause significant effects on the chromophoric pK's or to compete with the binding of halide or carboxylate anions which cause a perturbation of the pK_a.     

Heme-linked ionization and chloride binding in intestinal peroxidase and lactoperoxidase.

Hog intestinal peroxidase and bovine lactoperoxidase exhibited similar spectral shifts upon pH alteration. From spectrophotometric titrations, it was found that there are hemelinked ionizations of pK_a = 4.75 in intestinal peroxidase and pK_a = 3.5 in lactoperoxidase. The apparent pK_a (pK_a′) increased with the increase in chloride concentration. The pK_a′ vs log[Cl^?] plots showed that the chloride forms complex with the acid forms of these enzymes with a dissociation constant (pK = 2.7). Although the dissociation constant (K_d) of the peroxidase-cyanide complexes is nearly independent of pH, cyanide competed with chloride in the acidic pH region. The slopes of logK_d vs log[Cl^?] were 1.0 for intestinal peroxidase and 0.5 for lactoperoxidase. The reaction of hydrogen peroxide with these peroxidases was also affected by chloride, similarly as the reaction with cyanide was. The results were explained by assuming that protonation occurs at the distal base and destroys the hydrogen bond between the base and a water molecule at the sixth coordinate position of the heme iron.     

Determination of 1-aryl-4-propylpiperazine pKa values: The substituent on aryl modulates basicity

In order to design a potential drug, it is important to know its pK_a because the protonation state of the molecule will be critical for ligand–receptor interaction and for the pharmacokinetic of the molecule. pK_a values of a series of 1-(substitutedphenyl)-4-propylpiperazines were measured to study how the presence of a substituent on the phenyl ring modulates the basicity of N-4 nitrogen. pK_a values indicated that the position of the substituent was crucial. In general, the introduction of the substituent in ortho-position of the phenyl ring increased the basicity of the molecule. This effect appeared to be related to steric and conformational effects and not to the electronic properties of the substituent. On the other hand, meta- and para-substituted derivatives showed a slight decrease of pK_a that was qualitatively consistent with the electronic properties of the substituent.     

Conformational stability and dynamics of cytochrome <Emphasis Type="Italic">c</Emphasis> affect its alkaline isomerization

The alkaline isomerization of horse heart ferricytochrome c (cyt c) has been studied by electronic absorption spectroscopy in the presence of the Hofmeister series of anions: chloride, bromide, rhodanide and perchlorate. The anions significantly affect the apparent pK _a value of the transition in a concentration-dependent manner according to their position in the Hofmeister series. The Soret region of the absorption spectra is not affected by the presence of the salts and shows no significant structural perturbation of the heme crevice. In the presence of perchlorate and rhodanide anions, the cyanide exchange rate between the bulk solvent and the binding site is increased. These results imply higher flexibility of the protein structure in the presence of chaotropic salts. The thermal and isothermal denaturations monitored by differential scanning calorimetry and circular dichroism, respectively, showed a decrease in the conformational stability of cyt c in the presence of the chaotropic salts. A positive correlation between the stability, ΔG, of cyt c and the apparent pK _a values that characterize the alkaline transition indicates the presence of a thermodynamic linkage between these conformational transitions. In addition, the rate constant of the cyanide binding and the partial molar entropies of anions negatively correlate with the pK _a values. This indicates the important role of anion-induced solvent reorganization on the structural flexibility of cyt c in the alkaline transitions. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Hemoglobins with multiple reactive sulphydryl groups: The reaction of pigeon hemoglobin with 5,5′-dithiobis (2-nitrobenzoic acid)

Pigeon hemoglobin has eight reactive sulphydryl groups per (tetramer) molecule, as determined by Boyer titration with p-chloromercuribenzoate. However, only four of these are titra-table with 5,5′-dithiobis(2-nitrobenzoate) under the same experimental conditions. The time course of the reaction of pigeon hemoglobin with 5,5′-dithiobis(2-nitrobenzoate) is biphasic. In thepH range 6–9, the fast phase is between one and two orders of magnitude faster than the slow phase. For the fast phase,k _app, the apparent second-order rate constant, increases monotonously withpH. Quantitative analysis reveals that the reactionof the sulphydryl group responsible for this phase is coupled to the ionization of two groups with pK _a values of 6.15±0.1 and 8.5±0.1. These pK _a values are assigned to HisHC3(146)β and to the CysF9(93)β sulphydryl group, respectively. For the slow phase thek _app vs.pH profiles are bowl-shaped. Analysis reveals that the reaction of the sulphydryl group to which this phase may be attributed is coupled to the ionization of two groups with mean pK _a values of 6.53±0.1 and 8.25±0.1. Examination of the structure of hemoglobin allows us to assign these values to HisG19(117)β and CysB5(23)β, respectively. The CysB5(23)β sulphydryl is in the region of the molecule where amino acid substitutions have been found to give rise to significant changes in the oxygen affinity of hemoglobin [Huanget al. (1990),Biochemistry 29, 7020–7023.     

Solvent isotope effects on α-glucosidase

The solvent kinetic isotope effects (SKIE) on the yeast α-glucosidase-catalyzed hydrolysis of p-nitrophenyl and methyl-d-glucopyranoside were measured at 25 °C. With p-nitrophenyl-d-glucopyranoside (pNPG), the dependence of k_cat/K_m on pH (pD) revealed an unusually large (for glycohydrolases) solvent isotope effect on the pL-independent second-order rate constant, ^DOD(k_cat/K_m), of 1.9 (±0.3). The two pK_as characterizing the pH profile were increased in D₂O. The shift in pK_a2 of 0.6 units is typical of acids of comparable acidity (pK_a=6.5), but the increase in pK_a1 (=5.7) of 0.1 unit in going from H₂O to D₂O is unusually small. The initial velocities show substrate inhibition (K_is/K_m～200) with a small solvent isotope effect on the inhibition constant [^DODK_is=1.1 (±0.2)]. The solvent equilibrium isotope effects on the K_is for the competitive inhibitors d-glucose and α-methyl d-glucoside are somewhat higher [^DODK_i=1.5 (±0.1)]. Methyl glucoside is much less reactive than pNPG, with k_cat 230 times lower and k_cat/K_m 5×10⁴ times lower. The solvent isotope effect on k_cat for this substrate [=1.11 (±0. 02)] is lower than that for pNPG [=1.67 (±0.07)], consistent with more extensive proton transfer in the transition state for the deglucosylation step than for the glucosylation step.     

Specific modification of gastric K+-stimulated ATPase activity by thimerosal

Treatment of hog gastric microsomes with the sulfhydryl reagent, thimerosal (ethylmercurithiosalicylate), produced differential effects on the K⁺-ATPase and the K⁺-stimulated p-nitrophenylphosphatase activities. For example, exposure to 2 mM thimerosal for 3 min severely reduced the activity of K⁺-stimulated ATPase, while K⁺-p-nitrophenylphosphatase activity was enhanced 2- to 3-fold. Higher concentration of thimerosal, or longer incubation times, also led to inhibition of K⁺-p-nitrophenylphosphatase. The activated state of p-nitrophenylphosphatase could be sustained by a 20-fold, or greater, dilution of treated membranes, and could be reversed by reduction of membrane SH groups by exogenous thiols. Significant activation of K⁺-p-nitrophenylphosphatase was not produced by p-chloromercuribenzene sulfonate, p-chloromercuribenzoate or mersalyl; however, ethyl mercuric chloride had qualitatively similar activity effects as thimerosal. Kinetics of K⁺-p-nitrophenylphosphatase for thimerosal-treated membranes were altered as follows: V increased; K_m for p-nitrophenylphosphate unchanged for K_a for K⁺ increased. ATP, which is a potent inhibitor of K⁺-p-nitrophenylphosphatase activity in native membranes (K_I ≈ 200 μM). These data suggest that there are multiple SH groups which differentially influence the gastric K⁺-stimulated ATPase activity. Defined treatments with thimerosal are interpreted as an uncoupling of the K⁺-stimulated phosphatase component of the enzyme (for which p-nitrophenylphosphatase is a presumed model reaction). Such differential modifications can be usefully applied to the study of partial reactions of the enzyme and their specific role in the related H⁺-transport reaction.     

The reactive tyrosine residue of human serum albumin: characterization of its reaction with diisopropylfluorophosphate.

The rapid reaction of diisopropylfluorophosphate with a tyrosine residue of human serum albumin at 0.02 m ionic strength involves prior rapid reversible binding characterized by a dissociation constant of 3.6 × 10^?3m and an apparent pK_a of 8.3. The rapid reaction of p-nitrophenyl acetate with human serum albumin (G. E. Means and M. L. Bender, 1975, Biochemistry14, 4989–4994) appears to involve the same tyrosine residue and is thus stoichiometrically inhibited by prior reaction with diisopropylfluorophosphate. Both reactions are strongly inhibited by decanoate anion, strongly retarded at higher ionic strength, and reflect strong rapidly reversible binding and abnormally low tyrosine pK_a values. This reactive tyrosine residue thus appears to be located in a primary binding site for small apolar anions and to be closely associated with several cationic groups.     

Structure–activity relationships for 4-anilinoquinoline derivatives as inhibitors of the DNA methyltransferase enzyme DNMT1

A series of 4-anilinoquinoline derivatives related to the known inhibitor SGI-1027, containing side chains of varying pK_a, were prepared by acid-catalysed coupling of the pre-formed side chains with 4-chloroquinolines. The compounds were evaluated for their ability to reduce the level of DNMT1 protein in HCT116 human colon carcinoma cells by Western blotting. With a very strongly basic N-methylpyridinium side chain, only NHCO-linked compounds were effective, whereas less strongly basic ((diaminomethylene)hydrazono)ethyl or 3-methylpyrimidine-2,4-diamine side chains allowed both NHCO- and CONH-linked compounds to show activity. In contrast, the pK_a of the quinoline unit had little apparent influence on activity.     

Kinetics of cyanide binding to chloroperoxidase in the presence of nitrate: detection of the influence of a heme-linked acid group by shift in the appa

The kinetics of the binding of cyanide to ferric chloroperoxidase have been studied at 25°C and ionic strength 0.11 M using a stopped-flow apparatus. The dissociation constant (K_CN) of the peroxidase-cyanide complex and both forward (k₊) and reverse (k_?) rate constants are independent of the H⁺ concentration over the pH range 2.7 to 7.1. The values obtained are k_cn = (9.5 ± 1.0) × 10^-5 M, k₊. = (5.2 ± 0.5) × 10⁴ M^?1 sec^?1 and k_- = (5.0± 1.4) sec^-1. In the presence of 0 06 M potassium nitrate the affinity of cyanide for chloroperoxidase decreases due to the inhibition of the forward reaction. The dissociation rate is not affected. The nitrate anion exerts its influence by binding to a protonated form of the enzyme, whereas the cyanide binds to the unprotonated form. Binding of nitrate results in an apparent shift towards higher pK_a values of the ionization of a crucial heme-linked acid group. Hence the influence of this group can be detected in the accessible pH range. Extrapolation to zero nitrate concentration yields a value of 3.1±0.3 for the pK_a of the heme-linked acid group.     

Functional tuning of the catalytic residue pKa in a de novo designed esterase

AlleyCatE is a de novo designed esterase that can be allosterically regulated by calcium ions. This artificial enzyme has been shown to hydrolyze p‐nitrophenyl acetate (pNPA) and 4‐nitrophenyl‐(2‐phenyl)‐propanoate (pNPP) with high catalytic efficiency. AlleyCatE was created by introducing a single‐histidine residue (His¹⁴⁴) into a hydrophobic pocket of calmodulin. In this work, we explore the determinants of catalytic properties of AlleyCatE. We obtained the pK_a value of the catalytic histidine using experimental measurements by NMR and pH rate profile and compared these values to those predicted from electrostatics pK_a calculations (from both empirical and continuum electrostatics calculations). Surprisingly, the pK_a value of the catalytic histidine inside the hydrophobic pocket of calmodulin is elevated as compared to the model compound pK_a value of this residue in water. We determined that a short‐range favorable interaction with Glu¹²⁷ contributes to the elevated pK_a of His¹⁴⁴. We have rationally modulated local electrostatic potential in AlleyCatE to decrease the pK_a of its active nucleophile, His¹⁴⁴, by 0.7 units. As a direct result of the decrease in the His¹⁴⁴ pK_a value, catalytic efficiency of the enzyme increased by 45% at pH 6. This work shows that a series of simple NMR experiments that can be performed using low field spectrometers, combined with straightforward computational analysis, provide rapid and accurate guidance to rationally improve catalytic efficiency of histidine‐promoted catalysis. Proteins 2017; 85:1656–1665. © 2017 Wiley Periodicals, Inc.     

Differentiation of various types of biological oxidation of nitrogen in organic compounds

The various types of nitrogen which occur in organic compounds and which are susceptible to biological oxidation are clearly divided into groups depending upon the pK_a, of the constituent nitrogen. The enzymatic processes which give rise to the N-oxidation products are reviewed by a consideration of species differences, age of animal, pH optima, influence of inducing agents, inhibitors and microsomal pretreatments, as well as the stereochemistry of the nitrogen atom.From the data collected, a concept is developed which suggests that all basic amines (group I) are oxidised by a flavine adenine nucleotide (FAD)-dependent enzyme system, whereas non-basic nitrogen-containing compounds (group III) are oxidised by a cytochrome P450-dependent system.It is further suggested that compounds of intermediary pK_a,i.e. between 1 and 7 (group II), may be substrates for both enzyme systems, which would yield the same products, but by different processes. The extent to which N-oxidation occurs in a species would therefore depend on the pK_a of the substrate and the amounts and ratio of the two enzymes present, a lower pK_a favouring oxidation by the cytochrome P450 system and a higher pK_a favouring oxidation by the FAD system.In a similar manner, it is suggested that the oxidation of aromatic heterocyclic amines depends upon the pK_a of the nitrogen, compounds having a low pK_a being preferentially metabolised by nitrogen oxidation.     

Mechanism of action of α-galactosidase

The effect ofpH on K_m and V_max values of coconut α-galactosidase indicates the involvement of two ionizing groups with pK_a values of 3.5 and 6.5 in catalysis. Chemical modification has indicated the presence of two carboxyl groups, a tryptophan and a tyrosine, at or near the active site of α-galactosidase. Based on these facts a new mechanism of action for α-galactosidase is proposed in which the ionizing group with a pK_a of 3.5 is a carboxyl group involved in stabilizing a carbonium ion intermediate and the ionizing group with a pK_a of 6.5 is a carboxyl group perturbed due to the presence of a hydrophobic residues in its vicinity which donates a H⁺ ion in catalysis.     

Kinetics of interaction of some α- and β-D-monosaccharides with concanavalin A

The rates of formation and dissociation of concanavalin A with some 4-methylumbelliferyl and p-nitrophenyl derivatives of α- and β-D-mannopyranosides and glucopyranosides were measured by fluorescence and spectral stopped-flow methods. All process examined were uniphasic. The second-order formation rate constants varied only from 6.8 · 10⁴ to 12.8 · 10⁴ M^?. s^?1, whereas the first-order dissociation rate constants ranged from 4.1. to 220 s^?1, all at ph 5.0, I = 0.3 M, and 25°C. Dissociation rates thus controlled the value of binding constant. The effect of temperature on these reactions was examined, from which enthalpies and entropies of activation and of reaction could be calculated. The effects of pH at 25°C on the reaction rates of 4-methylumbelliferyl α-D-mannopyranoside and 4-methylumbelliferyl α-D-glucopyranoside with concanavalin A were examined. The value of the binding constant K_ap (derived from the kinetics) at any pH could be related to the intrinsic binding constant K by the expression K_ap = K_aK(K_a + [H⁺])^?1. The values of K_a, the ionization constant of the protein segment responsive to sugar binding, were 3 · 10^?4 M and 1 · 10^?4 M for 4-methylumbelliferyl α-D-mannopyranoside and 4-methylumbelliferyl α-D-glucopyranoside, respectively. The binding constant of p-nitrophenyl α-D-mannopyranoside is surprisingly much less sensitive to a pH change from 5.0 to 2.7. Ionic strength had little effect on the binding characteristics of 4-methylumbelliferyl α-D-mannopyranoside to concanavalin A at pH 5.2 and 25°C.     

Hemin-mediated para-hydroxylation of aniline: A potential model for oxygen activation and insertion reactions of mixed function oxidases

The activation of molecular oxygen by alkaline hemin (ferriprotoporphyrin IX) has been studied. In the presence of reductant nicotineamide adenine dinucleotide (NADH) or nicotineamide adenine dinucleotide phosphate (NADPH) and organic substrate, aniline, hemin activates oxygen to the hydroperoxide anion (HO₂^?) and subsequently mediates insertion of active oxygen into the benzene ring of the substrate to form p-aminophenol, with a high degree of regiospecificity. Oxygen activation does not occur in the absence of aniline. Stoichiometry of the reaction indicates that two electrons are required per molecule of oxygen activated or atom of oxygen inserted into the substrate aromatic ring system. Direct measurements of H₂O₂ and of the pK_a for maximum rate of p-aminophenol formation (11.7 ± 0.1) indicate participation of the hydroperoxide anion as the active oxygen species in the rate-determining step of the insertion reaction. Powerful scavengers of the hydroxyl radical (OH′) have little effect on the formation of H₂O₂ or p-aminophenol by the system. Superoxide dismutase (10^?7 mol dm^?3) inhibited both p-aminophenol and H₂O₂ formation, when added to the system immediately prior to initiation of the reaction. Studies involving N-phenylhydroxylamine indicate that aromatic ring hydroxylation is occurring directly and not by rearrangement of an N-hydroxylated intermediate. Implications of hemin-mediated hydroxylation reactions for those of enzymatic mixed function oxidase activity are discussed.     

How enzymes harness highly unfavorable proton transfer reactions

Acid–base reactions that are exceedingly unfavorable under standard conditions can be catalytically important at enzyme active sites. For example, in triose phosphate isomerase, a glutamate side chain (nominal pK _a ≈ 4 in solution) can in fact deprotonate a CH group that is vicinal to a carbonyl (pK _a ≈ 18 in solution). This is true because of three distinct interactions: (a) ground state pK _a shifts due to environment polarity and electrostatics; (b) dramatic increases in effective molarity due to optimization of proximity and orientation; and (c) transition state pK _a shifts due to binding interactions and the formation of strong low barrier hydrogen bonds. In this report, we review the literature showing that the sum of these three effects supplies more than enough free energy to push forward proton transfer reactions that under standard conditions are exceedingly nonspontaneous and slow.     

Metal ion-biomolecule interactions. II. Methylmercuration of the deprotonated amino groups in adenine,guanine, and cytosine derivatives,and its relationship to amino group acidity

Proton nmr spectroscopic evidence is presented for methylmercury(II) binding to the deprotonated amino groups in adenosine, 9-methyladenine, guanosine, 1-methylguanosine, and cytidine under basic conditions. Except for the guanosine case, ¹H nmr spectra of the products from aqueous or ethanolic 1:1 mixtures of substrate and MeHgOH are consistent with methylmercuration of the deprotonated amino groups. Guanosine undergoes initial binding of MeHg to N₁, and a second equivalent of MeHgOH is necessary to effect amino binding. The nmr spectra of the complexed adenine derivatives suggest that different geometrical isomers exist in (CD₃)₂SO solution, reflecting the partial double bond character of the C₆N bond in these systems. Using a correlation relating the magnitude of the ¹⁹⁹Hg-¹H coupling constant (J) for MeHg-ligand complexes with the ligand pK_a (J = ?3.88 pK_a + 248.5, extending over 13 pK units, based on a variety of N and O donor ligands), estimates (± 0.3 pK unit) of the pK_as of the amino groups of the above substrates have been made. In this way, pK_a values of 15.5 (cytidine), 17.0 (adenosine and 9-methyladenine), 15.1 (guanosine), and 14.9 (1-methylguanosine) are obtained. In the cases where comparisons with literature pK_a data can be made, good agreement is found.