Electrostatic contributions to the stability of the GCN4 leucine zipper structure

Ion pairs are ubiquitous in X-ray structures of coiled coils, and mutagenesis of charged residues can result in large stability losses. By contrast, pK_a values determined by NMR in solution often predict only small contributions to stability from charge interactions. To help reconcile these results we used triple-resonance NMR to determine pK_a values for all groups that ionize between pH 1 and 13 in the 33 residue leucine zipper fragment, GCN4p. In addition to the native state we also determined comprehensive pK_a values for two models of the GCN4p denatured state: the protein in 6 M urea, and unfolded peptide fragments of the protein in water. Only residues that form ion pairs in multiple X-ray structures of GCN4p gave large pK_a differences between the native and denatured states. Moreover, electrostatic contributions to stability were not equivalent for oppositely charged partners in ion pairs, suggesting that the interactions between a charge and its environment are as important as those within the ion pair. The pH dependence of protein stability calculated from NMR-derived pK_a values agreed with the stability profile measured from equilibrium urea-unfolding experiments as a function of pH. The stability profile was also reproduced with structure-based continuum electrostatic calculations, although contributions to stability were overestimated at the extremes of pH. We consider potential sources of errors in the calculations, and how pK_a predictions could be improved. Our results show that although hydrophobic packing and hydrogen bonding have dominant roles, electrostatic interactions also make significant contributions to the stability of the coiled coil.     

Reactions of the amino groups of RNAse A: III. The existence of pH-dependent values of pK

The rates of the trinitrophenylation of the amino groups of ribonuclease A (RNAse) with the specific reagent trinitrobenzene sulfonic acid have been studied at 27°C, between pH 7.0 and 9.9. From the variation of the velocity constants with pH it has been shown that the reaction is biphasic in the sense that for each amino group two pKs have been found: one (pK = 7.3–7.52) in the range of pH between 7.0 and 8.3 and the other (pK = 9.28–9.69) in the pH range 8.5–9.9. It is pointed out that when the experimental conditions approached one another, there was agreement between the pK values obtained from titrimetric and kinetic studies. Evidence is presented from the literature concerning the validity of the pK value near 7.5 for the ε-amino groups in RNAse. The studies were repeated with performic acid oxidized RNAse and the 10 ε-amino groups were found to be monophasic with pK values between 8.01 and 8.10. The α-amino group of the N-terminal lysine was biphasic with a pK of 7.26 (pH range 7–8) and 8.13 (pH range 8.2–9.5).     

A physical difference between the fast- and slow-refolding forms of nitrotyrosyl ribonuclease A: the pK values of the nitrotyrosyl groups.

In the preceding paper we present kinetic evidence for a slow equilibrium between two conformational forms of heat-unfolded ribonuclease A whose rates of refolding differ 100-fold. In a search for physical differences between these two forms, we undertook a study of the pK changes during refolding of a specific set of freely ionizing surface groups. By use of a standard procedure the three freely ionizing tyrosine groups (pK ∼- 10) have been nitrated by tetranitromethane, yielding three nitrotyrosine groups (pK ∼- 6.8). Nitrotyrosyl ribonuclease A closely resembles the unmodified enzyme as regards: (1) enzymatic activity; (2) thermal unfolding transition at neutral pH; and (3) kinetics of refolding. In particular, stopped-flow measurements of 2′CMP binding during refolding show that the fast-refolding reaction is unchanged by nitration and yields fully folded enzyme able to bind 2′CMP.The pK change of the nitrotyrosyl groups upon refolding is quite different in the fast- and slow-refolding reactions. In the slow reaction it is small (− 0.046 ± 0.006 pH unit) but easily measureable, whereas in the fast-reaction it is too small to be detected (− ΔpK less than 0.02 pH unit). This difference in pK change upon refolding can be attributed to different pK values of the nitrotyrosyl groups in the slow-refolding and fast-refolding forms of the heat-unfolded protein. Presumably the same structural differences between these two heat-unfolded forms are responsible both for the pK difference and for the 100-fold difference in rates of refolding.These results support the simple three-species mechanism for refolding discussed in the preceding paper. (a) They demonstrate a physical difference between the fast- and slow-refolding species. (b) They do not show any additional kinetic complexity when refolding is measured by a property that distinguishes between the fast- and slow-refolding species.     

Conditionally lethal mutants of bacteriophage T4 defective in production of a transfer RNA

The two buried carboxyls (Asp-102 and Asp-194) in both chymotrypsin and chymotrypsinogen are ionized at pH values greater than 4.2 and may be ionized even as low as pH 3.This was demonstrated by coupling most of the surface carboxyis of the proteins by a carbodi-imide with glycinamide or semicarbazide to diminish the groups ionizing at low pH and then titrating the proton uptake on denaturation by sodium dodecyl sulphate between pH 3.0 and 4.6. At pH values greater than 4.2 all unblocked carboxyls are ionized. The proton uptake during the conformational change on denaturation was determined by a stopped-flow procedure and found to be about 2H⁺/mol between pH 3.0 and 3.6. The rate constant for the uptake of protons is the same as that for the exposure of tryptophan and lies in the tens of millisecond region.The buried negative charge at the active site appears to be mainly on Asp-102 rather than on His-57, the pK_a of which must be raised by the buried charge. This enhances its efficacy as a base catalyst in the “charge relay system”.The presence of an intact charge relay system in the inactive zymogen illustrates the importance of stereochemical fit between enzyme and substrate. Enzyme catalysis could hardly be mediated by a catalyst which is uniquely reactive in the absence of correct enzyme-substrate orientation as this would be inconsistent with its specificity.     

Glycine transport by hemolysed and restored pigeon red cells effects of a domnan-induced electrical potential on entry and exit kinetics

The influence of a Donnan effect on the transport of glycine by hemolysed and restored pigeon red cells was examined. The Donnan effect was produced by replacing Cl^? with 2,4-toluenedisulfonate or glutamate. The effects of the associated membrane potential and inside-outside pH difference on glycine entry and exit rates were examined. The effects of pH on entry and exit rates in the absence of a Donnan effect were also examined.In the absence of a Donnan effect, Na⁺-dependent glycine entry requires the protonated form of a group with a pK_app of 7.9 and the depronated form of another group with a pK_app of 6.8. Neither of these are required for exit but the deprotonated form of a group(s) with a pK_app of 6.2 is required. The pK 7.9 group and pK 6.2 group probably react with H⁺ at the inner face of the membrane and the pK 6.8 group probably reacts at the outer face.The V for glycine entry was determined for cells with their Cl^? largely replaced by toluenedisulfonate and without such replacement. Between pH 6.1 and 7, the ratio of the respective V values, V_T/V_Cl, was 1.5–1.7. V_T/V_Cl rose above pH 7 to near 4 at pH 8.3. At pH 6.9, with glutamate replacing cell Cl^?, the analogous ratio (V_Glu/V_Cl) was 1.7. The increase of V_T/V_Cl above pH 7 could be quantitatively accounted for by the increase in cell [H⁺]/medium [H⁺] caused by the Donnan effect together with the assumption that the pK 7.9 group reacts with H⁺ at the inner face of the membrane.When cell Cl^? was replaced by toluenedisulfonate or glutamate there was a drop in the term in the glycine K_m describing Na⁺ dependence of glycine entry. When cell Cl^? was replaced by toluenedisulfonate there was a rise in the Na⁺-independent term in the glycine entry K_m. By replacing varying amounts of cell Cl^? with either toluenedisulfonate or glutamate, plots were obtained of entry rates vs. the cell [Cl^?]/medium [Cl^?] ratio consistent with the assumption that the Donnan-induced membrane potential acts on a “moving” charge. Glycine exit was only slightly accelerated by trans-toluenedisulfonate. The ratio, exit rate into toluenedisulfonate medium/exit rate into Cl^? medium rose with decreasing pH. This rise could be accounted for by a Donnan-induced inside-outside pH difference which affects a pK_app 6.2 group reacting with internal H⁺.The observed influences of the Donnan effect on V(glycine entry), on both components of K_m(glycine entry), on the shape of the plot of glycine entry rate vs. the cell [Cl^?]/medium [Cl^?] ratio and on glycine exit all fit the assumptions that when the empty porter reorients, one unit of negative charge accompanies it “across” the membrane and that no other steps involve charge movement.The properties of the system seem inconsistent with a translational (“ferry boar”) mobile carrier.     

pK determinations via pH-mobility curves obtained by isoelectric focusing-electrophoresis: Theory and experimental verification

Basic equations have been derived linking the electrophoretic migration in a stationary pH gradient of simple, singly charged cations or anions and of mono- mono- valent ampholytes with the pKs of their ionizable groups. In the case of diprotic ampholytes, an equation and a curve are described calculating a correction factor to be applied to the mobility measurements, accounting for the influence of the opposite charge species on the mobility curve of the ion being measured. This correction factor is a function of ΔpK and increases exponentially with decreasing values of ΔpK. These theoretical considerations have been experimentally verified by running pH-mobility curves of colored compounds, such as methyl red, neutral red and dexorubicin. The pKs thus measured were in excellent agreement with the pKs obtained independently by spectrophotometric titrations.     

Isocitrate lyase from Neurospora crassa: pH dependence of catalysis and interaction with substrates and inhibitors.

The maximal velocity, V, for isocitrate cleavage by isocitrate lyase from Neurospora crassa is dependent on two dissociable groups with pK_a values of 6.1 and 8.6. A dissociable group with a pK_a of 8.5 on the enzyme-substrate complex affects the pK_m for isocitrate. The pK_i for homoisocitrate is affected in a like manner. The pH dependence of the pK_i's for succinate, a product of isocitrate cleavage, and the succinate analog maleate is similar to the pH dependence of the pK_m of isocitrate below pH 7.3, but is markedly different above this pH. Both the K_m for isocitrate and the K_i for succinate were dependent upon Mg²⁺ concentration. The pK_i for oxalate, an analog of glyoxylate which is also a product of isocitrate cleavage, is dependent on a group with a pK_a of 6.8 on the enzyme-inhibitor complex. The pH dependence of the pK_i for phosphoenolpyruvate, which binds to the succinate site, suggests that it is dependent on two dissociable groups, one on phosphoenolpyruvate and one, by analogy to the pK_m for isocitrate, on the enzyme-glyoxylate-inhibitor complex.     

Determination of proton dissociation constants by ion-exchange high-performance liquid chromatography

The common methods to determine dissociation constants of solutes, e.g., uv spectrophotometry, potentiometry, and conductimetry, are accurate but require at least 1 nmol of compound. High-performance liquid chromatography (HPLC) allows 1 pmol of a uv-absorbing compound to be detected. By adjusting the polarity of the mobile phase, reverse and normalphase properties of an ion-exchanger can be minimized, resulting in a high correlation between charge and retardation of the solute. Thus, the degree of ionization of several compounds was monitored in mobile-phase compositions of different pH values using cation exchange. The pK values of several pterin derivatives corresponded to those obtained by other methods. In addition, pK values of two unidentified pterin derivatives were determined, using only 20 pmol of each.     

Isoelectric focusing in immobilized pH gradients: Generation of extended pH intervals

A new technique for generatiing extended pH gradients (3–4 pH units) in Immobiline gels for isoelectric separations is described. A five-chamber gradient mixer has been built, based on the ‘Varigard’-type mixers of Peterson and Sober (Anal. Chem. 31, 1959, 857–862). Each chamber contains one of the following Immobilines, in this order: pK values 4.4, 4.6, 6.2, 7.0 and 8.5, titrated in the pH 4–8 interval with non-buffering Immobilines pK 9.3 (in the case of the two acidic Immobilines) and pK 3.6 (in the case of the three basic Immobilines). In this way it is possible to cast, in a highly reproducible way, an immobilized pH gradient in thepH range 4.0 to 7.5, which should be ideal for isoelectric separations in the first dimension of two-dimensional techniques. A computer program is also described which, given the molarities and pK values of the different Immobilines in the chambers of the Varigrad mixer, can generate the theoretical pH profile, together with the buffering capacity (β) and ionic strength (I) courses.     

One-electron reduction of adriamycin: Properties of the semiquinone

Pulse radiolysis of aqueous solutions containing adriamycin and redox indicators of known one-electron reduction potential (E¹) shows that its E¹ at pH 7 is ?328 mV (vs NHE). The variation E¹ with pH in the range 6–12 shows that the net charge on the semiquinone at pH 7 is zero. As well as the pK_a values of 2.9 and ≥ 14 established independently, the semiquinone has a pK_a close to 9.2. The new data enable the structure and likely reactivity of the semiquinone to be specified.     

Surface charges on chloroplast membranes as studied by particle electrophoresis

1. Particle microelectrophoresis mobility studies have been conducted with chloroplast thylakoid membranes and with isolated intact chloroplasts.2. The pH dependence of the electrophoretic mobility indicated that at pH values above 4.3 both membrane systems carry a net negative charge.3. Chemical treatment of thylakoids has shown that neither the sugar residues of the galactolipids in the membrane nor the basic groups of the membrane proteins having pK values between 6 and 10 are exposed at the surface.4. However, treatment with 1-ethyl-3(3-dimethylaminopropyl)carbodiimide, together with glycine methyl ester, neutralized the negative charges on the thylakoid membrane surface indicating the involvement of carboxyl groups which, because of their pH sensitivity, are likely to be the carboxyl groups of aspartic and glutamic acid residues.5. The nature of the protein giving rise to the negative surface charges on the thylakoids is not known but is shown not to involve the coupling factor or the light harvesting $\text{chlorophyl}\text{a}\text{chlorophyll}\text{b}\text{pigment · protein complex}$.6. No significant effect of light was observed on the electrophoretic mobility of either thylakoids or intact chloroplasts.7. The striking difference in the ability of divalent and monovalent cations to screen the surface charges was demonstrated and explained in terms of the Gouy-Chapman theory.8. Calculations of the ζ-potentials for thylakoid membranes gave values for the charge density at the plane of shear to be in the region of one electronic charge per 1500–2000 Ų.9. The significance of the results is discussed in terms of cation distribution in chloroplasts and the effect of cations on photosynthetic phenomena.     

Ionization behavior of proteins. I. Spectral titration of the tyrosyl groups of chymotrypsinogen and nitrated-chymotrypsinogen

The ionization constants of the tyrosyl groups of chymotrypsinogen and of nitrated-chymotrypsinogen (two tyrosyl residues nitrated) have been determined by difference spectrophotometry. In chymotrypsinogen, two of the four tyrosyl groups ionize without any time dependence. Above pH greater than ca. 12.5, time-dependent spectral changes are seen for 0.7 group equivalent. The data can be fitted to the values of pK′₁ 9.75 ± 0.07, pK′₂ 11.55 ± 0.05, pK′₃ 13.30 ± 0.05. In nitrated-chymotrypsinogen, the two nitrated tyrosyl residues have pK′₁ 6.44 and pK′₂ 8.30. For both proteins, these pK′ values are in agreement with those evaluated from potentiometric titration and calorimetric data using computer-assisted curve-fitting analysis.     

Protein Ionizable Groups: pK Values and Their Contribution to Protein Stability and Solubility

The structure, stability, solubility, and function of proteins depend on their net charge and on the ionization state of the individual residues. Consequently, biochemists are interested in the pK values of the ionizable groups in proteins and how these pK values depend on their environment. We review what has been learned about pK values of ionizable groups in proteins from experimental studies and discuss the important contributions they make to protein stability and solubility.     

pH Variation of midpoint potential for three photosynthetic bacterial cytochromes c′. A link between physical and functional properties

Midpoint redox potential (E_M) versus pH curves are reported over the pH range 5 to 10 for the cytochromes c′ from three species of purple photosynthetic bacteria: Rhodospirillum rubrum, Rhodopseudomonas palustris and Chromatium vinosum. In each case, theoretical curves are fitted to the data and pK values for the reduced (pH 5–5.5) and oxidized (pH 8–8.5) forms of the protein are found to influence the midpoint redox potentials. The oxidized form pK values in each case are found to correlate with previously determined pK values for variation in physical and/or spectroscopic properties. This correlation of functional and physical observables is discussed in terms of a possible mechanism of control of midpoint redox potential through heme iron-ligand bonding as moderated by the protein conformation in response to solution conditions. The reduced form pK values are discussed in terms of a mechanism which would alter the polarity of the heme environment, thereby influencing redox potentials.     

Reactions of the amino groups in ribonuclease A: II. Identification of reactive amino groups in ribonuclease

Ribonuclease A has been trinitrophenylated to varying degrees by reaction with trinitrobenzenesulfonic acid. The reactive amino groups were identified by use of the peptides obtained from the oxidized TNP-RNase by tryptic and chymotryptic hydrolysis. From a quantitative study of the TNP-peptides it was possible to associate each amino group with values of pK_ma. It was shown that the lys-41 amino group had a pK_a of 9.03 in TEA buffer. The pK_a values of all of the other amino groups were dependent on the nature of the buffer (triethanolamine and phosphate) and on the pH.     

Modification of (Na+ + K+)-dependent ATPase by fluorescein isothiocyanate: evidence for the involvement of different amino groups at different PH values

Fluorescein isothiocyanate (FITC) reactivity with the (Na⁺ + K⁺)-ATPase was studied at pH 6.5 and 9.0. Reaction with FITC is nearly complete in 30 min and is irreversible at both pH values. Differential inhibition of enzyme activity is observed at the two pH values as follows: at pH 6.5 the maximal inhibition reached is only 35–45% of the ATPase or p-nitrophenylphosphatase activities, whereas at pH 9.0 ATPase activity can be completely inhibited while maximal phosphatase inhibition is ca. 50%. At all concentrations of FITC tested, more FITC is incorporated into the enzyme at pH 9.0 than at 6.5. At both pH values NaCl increases the inhibition due to FITC while KCl protects against the inhibition. ATP protects the enzyme at both pH values with a K_0.5 in the range of 8–20 μm. Enzyme that is partially inactivated at either pH shows no significant change in the K_0.5 values for Na⁺ or K⁺ or in the K_{m app} for ATP or p-nitrophenylphosphate for the remaining activity. The binding of ⁴⁸VO₄ is not changed by reaction with FITC at either pH, while [³H]ouabain binding is inhibited after reaction at pH 9.0 only in the presence of Mg⁺² + Na⁺ + ATP. [³H]Ouabain binding in the presence of Mg⁺² + inorganic phosphate is not inhibited by FITC reaction. Enzyme reacted at both pH values exhibits the expected fluorescein fluorescence (λ_ex = 490, λ_em = 520) but only with enzyme reacted at pH 9.0 is fluorescence quenching by K⁺ or reversal by Na⁺ observed. These results suggest that different classes of amino groups react with FITC at the two pH values tested, and that these groups have distinct roles in the different activities of the enzyme.     

Effects of 2,4-substituents of deuteropheme upon redox potentials of horseradish peroxidases.

The effects of pH on redox potentials of horseradish peroxidase-A and -(B + C) and of their heme-substituted enzymes with mesoheme, deuteroheme, chlorocruoroheme, and diacetyldeuteroheme were investigated. The slope in the plot of E_o against pK₃ (a measure of basicity of pyrrole nitrogen) was found to be close upon 59 $\text{mV}\text{p}\text{K}{}_3$ unit. It was also found that the ratio of ΔpK_r to ΔpK₃ was about 0.1 while that of ΔpK_o to ΔpK₃ was almost unity. Here, K_r and K_o stand for heme-linked proton dissociation constants in the ferrous and ferric peroxidases, respectively. The difference of either pK_r or pK_o between two isoenzyme preparations was about 1.6. These results support the previous conclusion (Arch. Biochem. Biophys. 165, 725, 1974 that K_r represents a proton dissociation constant of a distal amino acid residue and that there is a strong hydrogen bonding between its base and the water oxygen atom as a sixth ligand in the ferric state of peroxidases. The difference of redox potentials at pH 8.5 between two natural isoenzyme preparations, amounting to 88 mV, was attributed to the change in the hydrogen bonding strength caused by the difference in basicity of two distal amino acid residues. A possibility that approximate redox potentials of hemoproteins can be determined by analysis of several factors is discussed.     

Carboxyl pKa Values and Acid Denaturation of BBL

The protein BBL undergoes structural transitions and acid denaturation between pH 1.2 and 8.0. Using NMR spectroscopy, we measured the pK_a values of all the carboxylic residues in this pH range. We employed ¹³C direct-detection two-dimensional IPAP (in-phase antiphase) CACO NMR spectroscopy to monitor the ionization state of different carboxylic groups and demonstrated its advantages over other NMR techniques in measuring pK_a values of carboxylic residues. The two residues Glu161 and Asp162 had significantly lowered pK_a values, showing that these residues are involved in a network of stabilizing electrostatic interactions, as is His166. The other carboxylates had unperturbed values. The pH dependence of the free energy of denaturation was described quantitatively by the ionizations of those three residues of perturbed pK_a, and, using thermodynamic cycles, we could calculate their pK_as in the native and denatured states as well as the equilibrium constants for denaturation of the different protonation states. We also measured ¹³C^α chemical shifts of individual residues as a function of pH. These shifts sense structural transitions rather than ionizations, and they titrated with pH consistent with the change in equilibrium constant for denaturation. Kinetic measurements of the folding of BBL E161Q indicated that, at pH 7, the stabilizing interactions with Glu161 are formed mainly in the transition state. We also found that local interactions still exist in the acid-denatured state of BBL, which attenuate somewhat the flexibility of the acid-denatured state.     

Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding

This work investigates statistical prevalence and overall physical origins of changes in charge states of receptor proteins upon ligand binding. These changes are explored as a function of the ligand type (small molecule, protein, and nucleic acid), and distance from the binding region. Standard continuum solvent methodology is used to compute, on an equal footing, pK changes upon ligand binding for a total of 5899 ionizable residues in 20 protein-protein, 20 protein-small molecule, and 20 protein-nucleic acid high-resolution complexes. The size of the data set combined with an extensive error and sensitivity analysis allows us to make statistically justified and conservative conclusions: in 60% of all protein-small molecule, 90% of all protein-protein, and 85% of all protein-nucleic acid complexes there exists at least one ionizable residue that changes its charge state upon ligand binding at physiological conditions (pH = 6.5). Considering the most biologically relevant pH range of 4-8, the number of ionizable residues that experience substantial pK changes (ΔpK > 1.0) due to ligand binding is appreciable: on average, 6% of all ionizable residues in protein-small molecule complexes, 9% in protein-protein, and 12% in protein-nucleic acid complexes experience a substantial pK change upon ligand binding. These changes are safely above the statistical false-positive noise level. Most of the changes occur in the immediate binding interface region, where approximately one out of five ionizable residues experiences substantial pK change regardless of the ligand type. However, the physical origins of the change differ between the types: in protein-nucleic acid complexes, the pK values of interface residues are predominantly affected by electrostatic effects, whereas in protein-protein and protein-small molecule complexes, structural changes due to the induced-fit effect play an equally important role. In protein-protein and protein-nucleic acid complexes, there is a statistically significant number of substantial pK perturbations, mostly due to the induced-fit structural changes, in regions far from the binding interface.     

Isocitrate lyase from Pseudomonas indigofera: pH dependence of catalysis and binding of substrates and inhibitors.

The maximal velocity, V, for isocitrate cleavage by isocitrate lysase from Pseudomonas indigofera was dependent on two dissociable groups (pK_a's of 6.9 and 8.6). The pH dependence of the pK_i for succinate, a product of isocitrate cleavage, implied that a dissociable group (pK_a of 6.0) on the enzyme functions in binding succinate. The pK_i's for maleate and itaconate (succinate analogs) were similarly pH dependent. The pK_i for oxalate, an analog of glyoxylate which is also a product of isocitrate cleavage, was pH independent. In contrast the pK_i's of the four-carbon dicarboxylic acid inhibitors, fumarate and meso-tartrate, both of which affect the glyoxylate site, were dependent on a dissociable group on the enzyme-inhibitor complex. Comparison of the pH dependence of the pK_m for isocitrate and the pK_i for succinate (and succinate analogs) indicated that the binding of isocitrate was dependent on an acidic dissociable group on the enzyme (pK_a of 5.8). The pH dependence of the pK_i for homoisocitrate was similar. In addition the K_i for succinate and K_m for isocitrate were dependent upon Mg²⁺ concentration. Inhibition by phosphoenolpyruvate, which binds to the succinate site and may regulate isocitrate lyase from P. indigofera, was twice as pH dependent as that for succinate. Two dissociable groups, one on the enzyme (pK_a of 5.8) and one on phosphoenolpyruvate (pK_a of 6.35), contributed to the pH dependence observed with phosphoenolpyruvate.