pK Alpha Values Research Articles

Influence of sample pH on the conformational backbone dynamics of a pseudotripeptide (H‐Tyr‐TicΨ[CH2‐NH] Phe‐OH) incorporating a reduced peptide bond: An NMR investigation

In the present paper we investigate the influence of sample pH on the conformational and dynamical properties of the pseudotripeptide H-Tyr-Tic psi [CH2-NH]Phe-OH (TIP[psi]; Tic: 1,2,3,4,-tetrahydroisoquinoline-3-carboxylic acid) using various one- and two-dimensional nmr techniques in conjunction with molecular modeling. Studies were conducted at three different pH levels corresponding to the zwitterionic peptide containing a formal positive charge (pH 3.1), the deprotonated molecule (pH 9.1), and a situation at neutral pH (pH 7.2) involving both protonated and deprotonated states of the reduced peptide bond. Analysis of the one-dimensional1H-nmr spectra reveals that in solution TIP[psi] is in slow dynamic exchange between conformations containing cis and trans configurations of the Tyr-Tic bond. An nmr pH dependence study of the cis:trans ratio indicated that the exchange process was governed by the protonation state of the reduced bone amine. From the nmr data, reduced peptide bond pK alpha values of 6.5 and 7.5 were determined for the cis and trans conformers, respectively. It was concluded that conformations containing a trans Tyr-Tic bond are stabilized at low pH by an intramolecular hydrogen bond between the Tyr carbonyl and the reduced peptide bond protonated amine. This observation was corroborated by molecular mechanics investigations that revealed low energy trans structures compatible with nmr structural data, and furthermore, were consistently characterized by the existence of a strong N+ H ... O = C interaction closing a seven-membered cycle. The dynamics of cis-trans isomerization about the Tyr-Tic peptide bond were probed by nmr exchange experiments. The selective presaturation of exchanging resonances carried out at several temperatures between 50 and 70 degrees C allowed the determination of isomerization rate constants as well as thermodynamic activation parameters. delta G not equal to values were in close agreement with the cis-->trans energy barrier found in X-Pro peptide fragments (approximately 83 kJ/mol). A large entropic barrier determined for the trans-->cis conversion of TIP[psi] (5.7 JK-1 mol-1 at pH 3.1;6.5 J K-1 mol-1 at pH 9.1) is discussed in terms of decreased solvent molecular ordering around the conformers possessing a trans Tyr-Tic bond. Evidence that the neutral form of the reduced peptide bond gains rigidity upon protonation was obtained from relaxation measurements in the rotating frame. T1 rho measurements of several protons in the vicinity of the reduced peptide bond were made as a function of spin-lock field.(ABSTRACT TRUNCATED AT 400 WORDS)

Analysis of the Binding of Xenopus Ribosomal Protein L5 to Oocyte 5 S rRNA: THE MAJOR DETERMINANTS OF RECOGNITION ARE LOCATED IN HELIX III-LOOP C

Xenopus ribosomal protein L5 was expressed in Escherichia coli and exhibits high affinity (Kd = 2 nM) and specificity for oocyte 5 S rRNA. The pH dependence of the association constant for the complex reveals an ionization with a pK alpha value of 10.1, indicating that tyrosine and/or lysine residues are important for specific binding of L5 to the RNA. Formation of the L5.5 S rRNA complex is remarkably insensitive to ionic strength, providing evidence that nonelectrostatic interactions make significant contributions to binding. Together, these results suggest that one or more tyrosine residues may form critical contacts through stacking interactions with bases in the RNA. In order to locate recognition elements within 5 S rRNA, we measured binding of L5 to a collection of site-specific mutants. Mutations in the RNA that affected the interaction are confined to the hairpin structure comprised of helix III and loop C. Earlier experiments with a rhodium structural probe had shown that the two-nucleotide bulge in helix III and the intrinsic structure of loop C create sites in the major groove that are opened and accessible to stacking interactions with the metal complex. In the present studies, we detect a correlation between the intercalative binding of the rhodium complex to mutants in the hairpin and binding of L5, supporting the proposal that binding of the protein is mediated, in some part, by stacking interactions. Furthermore, the results from mutagenesis establish that, despite overlapping binding sites on 5 S rRNA, L5 and transcription factor IIIA utilize distinct structural elements for recognition.

Prototropic Control of Intramolecular Electron Transfer in Trimethylamine Dehydrogenase

The pH dependence of static optical/EPR spectra of trimethylamine dehydrogenase reduced to the level of two equivalents (TMADH2eq) has been examined and indicates the existence of three different states for this iron-sulfur flavoprotein. At pH 6, TMADH2eq exists principally in a form possessing flavin mononucleotide hydroquinone, with its iron-sulfur center oxidized. At pH 8, the enzyme principally contains flavin mononucleotide semiquinone and reduced iron-sulfur, but despite the proximity of the two centers to one another, their magnetic moments do not interact. At pH 10, TMADH2eq exhibits the EPR spectrum that is diagnostic of a previously characterized spin-interacting state in which the magnetic moments of the flavin semiquinone and reduced iron-sulfur center are strongly ferromagnetically coupled. The kinetics of the interconversion of these three states have been investigated using a pH jump technique in both H2O and D2O. The observed kinetics are consistent with a reaction mechanism involving sequential protonation/deprotonation and intramolecular electron transfer events. All reactions studied show a normal solvent kinetic isotope effect. Proton inventory analysis indicates that at least one proton is involved in the reaction between pH 6 and 8, which principally controls intramolecular electron transfer, whereas at least two protons are involved between pH 8 and 10, which principally control formation of the spin-interacting state. The results of these and previous studies indicate that for TMADH2eq, between pH 10 and 6, at least three protonation/deprotonation events are associated with intramolecular electron transfer and formation of the spin-interacting state, with estimated pK alpha values of 6.0, 8.0, and approximately 9.5. These pK alpha values are attributed to the flavin hydroquinone, flavin semiquinone, and an undesignated basic group on the protein, respectively.

Kinetic and Mechanistic Characterization of a Mammalian Protein-tyrosine Phosphatase, PTP1

The kinetic mechanism of the hydrolysis of phosphate monoesters catalyzed by a soluble form of rat protein-tyrosine phosphatase (PTPase), PTP1, was probed with a variety of steady-state and pre-steady-state kinetic techniques. Product inhibition and 18O exchange experiments are consistent with the enzymatic reaction proceeding through two chemical steps, i.e. formation and breakdown of a covalent phosphoenzyme intermediate. The variation of kcat/Km with pH indicates that three ionizable groups are involved in enzyme substrate binding and catalysis. The first group must be deprotonated and is attributed to the second ionization of the substrate. The other two groups with pK alpha values of 5.1 and 5.5 correspond to two enzyme active site residues. The kcat-pH profiles for both p-nitrophenyl phosphate and beta-naphthyl phosphate are bell-shaped and are superimposable, with the apparent pK alpha values derived from the acidic limb and the basic limb of the profile being 4.4 and 6.8, respectively. This suggests that the rate-limiting step corresponds to the decomposition of the phosphoenzyme intermediate at all pH values. Results from leaving group dependence of kcat at two different pH values support the above conclusion. Furthermore, burst kinetics have been demonstrated with PTP1 using p-nitrophenyl phosphate as a substrate. The rate constants for the formation and the breakdown of the intermediate are 241 and 12 s-1, respectively, at pH 6.0 and 3.5 degrees C. A normal D2O solvent isotope effect (kcatH/kcatD = 1.5) is associated with the breakdown of the phosphoenzyme intermediate, indicating a solvent-derived proton in the transition state. The leaving group dependence of kcat/Km suggests that there is a strong electrophilic interaction between the enzyme and the leaving group oxygen in the transition state of the phosphorylation event. These results are compared with those of the Yersinia PTPase and suggest that the mechanism for PTPase-catalyzed phosphate monoester hydrolysis is conserved from bacterial to mammals.

Heme Oxygenase-2: PROPERTIES OF THE HEME COMPLEX OF THE PURIFIED TRYPTIC FRAGMENT OF RECOMBINANT HUMAN HEME OXYGENASE-2

Recombinant human microsomal heme oxygenase-2 was expressed in Escherichia coli. Tryptic digestion of the membrane fraction, in which the wild-type enzyme was localized, yielded a soluble tryptic peptide of 28 kDa, which retained the ability to accept electrons from NADPH-cytochrome P-450 reductase and the enzymatic activity for conversion of heme to biliverdin. The tryptic fragment, when purified to apparent homogeneity, bound one equivalent of heme to form a substrate-enzyme complex that had spectroscopic properties characteristic of heme proteins, such as myoglobin and hemoglobin. Optical absorption, Raman scattering, and EPR studies of the heme-tryptic fragment complex revealed that the ferric heme was six coordinate high spin at neutral pH and six coordinate low spin at alkaline pH, with a pK alpha value of 8.5. EPR and Raman scattering studies indicated that a neutral imidazole of a histidine residue served as the proximal ligand in the heme-heme oxygenase-2 fragment complex. The reaction with hydrogen peroxide converted the heme of the heme oxygenase-2 fragment complex into a verdoheme-like intermediate, while the reaction with m-chloroperbenzoic acid yielded a oxoferryl species. These spectroscopic properties are similar to those obtained for heme oxygenase-1, and thus the catalytic mechanism of heme oxygenase-2 appears to be similar to that of heme oxygenase-1.

Site-directed Mutagenesis of Human Glutathione Transferase P1-1: SPECTRAL, KINETIC, AND STRUCTURAL PROPERTIES OF Cys-47 AND Lys-54 MUTANTS

In the human placental glutathione transferase, Cys-47 possesses, at physiological pH values, a pK alpha value of 4.2 and may exist as an ion pair with the protonated epsilon-amino group of Lys-54. Using site-directed mutagenesis we investigate spectral, kinetic, and structural properties of Cys-47 and Lys-54 mutants. The results shown indicate that the thiolate ion detected at 229 nm should be assigned exclusively to Cys-47. The contribution of Lys-54 to the activation of Cys-47 is assessed by the spectral properties of the K54A mutant enzyme. The induced cooperativity toward glutathione, as a consequence of mutation of Lys-54 to alanine, clearly parallels that observed for the Cys-47 mutant enzymes (see the preceding paper (Ricci, G., Lo Bello, M., Caccuri, A. M., Pastore, A., Nuccetelli, M., Parker, M. W., and Federici, G. (1995) J. Biol. Chem. 270, 1243-1248) and points out the importance of this electrostatic interaction in shaping the correct spatial arrangement for the binding of glutathione and in anchoring the flexible helix alpha 2. When this ion pair is disrupted, by mutation of either residue, the flexibility of this region could be greatly increased, causing helix alpha 2 to come in contact with the other subunit and generating a structural communication, which is the basis of the observed cooperativity.

Kinetic and site-directed mutagenesis studies of the cysteine residues of bovine low molecular weight phosphotyrosyl protein phosphatase.

The roles of the 8 conserved cysteines and 1 arginine in the low molecular weight phosphotyrosyl protein phosphatases were investigated using site-directed mutagenesis of the recombinant bovine heart enzyme. Single mutants of cysteine to serine were studied for each cysteine; alanine replacements were also made for Cys-12, Cys-17, and Arg-18. The CD spectra of the purified proteins were effectively superimposable, consistent with the conclusion that no major structural alterations had occurred, but 1H NMR spectroscopy did reveal some spectral shifts in the aromatic region. Kinetic analysis of the mutant proteins demonstrated that only Cys-12, Cys-17, and Arg-18 had significantly altered catalytic activity toward the substrate p-nitrophenyl phosphate at pH 5. The Cys-12 and Arg-18 mutants were effectively inactive. Thus, it is concluded that Cys-12 is the catalytic nucleophile, and Arg-18 presumably serves an essential function in substrate binding. The C17S mutant had 6% residual activity compared with wild type protein, whereas the C17A mutant had 37% activity. Consistent with the observed activity of the Cys-17 mutant, a covalent phosphocysteine intermediate was trapped and identified by 31P NMR. Further kinetic analysis of C17A using several aryl phosphate monoester substrates with different leaving group pK alpha values indicated that no change in the rate-determining step of the catalytic mechanism had occurred, that is, dephosphorylation of the covalent phosphoenzyme intermediate remains rate-limiting. The C17A mutant had a 4-fold higher phosphate Ki and slightly higher Km values for p-nitrophenyl phosphate suggesting that Cys-17 may be important for optimal positioning of the substrate phosphate moiety.

Conformation of apolipoprotein E in lipoproteins.

Lysine (Lys) residues in apolipoprotein (apo) E are known to be involved in binding of apoE-containing lipoproteins to the low density lipoprotein (LDL) receptor. To examine the microenvironments of the Lys residues of apoE-3 in a variety of lipid-associated states, we have used a high resolution 13C-NMR method in which Lys were reductively methylated with [13C] formaldehyde. Over a wide pH range, the spectrum of apoE in canine HDLc, a spherical lipoprotein particle, exhibited two peaks from Lys epsilon-amino groups. The two pools of Lys in HDLc titrate with pK alpha values of 10.4 ("normal") and 9.3 ("active"). In contrast, eight epsilon-[13CH3]2Lys peaks (delta = 42.5-44.5 parts/million) with pK alpha values ranging from 8.2 to 10.1 and 7.8 to 10.5 were observed at pH 9.5 for human and canine apoE, respectively, in discoidal complexes with dimyristoyl glycerophosphocholine. A single Lys microenvironment was observed for apoE present in a disordered, lipid-free, state in 8 M urea, confirming the fact that the lipid environment is modulating the conformation of apoE. The above data demonstrate that the conformation of apoE, as reflected by the Lys microenvironments, on spherical HDLc particles is different from that on discoidal complexes.

Tautomeric states of the active‐site histidines of phosphorylated and unphosphorylated IIIGlc, a signal‐transducing protein from escherichia coli, using two‐dimensional heteronuclear NMR techniques

IIIGlc is an 18.1-kDa signal-transducing phosphocarrier protein of the phosphoenolpyruvate:glycose phosphotransferase system from Escherichia coli. The 1H, 15N, and 13C histidine ring NMR signals of both the phosphorylated and unphosphorylated forms of IIIGlc have been assigned using two-dimensional 1H-15N and 1H-13C heteronuclear multiple-quantum coherence (HMQC) experiments and a two-dimensional 13C-13C-1H correlation spectroscopy via JCC coupling experiment. The data were acquired on uniformly 15N-labeled and uniformly 15N/13C-labeled protein samples. The experiments rely on one-bond and two-bond J couplings that allowed for assignment of the signals without the need for the analysis of through-space (nuclear Overhauser effect spectroscopy) correlations. The 15N and 13C chemical shifts were used to determine that His-75 exists predominantly in the N epsilon 2-H tautomeric state in both the phosphorylated and unphosphorylated forms of IIIGlc, and that His-90 exists primarily in the N delta 1-H state in the unphosphorylated protein. Upon phosphorylation of the N epsilon 2 nitrogen of His-90, the N delta 1 nitrogen remains protonated, resulting in the formation of a charged phospho-His-90 moiety. The 1H, 15N, and 13C signals of the phosphorylated and unphosphorylated proteins showed only minor shifts in the pH range from 6.0 to 9.0. These data indicate that the pK alpha values for both His-75 and His-90 in IIIGlc and His-75 in phospho-IIIGlc are less than 5.0, and that the pK alpha value for phospho-His-90 is greater than 10. The results are presented in relation to previously obtained structural data on IIIGlc, and implications for proposed mechanisms of phosphoryl transfer are discussed.

Role of histidine 124 in the catalytic function of ribonuclease HI from Escherichia coli.

The role of the conserved histidine residue (His124) in the catalytic function of Escherichia coli ribonuclease HI was probed by the use of the pH titration experiments with 1H NMR and site-directed mutagenesis. His124 is located close to the catalytic triad formed by the three carboxylates. The C2H proton resonance of His124, as well as those of four other His residues, in the enzyme were assigned by comparing the 1H NMR spectrum of the wild-type enzyme to the spectra of the five mutant enzymes, each of which lacked a different His residue. From the analysis of the pH titration shifts of these resonances, the pK alpha values of all His residues were determined. The pK alpha value of His124 was 7.1, which is slightly higher than, but close to, the normal value of the imidazole group. This result suggests that His124 is located in an acidic environment but does not interact directly with a carboxyl group in the solution structure. Three mutant enzymes, in which His124 was replaced by Lys, Gln, or Glu were constructed. The kinetic parameters of these mutant enzymes were determined by using the M13 DNA/RNA hybrid as a substrate. Substitution of Lys, Gln, or Glu for His124 dramatically lowered the Vmax value by 30-100-fold, without significantly affecting the Km value, as compared to those of the wild-type enzyme. In addition, any mutation impaired the in vivo function of the enzyme. These results indicate that His124 is involved in the catalytic function of the enzyme. We propose that His124 changes its conformation in the catalytic reaction and enhances the catalytic efficiency by removing a proton from a catalytically essential carboxylate.

Thyrotropin-releasing hormone binding to the mouse pituitary receptor does not involve ionic interactions. A model for neutral peptide binding to G protein-coupled receptors.

Thyrotropin-releasing hormone, TRH (< Glu-His-Proamide), and [N tau-Me-His]TRH (MeTRH) are present as neutral and positively charged forms at physiologic pH, and it was possible that they bind to the TRH receptor (TRH-R) as charged (protonated) species. Binding affinities of TRH and MeTRH to endogenous rat TRH-Rs and to transfected wild type mouse TRH-Rs decreased below pH 7.1. Half-maximal decreases in binding occurred at the approximate pK alpha values of these ligands. Asp to Ala mutations in extracellular loop 1, TM-4, and TM-5 did not decrease binding affinity, but an Asp to Ala mutation in TM-2 caused the affinity to decrease 8-fold. The pH dependences of binding of MeTRH, however, were similar in wild type and all mutant receptors and were consistent with the protonated form of MeTRH binding less well. Thus, the binding of TRH to its receptor does not involve ionic interactions and may be a prototype for binding of neutral peptide ligands to G protein-coupled receptors.

Site-directed mutagenesis of glutathione S-transferase YaYa. Important roles of tyrosine 9 and aspartic acid 101 in catalysis.

The roles of tyrosine 9 and aspartic acid 101 in the catalytic mechanism of rat glutathione S-transferase YaYa were studied by site-directed mutagenesis. Replacement of tyrosine 9 with phenylalanine (Y9F), threonine (Y9T), histidine (Y9H), or valine (Y9V) resulted in mutant enzymes with less than 5% catalytic activity of the wild type enzymes. Kinetic studies with purified Y9F and Y9T mutants demonstrated poor catalytic efficiencies which were largely due to a drastic decrease in kcat. The estimated pK alpha values of the sulfhydryl group of glutathione bound to Y9F and Y9T mutant enzymes were 8.5 to 8.7, similar to the chemical reaction, in contrast to the estimated pK alpha value of 6.7 to 6.8 for the glutathione enzyme complex of wild type glutathione S-transferase. These results indicate that tyrosine 9 is directly responsible for the lowering of the pKa of the sulfhydryl group of glutathione, presumably due to the stabilization of the thiolate anion through hydrogen bonding with the hydroxyl group of tyrosine. To examine the role of aspartic acid in the binding of glutathione to YaYa, 4 conserved aspartic acid residues at positions 61, 93, 101, and 157 were changed to glutamic acid and asparagine. All mutant enzymes retained either full or partial activity except D157N, which was virtually inactive. Kinetic studies with four mutant enzymes (D93E, D93N, D101E, and D101N) indicate that only D101N exhibited a 5-fold increase in Km toward glutathione. Also, the binding of this mutant to the affinity column was greatly reduced. These results demonstrate that aspartic acid 101 plays an important role in glutathione interaction to YaYa. The role of aspartic acid 157 in catalysis remains to be determined.

PH dependence of kinetic parameters of pepsin, rhizopuspepsin, and their active-site hydrogen bond mutants.

The pH dependence of the kinetic parameters of pepsin, rhizopuspepsin, and their active-site hydrogen bond mutants has been determined. These data have permitted the calculation of two active-site ionization constants in the free enzymes (pKe1 and pK32) and in the enzyme-substrate complexes (pKes1 and pKes2). The pKe1 of rhizopuspepsin (2.8) is near that of a normal carboxyl group and near the pKe1 of human immunodeficiency virus type 1 (HIV-1) protease (3.32) (Ido, E., Han, H. P., Kezdy, F. J., and Tang, J. (1991) J. Biol. Chem. 266, 24359-24366). The pKe1 of pepsin (1.57) is thus abnormally low. The pKe2 of rhizopuspepsin (4.44) is lower than that of pepsin (5.02) and HIV protease (6.80). The binding of substrate to rhizopuspepsin causes the lowering of pKes1 to 1.8 and the elevating of pKes2 to above 6. The pK alpha shifts due to substrate binding are much less pronounced in pepsin. Thus, the two enzyme-substrate complexes have similar pK alpha values. For both pepsin and rhizopuspepsin, the removal of hydrogen bonds to the active-site carboxyls by mutagenesis results in negligible changes in the four pK alpha values. The major alteration caused by these mutations is the decrease in kcat values, while there is little change in Km. These observations suggest that these hydrogen bonds to the active-site aspartyls contribute little to the pH-activity relationships of the aspartic proteases. The role of the active-site hydrogen bonds may well be to preserve the conformational rigidity of the catalytic apparatus.

Temperature- and pH-dependent changes in the coordination sphere of the heme c group in the model peroxidase N alpha-acetyl microperoxidase-8.

The pH- and temperature-dependent changes in the coordination sphere of the heme c group of N alpha-acetyl microperoxidase-8 (Ac-MP-8) have been studied by examining its optical, resonance Raman, electron paramagnetic resonance, and magnetic circular dichroism spectra. An optical titration indicates that Ac-MP-8 exists in three major ionization forms over the pH 1-12 range that are linked by pK alpha values of approximately 3 and 9. The acid form that is present at pH 1.5 exists as a mixture of five- and six-coordinate high-spin species and most likely has water or buffer ions as axial ligand(s). On titration to pH 7, the His18 residue is deprotonated and becomes the proximal ligand to the iron to give a six-coordinate neutral form that has water as the sixth ligand. This form exists in a thermal high-spin intermediate-spin state equilibrium. On raising the pH to 10, an alkaline form is generated which is predominantly a five-coordinate high-spin species. It is formed by ionization of the proximal His18 residue to its imidazolate form with concomitant dissociation of the water ligand at the sixth site. At concentrations of Ac-MP-8 greater than 10 microM, some six-coordinate low-spin species are formed that are attributed to a dimer in which a His18 residue from a second molecule of Ac-MP-8 coordinates to the sixth site of another to give a bis-His complex. Raising the pH to 11.5 does not produce an appreciable amount of the six-coordinate complex with hydroxide as the sixth ligand. These studies show that Ac-MP-8 is a good water-soluble model for the peroxidases that exhibits minimal aggregation at concentrations below 10 microM in the neutral and alkaline pH regions.

Replacement of lysine 269 by arginine in Escherichia coli tryptophan indole-lyase affects the formation and breakdown of quinonoid complexes.

Lysine 269 in Escherichia coli tryptophan indole-lyase (tryptophanase) has been changed to arginine by site-directed mutagenesis. The resultant K269R mutant enzyme exhibits kcat values about 10% those of the wild-type enzyme with S-(o-nitrophenyl)-L-cysteine, L-tryptophan, and S-benzyl-L-cysteine, while kcat/Km values are reduced to 2% or less. The pH profile of kcat/Km for S-benzyl-L-cysteine for the mutant enzyme exhibits two pK alpha values which are too close to separate, with an average value of 7.6, while the wild-type enzyme exhibits pK alpha values of 6.0 and 7.8. The pK alpha for the interconversion of the 335 and 412 nm forms of the K269R enzyme is 8.3, while the wild-type enzyme exhibits a pK alpha of 7.4. Steady-state kinetic isotope effects on the reaction of [alpha-2H]S-benzyl-L-cysteine with the K269R mutant enzyme (Dkcat = 2.0; D(kcat/Km) = 3.9) are larger than those of the wild-type enzyme (Dkcat = 1.4; D(kcat/Km) = 2.9). Rapid scanning stopped-flow kinetic studies demonstrate that the K269R mutant enzyme does not accumulate quinonoid intermediates with L-alanine, L-tryptophan, or S-methyl-L-cysteine, but does form quinonoid absorption peaks in complexes with S-benzyl-L-cysteine and oxidolyl-L-alanine, whereas wild-type enzyme forms prominent quinonoid bands with all these amino acids. Single wavelength stopped-flow kinetic studies demonstrate that the alpha-deprotonation of S-benzyl-L-cysteine is 6-fold slower in the K269R mutant enzyme, while the intrinsic deuterium kinetic isotope effect is less for the K269R enzyme (Dk = 4.2) than for the wild-type (Dk = 7.9). The decay of the K269R quinonoid intermediate in the presence of benzimidazole is 7.1-fold slower than that of the wild-type enzyme. These results demonstrate that Lys-269 plays a significant role in the conformational changes or electrostatic effects obligatory to the formation and decomposition of the quinonoid intermediate, although it is not an essential basic residue.

Are the histidine residues of glutathione S-transferase important in catalysis? An assessment by 13C NMR spectroscopy and site-specific mutagenesis.

To test the proposition that a histidine residue is essential in the catalytic mechanism of glutathione S-transferase, rat liver isoenzyme 3-3 specifically labeled with [ring-2-13C]histidine was prepared. The 13C NMR spectrum of the labeled enzyme revealed four resonances corresponding to the 4 histidine residues in the mu gene class type 3 subunit. Titration of the four resonances in the range of pH 4-9 both in the presence and absence of glutathione gave pK alpha values of much less than 4, 5.2, 7.1, and 7.8 for the four side chains that were identified by site-specific mutagenesis as His14, His83, His84, and His167, respectively. The magnetic resonance properties and titration behavior of His14 suggest that this residue is buried in a hydrophobic environment. Conservative replacement of each histidine with asparagine results in mutant enzymes that have catalytic properties very close to the native protein as assessed with three different substrates, 1-chloro-2,4-dinitrobenzene, 4-phenyl-3-buten-2-one, and phenanthrene 9,10-oxide. The results indicate clearly that none of the histidine residues of isoenzyme 3-3 is essential for stabilization of the bound glutathione thiolate or for any other aspect of catalysis.

6-Mercapto-FAD and 6-thiocyanato-FAD as active site probes of phenol hydroxylase

Recently, the synthesis and properties of several 6-substituted flavins as active site probes for flavoproteins have been reported (Ghisla, S., Massey, V., and Yagi, K. (1986) Biochemistry 25, 3282-3289). Here, we report results of experiments in which 6-thiocyanato-FAD and 6-mercapto-FAD have been substituted for the native flavin of phenol hydroxylase. The 6-SCN-FAD enzyme was converted spontaneously to the 6-mercaptoflavin form probably due to dissociation of flavin, followed by attack of external protein thiols. The pK alpha values of uncomplexed and phenol-bound 6-mercapto-FAD enzyme were determined. Both the spontaneously formed 6-mercapto-FAD enzyme and the enzyme reconstituted with preformed 6-mercapto-FAD were treated with a variety of thiol-specific reagents, and reaction rates were followed by spectroscopic means. Comparison with the corresponding rates found with free flavin suggested a high degree of accessibility to the flavin 6-position. Accessibility was somewhat decreased in the presence of phenol. Upon treatment with low concentrations of methyl methanethiosulfonate or N-ethylmaleimide (NEM), extremely rapid spectral changes were apparent. The former reaction, however, was reversed spontaneously within 2 h. Reaction with NEM was biphasic, with spectral changes consistent with the mechanism previously proposed (Steenkamp, D. J., McIntire, W., and Kenney, W. C. (1978) J. Biol. Chem. 253, 2818-2824), followed by a small absorbance decrease due to protein conformational changes. The NEM reaction is unusual, being easily reversed by addition of excess dithiothreitol.

Evidence for direct interaction between cysteine 138 and the flavin in thioredoxin reductase. A study using flavin analogs.

The flavoenzyme thioredoxin reductase from Escherichia coli contains an oxidation-reduction active disulfide made up of Cys135 and Cys138. Mutations changing each Cys residue to a Ser residue have been effected (Prongay, A. J., engelke, D. R., and Williams, C. H., Jr. (1989) J. Biol. Chem. 264, 2656-2664). The FAD prosthetic group of each altered thioredoxin reductase has been replaced with 1-deaza-FAD (a flavin analog with carbon substituted for nitrogen at position 1), 4-thio-FAD (a flavin analog with sulfur substituted for oxygen at position 4), and 6-thiocyanato-FAD. 1-Deaza-FAD-TRR(Cys135,Ser138) has absorbance and fluorescence spectral properties similar to the oxidized form of wild type apothioredoxin reductase reconstituted with 1-deaza-FAD. The absorbance spectrum of 1-deaza-FAD-TRR(Ser135,Cys138) is similar to the spectrum of the two-electron reduced form of wild type apothioredoxin reductase reconstituted with 1-deaza-FAD, indicating that it is a mixture of two species (O'Donnell, M. E., and Williams, C. H., Jr. (1984) J. Biol. Chem. 259, 2243-2251). The spectrum of one of these species of 1-deaza-FAD-TRR(Ser135,Cys138) resembles the spectrum of oxidized 1-deaza-FAD bound to wild type apothioredoxin reductase. The other species has an absorbance spectrum with a single peak at 400 nm (epsilon 400 = 11,100 M-1 cm-1) and resembles the spectrum of a thiolate adduct at the C4a position of the 1-deaza-FAD. The equilibrium between these species is pH-dependent, with a maximum of 50% C4a-adduct formation at low pH, and is linked to pK alpha values at 8.2 and 9.3. The absorbance spectrum of 4-thio-FAD-TRR(Cys135,Ser138) resembles the spectrum of the unbound 4-thio-FAD, whereas 4-thio-FAD-TRR(Ser135,Cys138) has a spectrum indicative of a mixture of 4-thio-FAD and FAD, suggesting a reaction between the 4-position of the flavin and Cys138. The binding of 6-thiocyanato-FAD to the apoprotein of the mutated enzymes showed no evidence for a reaction between the thiols and the group at the 6-position of the flavin.

Characterization of a tungsten-iron-sulfur protein exhibiting novel spectroscopic and redox properties from the hyperthermophilic archaebacterium Pyrococcus furiosus.

The archaebacterium, Pyrococcus furiosus, is a strict anaerobe that grows optimally at 100 degrees C by a fermentative-type metabolism in which H2 and CO2 are the only detectable products. Tungsten is known to stimulate the growth of this organism. A red-colored tungsten-containing protein (abbreviated RTP) that is redox-active and extremely thermostable has been purified. RTP is a monomer of Mr = 85,000 and contains approximately 6 iron, 1 tungsten, and 4 acid-labile sulfide atoms/molecule. Titrations using visible spectroscopy were consistent with the oxidation and reduction of the protein each requiring two electrons/molecule, suggesting that these metals and the sulfide are arranged in two redox active centers. P. furiosus ferredoxin served as an electron acceptor for the protein. Dithionite-reduced RTP exhibited a remarkable and complex EPR spectrum at 6 K with g values ranging from 1.3 to 10.0. This was shown to arise from the spin-coupling interaction of two paramagnetic centers. One (center A) has a S = 3/2 spin system (effective g values: gx = 3.33, gy = 4.75, and gz = 1.92, where D = 4.3 cm-1 and lambda = 0.135), whereas the EPR properties of the other (center B) could not be deduced. Nevertheless, theoretical analyses show how the redox properties of both centers may be determined using EPR spectroscopy. Their midpoint potentials (Em) at 20 degrees C and pH 8.0 are -410 mV (center A) and -500 mV (center B) with an effective potential for the spin coupled system (Em, A + B) of -505 mV. The Em values are dependent on temperature (delta Em/delta T = -2 mV/degrees C between 20 and 70 degrees C) and pH with pK alpha values of 8.0 (A) and approximately 8.5 (B). The Em values at 100 degrees C, the growth temperature, were estimated at -590, -650, and -660 mV for centers A, B, and A + B, respectively. These data indicate that RTP catalyzes a dehydrogenase-type reaction of extremely low potential, which involves the transfer of two protons and of two electrons, to and from two adjacent and interacting but nonidentical metal centers.

Endotoxin removal by anion‐exchange polymeric matrix

The effects of anion-exchange polymeric matrices on endotoxin removal from albumin and gamma-globulin solutions are evaluated. The positively charged cellulose acrylic media carrying DEAE or QAE functional groups remove significant amounts of endotoxin from tap water, but are less effective in protein solutions. With properly controlled pH levels and salt concentrations, the endotoxin level in a protein solution can be reduced; however, low endotoxin concentrations, less than 100 pg/ml, are more difficult to remove. The endotoxin removal capacity depends on the number of functional groups existing in the matrix, expressed as the number of milliequivalents (meq), and on the pH operable range, which is directly related to the pK alpha value of the matrix. The effects of pH and salt on endotoxin removal from albumin and gamma-globulin solutions by an anion-exchange polymeric matrix were evaluated statically in test tubes. In addition, a dynamic flow was performed under statically defined conditions on a 250-ml DEAE cartridge for the removal of endotoxin from albumin at a flow rate of 40 ml/min. A greater than 75% reduction in the endotoxin can be achieved, with protein loss occurring only in the early stage of removal. Such processes are useful for the reduction of endotoxin from biological solutions produced by natural sources or recombinant DNA technology.