Competitive partial inhibitors of serum albumin-catalyzed sulfur cyanolysis

Efforts to locate the active site for sulfur cyanolysis catalyzed by bovine serum albumin have led to systematic tests of several compounds that inhibit the catalyzed reaction. Hexanoate and 5-dimethylaminonaphthalene-1-sulfonate bind at the same site and are partial inhibitors competitive with cyanide, uncompetitive with respect to sulfur. Various dansyl amino acids and 1-anilino-8-naphthalene sulfonate display the same inhibitory behavior but bis (1-anilino-8-naphthalene sulfonate) is a total inhibitor competitive with cyanide. These findings are interpreted to indicate that the cyanolysis active site is near, but not at, one of the short-chain fatty acid binding sites on albumin subdomain 2-AB or 3-AB. Both ionic repulsion and steric considerations are implicated in the mechanisms of inhibition.     

The sulfur-cyanolysis sites of serum albumin: metabolite competition studies

In the presence of a source of sulfane sulfur, a cyanolysis reaction catalyzed by serum albumin may contribute to cyanide detoxication. The active site for this catalysis by serum albumin has been investigated in competition studies with ligands that have known albumin binding sites. Despite complications caused by the occurrence of multiple primary and secondary sites for many ligands, the results show that the primary sites for bilirubin, steroids, indoles, aspirin, and palmitate are distinct from that for sulfur. Laurate is a tight-binding partial inhibitor of the cyanolysis reaction, competitive with cyanide rather than with sulfur. In view of the formal mechanism previously established for the catalyzed reaction, this result indicates that the sulfur-cyanolysis site is probably near the site occupied by laurate.     

Serum albumin: Search for new sites of interaction with organophosphorus compounds by the example of soman

Albumin is known to be able to interact with organophosphorus compounds (OPCs), but neither amino acid residues of albumin that are responsible for this interaction nor the nature of the forming bonds have been finally established. Catalytic and pseudocatalytic functions of albumin are under consideration. Possible sites of interaction of albumin with soman have been elucidated by the methods of molecular modeling. Structures of the soman-albumin complexes have been determined by molecular docking. Stability of the obtained complexes has been evaluated by the method of molecular dynamics. The chemical bond between soman and the tyrosine-411 residue has been found to form only after deprotonation of the latter. The tyrosine-150 residue of albumin binds soman more effectively than tyrosine-411, and the tyrosine-150-deprotonation does not determine the efficacy of the binding (sorption) of soman, but affects the stability of the formed bound. It was proposed that the albumin residues of tyrosine-150 and serine-193 could serve as sites of the catalytic interaction with soman. We hypothesized that the deprotonation of an amino acid residue in one albumin site influenced initiation of the ligand binding in the other albumin site (allosteric albumin regulation).     

Critical residues influence the affinity and selectivity of alpha-conotoxin MI for nicotinic acetylcholine receptors.

The mammalian skeletal muscle acetylcholine receptor contains two nonequivalent acetylcholine binding sites, one each at the alpha/delta and alpha/gamma subunit interfaces. Alpha-Conotoxin MI, a 14-amino acid competitive antagonist, binds at both interfaces but has approximately 10(4) higher affinity for the alpha/delta site. We performed an "alanine walk" to identify the residues in alpha-MI that contribute to this selective interaction with the alpha/delta site. Electrophysiological measurements with Xenopus oocytes expressing normal receptors or receptors lacking either the gamma or delta subunit were made to assay toxin-receptor interaction. Alanine substitutions in most amino acid positions had only modest effects on toxin potency at either binding site. However, substitutions in two positions, proline-6 and tyrosine-12, dramatically reduced toxin potency at the high-affinity alpha/delta site while having comparatively little effect on low-affinity alpha/gamma binding. When tyrosine-12 was replaced by alanine, the toxin's selectivity for the high-affinity site (relative to that for the low-affinity site) was reduced from 45,000- to 30-fold. A series of additional amino acid substitutions in this position showed that increasing side chain size/hydrophobicity increases toxin potency at the alpha/delta site without affecting alpha/gamma binding. In contrast, when tyrosine-12 is diiodinated, toxin binding is nearly irreversible at the alpha/delta site but also increases by approximately 500-fold at the alpha/gamma site. The effects of position 12 substitutions are accounted for almost entirely by changes in the rate of toxin dissociation from the high-affinity alpha/delta binding site.     

Cyanolysis and azidolysis of epoxides by haloalcohol dehalogenase: theoretical study of the reaction mechanism and origins of regioselectivity

Haloalcohol dehalogenase HheC catalyzes the reversible dehalogenation of vicinal haloalcohols to form epoxides and free halides. In addition, HheC is able to catalyze the irreversible and highly regioselective ring-opening of epoxides with nonhalide nucleophiles, such as CN (-) and N 3 (-). For azidolysis of aromatic epoxides, the regioselectivity observed with HheC is opposite to the regioselectivity of the nonenzymatic epoxide-opening. This, together with a relatively broad substrate specificity, makes HheC a promising tool for biocatalytic applications. We have designed large quantum chemical models of the HheC active site and used density functional theory to study the reaction mechanism of the HheC-catalyzed ring-opening of ( R)-styrene oxide with the nucleophiles CN (-) and N 3 (-). Both the cyanolysis and the azidolysis reactions are shown to take place in a single concerted step. The results support the suggested role of the putative Ser132-Tyr145-Arg149 catalytic triad, where Tyr145 acts as a general acid, donating a proton to the substrate, and Arg149 interacts with Tyr145 and facilitates proton abstraction, while Ser132 positions the substrate and reduces the barrier for epoxide opening through interaction with the emerging oxyanion of the substrate. We have also studied the regioselectivity of ( R)-styrene oxide opening for both the cyanolysis and the azidolysis reactions. The employed active site model was shown to be able to reproduce the experimentally observed beta-regioselectivity of HheC. In silico mutations of various groups in the HheC active site model were performed to elucidate the important factors governing the regioselectivity.     

A single point mutation enhances hydroxynitrile synthesis by halohydrin dehalogenase

The cyanide-mediated ring opening of epoxides catalyzed by halohydrin dehalogenases yields β-hydroxynitriles that are of high interest for synthetic chemistry. The best studied halohydrin dehalogenase to date is the enzyme from Agrobacterium radiobacter, but this enzyme (HheC) exhibits only low cyanolysis activities. Sequence comparison between a pair of related halohydrin dehalogenases from Corynebacterium and Mycobacterium suggested that substitution of a threonine that interacts with the active site might be responsible for the higher cyanolytic activity of the former enzyme. Here we report that a variant of HheC in which this substitution (T134A) is adopted displays an up to 11-fold higher activity in cyanide-mediated epoxide ring-opening. The mutation causes removal of the hydrogen bond between residue 134 and the side chain O of the active site serine 132, which donates a hydrogen bond to the substrate oxygen. The mutation also increases dehalogenase rates with various substrates. Structural analysis revealed that the anion-binding site of the mutant enzyme remained unaltered, showing that the enhanced activity is due to altered interactions with the substrate oxygen rather than changes in the nucleophile binding site.     

Differences between the conformations of nitrotyrosyl-248 carboxypeptidase A in the crystalline state and in solution

In solution, nitrocarboxypeptidase A, modified at tyrosyl-248, exhibits a nitrotyrosyl pK apparent of 6.3. In the crystalline state, the pK apparent is about 8.2. This change in ionization is consistent with the hypothesis that crystallization of the enzyme causes a displacement of tyrosine-248 away from the active site zinc ion.     

Studies on the inhibition of human thrombin: effects of plasma and plasma constituents

The effects of blood plasma and some plasma constituents on several types of thrombin inhibitors were quite varied. Two active esters were rapidly destroyed by serum albumin; one of these reacted initially with Lys-199, the residue that is also acylated by aspirin. Of two sulfonyl fluorides one was unaffected by albumin, and the other bound reversibly to albumin; this binding was greater with albumin acetylated at Tyr-411 near the binding site for medium-chain fatty acids. The effects of a chloromethyl ketone were inhibited, apparently reversibly, by albumin but were practically abolished by glutathione. Of two potent reversible inhibitors one was unaffected by plasma constituents, while the other was over 10-fold less potent in plasma than in fibrinogen. The effect of plasma could be partially explained by binding to albumin and lipoproteins.     

Purification and characterization of an activated form of the protein tyrosine kinase Lck from an Escherichia coli expression system

The lymphocyte-specific, nonreceptor protein tyrosine kinase Lck has been purified from an Escherichia coli expression system using a monoclonal antibody column followed by dye-affinity chromatography. Polyacrylamide gel electrophoretic analysis of purified protein revealed a single 56 kDa band, indicating that recombinant Lck was purified to near-homogeneity. The purified enzyme displayed tyrosine kinase activity as measured by both autophosphorylation and phosphorylation of exogenous substrates. Biochemical properties including protein phosphorylation and kinetic characteristics of the enzyme have been assessed. Peptide map analysis revealed that bacterially expressed Lck is phosphorylated predominantly on the autophosphorylation site (tyrosine-394), which is characteristic for activated protein tyrosine kinases. Indeed, we found that the recombinant enzyme is approximately fivefold more active than Lck from resting T cells, which is extensively phosphorylated at the regulatory carboxy-terminal tyrosine residue (tyrosine-505). Thus, we have overproduced recombinant human Lck in E. coli and developed a simple two-step purification procedure which yields highly active enzyme. This will enable the identification and characterization of potential regulators and targets of Lck and thereby greatly facilitate studies which will clarify its role in T cell signal transduction. © 1994 Wiley-Liss, Inc.     

On the activation-inactivation coupling in Shaker potassium channels.

The 'ball-and-chain' model suggests the existence of a negative site which may attract the positively charged inactivation ball to occlude the pore when the channel is in the open state. For Shaker K+ channels, we propose that the state-dependent negative site be tryptophan-435, which becomes negatively charged after receiving an electron from tyrosine-445. The kinetic scheme for the channel's activation-inactivation coupling as derived from the YW-gated model resembles a successful 'scheme 8' proposed by Zagotta and Aldrich. Our model suggests that the final rapid voltage-independent transition to the open state is due to the deprotonation of tyrosine-445.     

Amino acid residues involved in the interaction of acetylcholinesterase and butyrylcholinesterase with the carbamates Ro 02-0683 and bambuterol, and with terbutaline.

In order to identify amino acids involved in the interaction of acetylcholinesterase (AChE; EC 3.1.1.7) and butyrylcholinesterase (BChE; EC 3.1.1.8) with carbamates, the time course of inhibition of the recombinant mouse enzymes BChE wild-type (w.t.), AChE w.t. and of 11 site-directed AChE mutants by Ro 02-0683 and bambuterol was studied. In addition, the reversible inhibition of cholinesterases by terbutaline, the leaving group of bambuterol, was studied. The bimolecular rate constant of AChE w.t. inhibition was 6.8 times smaller by Ro 02-0683 and 16000 times smaller by bambuterol than that of BChE w.t. The two carbamates were equipotent BChE inhibitors. Replacement of tyrosine-337 in AChE with alanine (resembling the choline binding site of BChE) resulted in 630 times faster inhibition by bambuterol. The same replacement decreased the inhibition by Ro 02-0683 ten times. The difference in size of the choline binding site in the two w.t. enzymes appeared critical for the selectivity of bambuterol and terbutaline binding. Removal of the charge with the mutation D74N caused a reduction in the reaction rate constants for Ro 02-0683 and bambuterol. Substitution of tyrosine-124 with glutamine in the AChE peripheral site significantly increased the inhibition rate for both carbamates. Substitution of phenylalanine-297 with alanine in the AChE acyl pocket decreased the inhibition rate by Ro 02-0683. Computational docking of carbamates provided plausible orientations of the inhibitors inside the active site gorge of mouse AChE and human BChE, thus substantiating involvement of amino acid residues in the enzyme active sites critical for the carbamate binding as derived from kinetic studies.     

Magnetic resonance investigation of ionizable residues at the active site of thermolysin.

The details of the pH dependence of the thermodynamic and magnetic interactions of the active-site region of thermolysin in which manganese has replaced the active-site zinc atom and the inhibitor N-trifluoroacetyl-D-phenylalanine have been examined. These show a number of ionizable groups in the active-site region. A cooperative displacement of manganese at the catalytic site is observed as pH is lowered. This appears to be the result of the protonation of histidine-142 and -146 which act as metal ligands. The metal is 50% displaced at pH 6.0. At higher pH values, the environment of the bound manganese changes as a result of the ionization of at least two groups of approximate pKa = 8.5 and 9.5. These values are assigned to tyrosine-157 and to the water molecule which acts as a metal ligand at the active site. The binding behavior of the inhibitor strongly suggests that two molecules of inhibitor bind to the enzyme. The weaker site is competitive with the synthetic substrate FAGLA (furylacryloylglycyl-leucinamide), while the strong site has no effect on FAGLA hydrolysis. This second site is in the vicinity of the active site with a distance of 8 A or less between the trifluoromethyl group and manganese bound at the active site.     

The Role of H2O2-Generated Myoglobin Radical in Crosslinking of Myosin

The mechanism of myoglobin/H₂O₂ derived peroxidation of myosin was studied by comparing the catalytic activity of myoglobin and horseradish peroxidase using O-dianisidine, N-acetyl tyrosine and myosin as substrates. It was found that both hemoproteins induced myosin crosslinking and concomitant tyrosines oxidation to bityrosines, suggesting inter-molecular coupling of tyrosines in the crosslinking. The enzymatic activity of both hemoproteins on myosin was weak compared to small substrates. While horseradish peroxidase was much more active than myoglobin on small substrates, the reverse was true for myosin peroxidation. Since the suicidal interaction of myoglobin with H₂O₂ forms unstable tyrosine radicals, we suggest that the increased activity of myoglobin on myosin results from an efficient electron transfer between surface tyrosines of myosin and myoglobin but not horseradish peroxidase. These conclusions were supported by evidence that sperm whale myoglobin, which contains two active tyrosines -the heme-adjacent (tyrosine-103) and the surface (tyrosine-151), is more active as a mediator of myosin peroxidation than horse heart myoglobin which is devoid of the surface tyrosine.     

Engineering surface charge. 2. A method for purifying heterodimers of Escherichia coli glutathione reductase.

Two gor genes encoding different mutants of Escherichia coli glutathione reductase have been expressed in the same E. coli cell, leading to the creation of a hybrid form of the enzyme dimer. One of the gor genes carried, in addition to various directed mutations, a 5' extension that encodes a benign penta-arginine "arm" added to the N-terminus of the glutathione reductase polypeptide chain [Deonarain, M.P., Scrutton, N.S., & Perham, R.N. (1992) Biochemistry (preceding paper in this issue)]. This made possible, by means of ion-exchange chromatography or nondenaturing polyacrylamide gel electrophoresis, the facile separation of the hybrid enzyme from the two parental forms. Moreover, the two subunits in the hybrid enzyme could be made to carry different mutations. In this way, glutathione reductases with only one active site per dimer were generated: the effects of replacing tyrosine-177 with glycine in the NADPH-binding site, which greatly diminishes the Km for glutathione and switches the kinetic mechanism from ping-pong to ordered sequential, and of replacing His-439 with glutamine in the glutathione-binding site, which greatly diminishes the Km for NADPH, were both found to be restricted to the one active site carrying the mutations. This system of generating separable enzyme hybrids is generally applicable and should make it possible now to undertake a more systematic study of catalytic mechanism and assembly for the many enzymes with quaternary structure.     

Structure and function of malic enzymes, a new class of oxidative decarboxylases

Malic enzyme is a tetrameric protein with double dimer structure in which the dimer interface is more intimately contacted than the tetramer interface. Each monomeric unit of the enzyme is composed of four structural domains, which show a different folding topology from those of the other oxidative decarboxylases. The active center is located at the interface between domains B and C. For human mitochondrial malic enzyme, there is an exo nucleotide-binding site for the inhibitor ATP and an allosteric site for the activator fumarate, located at the tetramer and dimer interfaces, respectively. Crystal structures of the enzyme in various complexed forms indicate that the enzyme may exist in equilibrium among two open and two closed forms. Interconversion among these forms involves rigid-body movements of the four structural domains. Substrate binding at the active site shifts the open form to the closed form that represents an active site closure. Fumarate binding at the allosteric site induces the interconversion between forms I and II, which is mediated by the movements of domains A and D. Structures of malic enzyme from different sources are compared with an emphasis on the differences and their implications to structure-function relationships. The binding modes of the substrate, product, cofactors, and transition-state analogue at the active site, as well as ATP and fumarate at the exo site and allosteric site, respectively, provide a clear account for the catalytic mechanism, nucleotide specificities, allosteric regulation, and functional roles of the quaternary structure. The proposed catalytic mechanism involves tyrosine-112 and lysine-183 as the general acid and base, respectively. In addition, a divalent metal ion (Mn(2+) or Mg(2+)) is essential in helping the catalysis. Binding of the metal ion also plays an important role in stabilizing the quaternary structural integrity of the enzyme.     

Molecular basis for a direct interaction between the Syk protein-tyrosine kinase and phosphoinositide 3-kinase

After engagement of the B cell receptor for antigen, the Syk protein-tyrosine kinase becomes phosphorylated on multiple tyrosines, some of which serve as docking sites for downstream effectors with SH2 or other phosphotyrosine binding domains. The most frequently identified binding partner for catalytically active Syk identified in a yeast two-hybrid screen was the p85 regulatory subunit of phosphoinositide 3-kinase. The C-terminal SH2 domain of p85 was sufficient for mediating an interaction with tyrosine-phosphorylated Syk. Interestingly, this domain interacted with Syk at phosphotyrosine 317, a site phosphorylated in trans by the Src family kinase, Lyn, and identified previously as a binding site for c-Cbl. This site interacted preferentially with the p85 C-terminal SH2 domain compared with the c-Cbl tyrosine kinase binding domain. Molecular modeling studies showed a good fit between the p85 SH2 domain and a peptide containing phosphotyrosine 317. Tyr-317 was found to be essential for Syk to support phagocytosis mediated by FcgammaRIIA receptors expressed in a heterologous system. These studies establish a new type of p85 binding site that can exist on proteins that serve as substrates for Src family kinases and provide a molecular explanation for observations on direct interactions between Syk and phosphoinositide 3-kinase.     

Preferential nitration with tetranitromethane of a specific tyrosine residue in penicillinase from Staphylococcus aureus PCl. Evidence that the preferentially nitrated residue is not part of the active site but that loss of activity is due to intermolecular cross-linking.

1. Nitration of tyrosine residues of staphylococal penicillinase was accompanied by a partial loss of enzymic activity, which was not readily explained by nitration of a single residue. 2. Loss of activity correlated with low recovery of tyrosine plus nitrotyrosine, which was consistent with cross-linking. 3. The fraction of treated enzyme that was eluted from Sephadex G-75 earlier than native penicillinase was similar to the fraction of enzyme activity lost. Protein eluted in positions corresponding to monomer, dimer and higher oligomers respectively showed major bands in corresponding positions in sodium dodecyl sulphate/polyacrylamide-gel electrophoresis, indicating that the increase in molecular weight was due to intermolecular cross-linking. Monomeric enzyme containing up to 4 mol of nitrotyrosine/mol retained full catalytic activity. Dimeric enzyme retained 50% of normal activity, whereas higher oligomers retained an average of 8-15% of normal activity. 4. Monomeric enzyme isolated after treatment with equimolar tetranitromethane was nitrated predominantly at tyrosine-72.5. Reaction of reduced nitrated monomer with 1,5-difluoro-2,4-dinitrobenzene gave a monomeric, apparently cross-linked product with full catalytic activity. 6. It is concluded that tyrosine-72 plays no part in the active site. Its preferential nitration may be due to its being insufficiently exposed to be available for intermolecular cross-linking. This poperty may make it useful for attachment of a reporter group.     

PTEN catalysis of phospholipid dephosphorylation reaction follows a two-step mechanism in which the conserved aspartate-92 does not function as the general acid--mechanistic analysis of a familial Cowden disease-associated PTEN mutation

PTEN exerts its tumour suppressor function by dephosphorylating the phospholipid second messenger phosphatidylinositol-3,4,5-trisphosphate (PIP(3)). Herein, we demonstrate that the PTEN-catalysed PIP(3) dephosphorylation reaction involves two-steps: (i) formation of a phosphoenzyme intermediate (PE) in which Cys-124 in the active site is thiophosphorylated, and (ii) hydrolysis of PE. For protein tyrosine- and dual-specificity phosphatases, catalysis requires the participation of a conserved active site aspartate as the general acid in Step 1. Its mutation to alanine severely limits PE formation. However, mutation of the homologous Asp-92 in PTEN does not significantly limit PE formation, indicating that Asp-92 does not act as the general acid. G129E is a common germline PTEN mutations found in Cowden syndrome patients. Mechanistic analysis reveals that this mutation inactivates PTEN by both significantly slowing down Step 1 and abolishing the ability to catalyse Step 2. Taken together, our results highlight the mechanistic similarities and differences between PTEN and the conventional protein phosphatases and reveal how a disease-associated mutation inactivates PTEN.     

Catalytic and noncatalytic nucleotide binding sites of the Escherichia coli F1 ATPase. Amino acid sequences of beta-subunit tryptic peptides labeled with 2-azido-ATP

Under appropriate conditions tight, noncovalent binding of 2-azido-adenine nucleotides to either catalytic or noncatalytic binding sites on the E. coli F1-ATPase occurs. After removal of unbound ligands, UV-irradiation results primarily in the covalent incorporation of nucleotide moieties into the beta-subunit in both catalytic and noncatalytic site labeling experiments. Minor labeling of the alpha-subunit was also observed. After trypsin digestion and purification of the labeled peptides, microsequencing studies identified two adjacent beta-subunit tryptic peptides labeled by 2-azido-ADP or -ATP. These beta-subunit peptides were labeled on tyrosine-331 (catalytic sites) and tyrosine-354 (noncatalytic sites) in homology with the labeling patterns of the mitochondrial and chloroplast enzymes.     

Deprotonation of tyrosines in bacteriorhodopsin as studied by Fourier transform infrared spectroscopy with deuterium and nitrate labeling

Fourier transform infrared (FTIR) difference spectra are presented for bacteriorhodopsin (BR) at low temperature. Previous FTIR measurements have identified several tyrosine residues that change their absorption characteristics between light-adapted BR and dark-adapted BR, or between intermediates K and M [Dollinger, G., Eisenstein, L., Lin, S.-L., Nakanishi, K., Odashima, K., & Termini, J. (1986) Methods Enzymol. 127, 649-662]. These changes were explained by protonation/deprotonation of tyrosine moieties and perturbation of the protein environment surrounding tyrosines. A tyrosine deprotonation was observed to occur between intermediates K and M. The present studies confine the deprotonation to being between intermediates L and M and show that no tyrosines undergo changes between the K and the L states. Evidence is presented that none of the tyrosines undergoing changes at low temperature can be assigned to tyrosine-64. The environmental changes of these tyrosines are discussed in relation to the proton pumping mechanism. Their spatial relation to the chromophore is also discussed. At least two tyrosines are suggested to reside close to the retinal binding site. The reactive groups of the nitrated tyrosine-64 are speculated to be remote from the Schiff base and the active tyrosines but can possibly interact sterically with the ionone ring of the retinal.