Characterization of the reversible nature of the reaction catalyzed by sphingolipid ceramide N-deacylase. A novel form of reverse hydrolysis reaction.

Sphingolipid ceramide N-deacylase catalyzes a reversible reaction in which the amide linkages of the ceramides of various sphingolipids are cleaved or synthesized. Hydrolysis of sphingolipids by the enzyme proceeded efficiently at acidic pH in the presence of high concentrations of detergents, whereas the reverse reaction tended to be favored at neutral pH with a decrease in the detergent concentration. Although the catalytic efficiency (V(max)/K(m)) of the hydrolysis and reverse reactions was changed mainly by the concentration of detergents in the reaction mixture, V(max) and K(m) for the reverse reaction were relatively higher than those for the forward reaction, irrespective of the detergent concentration. The reverse reaction proceeded most efficiently when the molar ratio of lyso-sphingolipids and fatty acids was fixed at 1 : 1-2, the yield of the reaction exceeding 70-80%. The reverse and exchange (transacylation) reactions did not require ATP, CoA, metal ions or addition of organic solvents. Studies using inhibitors and chemical modifiers of the enzyme protein suggested that both the hydrolysis and condensation reactions are catalyzed at the same catalytic domain. These results indicate that the reverse hydrolysis reaction of the enzyme is unique, being completely different from those of lipases, proteases and glycosidases reported to date.     

A convenient method for the synthesis of amine-terminated poly(ethylene oxide) and poly(epsilon-caprolactone)

A convenient synthetic route to prepare amine-terminated poly(ethylene oxide) (PEO) and poly(epsilon-caprolactone) (PCL) was described. The strategy involved two-step reactions, the condensation of hydroxyl-terminated PEO and PCL with N-benzyloxycarbonyl amino acid followed by the catalytic hydrogenation under mild conditions. NMR and GPC measurements indicated that the reactions proceeded nearly quantitatively. Amine-terminated PEO thus prepared was used to initiate the polymerization of alpha-(N(epsilon)-benzyloxycarbonyl-L-lysine) N-carboxy anhydride [lys(Z)-NCA], and the results confirmed that the reactivity of the amino group was high.     

Novel binuclear chiral zirconium catalysts used in enantioselective strecker reactions

A novel binuclear chiral zirconium catalyst was successfully used in enantioselective Strecker reactions. The catalyst was readily prepared from zirconium t-butoxide (Zr(OtBu)4), (R)-6,6'-dibromo-1, 1'-bi-2-naphthol ((R)-6-Br-BINOL), and (R)-3,3'-dibromo-1, 1'-bi-2-naphthol ((R)-3-Br-BINOL) to form unique binuclear structure. It was revealed that a combination of (R)-6-Br-BINOL and (R)-3-Br-BINOL was essential in these asymmetric reactions and that much lower selectivities were obtained by using other combinations. Two-component (an imine and hydrogen cyanide (HCN)) and three-component (an aldehyde, an amine, and HCN) Strecker reactions proceeded smoothly in the presence of a catalytic amount of the chiral zirconium catalyst to afford the corresponding alpha-amino nitrile derivatives in high yields with high enantioselectivities.     

The oxidative part of the glucose-oxidase reaction

1. Kinetic parameters of the oxidative part of glucose-oxidase reaction have been measured with 16 different electron-acceptors and glucose as a substrate. 2. In each case, the rate-limiting portion of the oxidative part of reaction was the formation of the E-FADH2.Acceptor-complex; this rate was pH-independent around the pH-optimum of the enzyme. 3. In each case, E-FADH2 acceptor-complex was undetectable in the steady-state kinetics, with the exception of cytochrome-c. 4. The rates of redox reactions between various forms of reduced 5-ethyl-lumiflavin and five different electron-acceptors have been examined with a conventional spectrophotometry. In each case, it was found that the reactions proceeded at high rates whenever thermodynamically feasible, and were totally prevented in the opposite case. 5. Molecular oxygen was able to oxidize only the neutral form of 5-ethyl-1,5-dihydrolumiflavin to its radical form, at a moderate rate; all other forms of reduced 5-ethyl-lumiflavin were not oxidized by O2. 6. By the comparison of enzymatic and model redox reactions, it was possible to establish the minimal mechanism of the oxidative part of the glucose-oxidase catalytic cycle.     

Surfactant-protease complex as a novel biocatalyst for peptide synthesis in hydrophilic organic solvents*

The peptide synthesis from N-acetyl-L-phenylalanine ethyl ester with alaninamide catalyzed by a surfactant-protease complex has been performed in anhydrous hydrophilic organic solvents. Proteases derived from various sources were converted to surfactant-coated complexes with a nonionic surfactant. The surfactant-subtilisin Carlsberg (STC) complex had a higher enzymatic activity than the other protease complexes and the initial reaction rate in tert-amyl alcohol was 26-fold that of STC lyophilized from an optimum aqueous buffer solution. Native STC hardly catalyzed the same reaction. The addition of water to the reaction medium activated the lyophilized STC, however, the reaction rate was much lower than that of the STC complex, and a hydrolysis reaction preferentially proceeded. The STC complex exhibited a high catalytic activity in hydrophilic organic solvents (e.g. tertiary alcohol). The addition of dimethylformamide as a cosolvent improved the solubility of amino acid amides and further activated the STC complex due to the water mimicking effect. When hydrophilic amino acid amides were employed as an acyl acceptor, the peptide formation proceeded efficiently compared to that using hydrophobic substrates. The surfactant-STC complex is a powerful biocatalyst for peptide synthesis because the STC complexes display a high catalytic activity in anhydrous hydrophilic organic solvents and did not require the excess amount of water. Thus the side (hydrolysis) reaction is effectively suppressed and the yield in the dipeptide formation is considerably high.     

Highly enantioselective alkynylation of aldehydes using a new BINOL/Ti(OiPr)4/chiral sulfonamide catalyst system

A series of sulfonamides (2-4) were prepared from natural amino acids and used as additives in the BINOL-Ti(OiPr)(4) catalyzed enantioselective alkynylation of aldehydes. The reactions proceeded smoothly with good yields and very high ee's (up to 99%) in most cases.     

Formation and reactions of the Wurster's blue radical cation during the reaction of N,N,N',N'-tetramethyl-p-phenylenediamine with oxyhemoglobin.

The aromatic amine N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) reacted directly with oxyhemoglobin in a catalytic reaction resulting in formation of ferrihemoglobin. The second order rate constant of the reaction was found to be 5.5 M-1.s-1. The stable Wurster's blue radical cation produced ferrihemoglobin at rates greater 10(3) M-1.s-1, i.e. more than two orders of magnitude faster than the parent amine. In contrast to the reactions of aminophenols with hemoglobin, free hydrogen peroxide was formed which additionally contributed to ferrihemoglobin formation. Since ferrihemoglobin formation proceeded by two orders of magnitude faster than autoxidation of TMPD, oxyhemoglobin itself acted as an oxidase/peroxidase resulting in electron abstraction from the amino alone pair electrons.     

Multifunctional hydrolytic catalysis: VI. Catalytic hydrolysis of p-nitrophenyl acetate by N-(4-imidazolylmethyl)benzohydroxamic acid

A bifunctional catalyst, N-(4-imidazolylmethyl)benzohydroxamic acid, was synthesized from benzohydroxamic acid and chloromethylimidazole, and used for the hydrolysis of p-nitrophenyl acetate. The reaction proceeded via the formation of the acetyl hydroxamate and its subsequent decomposition. The deacylation step was shown to be general base-catalyzed by the intramolecular imidazole group on the basis of the deuterium solvent kinetic isotope effect of 2.0. The efficiency of water attack on the acetyl hydroxamate was enhanced 130-fold by the imidazole group. The catalytic process is compared with the reactions of related monofunctional compounds, and finally its significance as a model of the charge relay system is discussed.     

Mechanisms of cytochrome P450 and peroxidase-catalyzed xenobiotic metabolism.

The cytochrome P450 enzyme systems catalyze the metabolism of a wide variety of naturally occurring and foreign compounds by reactions requiring NADPH and O2. Cytochrome P450 also catalyzes peroxide-dependent hydroxylation of substrates in the absence of NADPH and O2. Peroxidases such as chloroperoxidase and horseradish peroxidase catalyze peroxide-dependent reactions similar to those catalyzed by cytochrome P450. The kinetic and chemical mechanisms of the NADPH and O2-supported dealkylation reactions catalyzed by P450 have been investigated and compared with those catalyzed by P450 and peroxidases when the reactions are supported by peroxides. Detailed kinetic studies demonstrated that chloroperoxidase- and horseradish peroxidase-catalyzed N-demethylations proceed by a Ping Pong Bi Bi mechanism whereas P450-catalyzed O-dealkylations proceed by sequential mechanisms. Intramolecular isotope effect studies demonstrated that N-demethylations catalyzed by P450s and peroxidases proceed by different mechanisms. Most hemeproteins investigated catalyzed these reactions via abstraction of an alpha-carbon hydrogen whereas reactions catalyzed by P-450 and chloroperoxidase proceeded via an initial one-electron oxidation followed by alpha-carbon deprotonation. 18O-Labeling studies of the metabolism of NMC also demonstrated differences between the peroxidases and P450s. Because the hemeprotein prosthetic groups of P450, chloroperoxidase, and horseradish peroxidase are identical, the differences in the catalytic mechanisms result from differences in the environments provided by the proteins for the heme active site. It is suggested that the axial heme-iron thiolate moiety in P450 and chloroperoxidase may play a critical role in determining the mechanism of N-demethylation reactions catalyzed by these proteins.     

Total Synthesis of (+)-(2S,3R)-Piscidic Acid via Catalytic Asymmetric Dihydroxylation of a Trisubstituted Olefin

(+)-(2S,3R)-Piscidic acid was efficiently synthesized with high optical purity (90% e.e.) via Sharpless catalytic asymmetric dihydroxylation of a trisubstituted olefin in only 6 steps from commercially available 4-hydroxyphenylpyruvic acid as the starting material. The reaction proceeded with high optical purity by using the chiral ligands, dihydroquinidine 2,5-diphenyl-4,6-pyrimidinediyl diether or dihydroquinidine 1,4-anthraquinonediyl diether.     

Novel asymmetric oxy-michael addition reaction of the chiral ketones to the achiral gamma--or delta-hydroxy-alpha,beta-unsaturated carbonyl compounds

A novel asymmetric oxy-Michael addition reaction was developed. In the presence of a catalytic amount of base, chiral ketones 1 and 2, derived from D-glucose and D-fructose, respectively, reacted with omega-hydroxy enones or enoates 3a-e, 17 and 21 to form the hemiacetal-derived alkoxide which underwent stereoselective intramolecular Michael addition to give cyclic acetals. Although the stereoselectivities in the formation of the five-membered acetal rings were modest, six-membered ring formation proceeded with high stereoselectivity and the utility of the reaction was demonstrated by a simple syntheses of natural products.     

Purine nucleoside phosphorylase. Kinetic mechanism of the enzyme from calf spleen.

Ribose 1-phosphate, phosphate, and acyclovir diphosphate quenched the fluorescence of purine nucleoside phosphorylase at pH 7.1 and 25 degrees C. The fluorescence of enzyme-bound guanine was similar to that of anionic guanine in ethanol. Guanine and ribose 1-phosphate bound to free enzyme, whereas inosine and guanosine were not bound to free enzyme in the absence of phosphate. Thus, synthesis proceeded by a random mechanism, and phosphorolysis proceeded by an ordered mechanism. Steady-state kinetic data for the phosphorolysis of 100 microM guanosine were fitted to a bifunctional kinetic model with catalytic rate constants of 22 and 1.3 s-1. The dissociation rate constants for guanine from the enzyme-guanine complex at high and low phosphate concentrations were similar to the catalytic rate constants. Fluorescence changes of the enzyme during phosphorolysis suggested that ribose 1-phosphate dissociated from the enzyme ribose 1-phosphate-guanine complex rapidly and that guanine dissociated from the enzyme-guanine complex slowly. The association and dissociation rate constants for acyclovir diphosphate, a potent inhibitor of the enzyme (Tuttle, J. V., and Krenitsky, T. A. (1984) J. Biol. Chem. 259, 4065-4069), were also dependent on phosphate concentration. The effects of phosphate are discussed in terms of a dual functional binding site for phosphate.     

The hydrogenation of phospholipid-bound unsaturated fatty acids by a homogeneous, water-soluble, palladium catalyst

The hydrogenation of unsaturated phospholipids by palladium di(sodium alizarine monosulphonate) activated for 5 min under H2 proceeded rapidly at 20 degrees C and 1 atm. H2. Multibilayer liposomes of dioleoyl- and dilinolenoylphosphatidylcholine were hydrogenated at similar rates while dilinoleoyl- and 1-palmitoyl-2-oleoylphosphatidylcholine were hydrogenated at slightly slower rates. The reduction of polyunsaturated fatty acids gave rise to a variety of natural and unnatural positional cis and trans isomers which were largely reduced further to saturated fatty acids as the hydrogenation continued. Dioleoylphosphatidylethanolamine was attacked by the catalyst more slowly at 20 degrees C than was the equivalent phosphatidylcholine molecular species. Experiments conducted using mixtures of phosphatidylethanolamine and phosphatidylcholine in varying proportions also suggested that phospholipids are slightly more susceptible to catalytic hydrogenation in the bilayer phase than in the hexagonalII phase. Understanding the sequence of hydrogenation reactions involving these one and two component lipid preparations is useful in interpreting the action of the palladium catalyst on living cells under the same mild conditions.     

Facile synthesis of N-glycosyl amides using a N-glycosyl-2,4-dinitrobenzenesulfonamide and thioacids

N-Glucosyl-2,4-dinitrobenzenesulfonamide was prepared from N-acetyl-d-glucosamine and 2,4-dinitrobenzenesulfonyl chloride. Amidation of several thioacids using the N-glucosylsulfonamide donor proceeded smoothly to give the desired N-glucosylamides in good to high yields. The amidation reactions were carried out at room temperature, under mild conditions, and were completed in a very short time.     

Easy preparation of dehydroalanine building blocks equipped with oxazolidin-2-one chiral auxiliaries,and applications to the stereoselective synthesis of substituted tryptophans

Chiral dehydroamino acid building blocks are versatile starting materials for the preparation of optically active unusual amino acids and other compounds of pharmacological interest. Herein we disclose the expedient preparation of dehydroalanines (ΔAla) equipped with oxazolidin-2-one (Oxd) chiral auxiliaries, Ts-Oxd-ΔAla-OMe. These compounds have been obtained in high yields from dipeptides Ts-Ser/Thr/phenylSer-Ser-OMe by the one-pot cyclization–elimination reaction with N,N-disuccinimidyl carbonate and catalytic DIPEA. To test the efficacy of the chiral auxiliaries in controlling asymmetric transformations, the Friedel–Crafts alkylations of indoles carrying diverse substituents were performed in the presence of Lewis and Brønsted acids. The reactions proceeded with good to excellent diastereomeric ratios giving (S)- or (R)-tryptophan derivatives, isolated very conveniently by simple flash chromatography. To verify the utility of this approach, optically pure (S)-2-methyltryptophan and (S)-5-fluorotryptophan were obtained and utilized to prepare analogues of endogenous opioid peptide endomorphin-1, H-Tyr-Pro-Trp-PheNH₂.     

Mutational analysis of the conserved TGES loop of sarcoplasmic reticulum Ca2+-ATPase

Crystal structures have shown that the conserved TGES loop of the Ca2+-ATPase is isolated in the Ca2E1 state but becomes inserted in the catalytic site in E2 states. Here, we have examined the kinetics of the partial reaction steps of the transport cycle and the binding of the phosphoryl analogs BeF, AlF, MgF, and vanadate in mutants with alterations to the TGES residues. The mutations encompassed variation of size, polarity, and charge of the side chains. Differential effects on the Ca2E1P --> E2P, E2P --> E2, and E2 --> Ca2E1 reactions and the binding of the phosphoryl analogs were observed. In the E183D mutant, the E2P --> E2 dephosphorylation reaction proceeded at a rate as high as one-third that of the wild type, whereas it was very slow in the other Glu183 mutants, including E183Q, thus demonstrating the need for a negatively charged carboxylate group to catalyze dephosphorylation. By contrast, the Ca2E1P --> E2P transition was accomplished at a reasonable rate with glutamine in place of Glu183, but not with aspartate, indicating that the length of the Glu183 side chain, in addition to its hydrogen bonding potential, is critical for Ca2E1P --> E2P. This transition was also slowed in mutants with alteration to other TGES residues. The data provide functional evidence in support of the proposed role of Glu183 in activating the water molecule involved in the E2P --> E2 dephosphorylation and suggest a direct participation of the side chains of the TGES loop in the control and facilitation of the insertion of the loop in the catalytic site. The interactions of the TGES loop furthermore seem to facilitate its disengagement from the catalytic site during the E2 --> Ca2E1 transition.     

Disproportionation reaction of disulfides promoted by nitric oxide (NO) in the presence of oxygen.

Two disulfides brought about disproportionation reaction to afford an unsymmetrical disulfide in 50% yield with a catalytic amount of nitric oxide in the presence of oxygen. The reaction proceeded faster when alkyl disulfides were employed for the reaction, and the substituent effects suggested that the reaction commenced with an oxidative process.     

pH dependent kinetic studies of lipoamide dehydrogenase catalysis.

1. Kinetic studies of lipoamide dehydrogenase and its modified enzymes catalyzing lipoamide oxidoreduction and ancillary reactions at various pH are compared. 2. The asymptotic kinetics of lipoamide oxidoreductions switch between the ping pong and ordered mechanisms by varying pH of the reactions. 3. pH-rate profiles of these reactions are bell-shaped suggesting the participation of 2 ionizable residues with pK values of 6.6 +/- 0.5 and above 8 respectively. 4. The unusually high pK value for the catalytic site histidine is attributed to its involvement in an ion-pair formation. 5. In the absence of the catalytic site histidine, the pH-rate profile for the lipoamide reduction of the photooxidized enzyme is no longer bell-shaped but it is similar to those of the transhydrogenation and NADH-oxidation of the native enzyme. 6. This implies the participation of a low-pK protonated group in these reactions.     

A computational method for design of connected catalytic networks in proteins

Computational design of new active sites has generally proceeded by geometrically defining interactions between the reaction transition state(s) and surrounding side‐chain functional groups which maximize transition‐state stabilization, and then searching for sites in protein scaffolds where the specified side‐chain–transition‐state interactions can be realized. A limitation of this approach is that the interactions between the side chains themselves are not constrained. An extensive connected hydrogen bond network involving the catalytic residues was observed in a designed retroaldolase following directed evolution. Such connected networks could increase catalytic activity by preorganizing active site residues in catalytically competent orientations, and enabling concerted interactions between side chains during catalysis, for example, proton shuffling. We developed a method for designing active sites in which the catalytic side chains, in addition to making interactions with the transition state, are also involved in extensive hydrogen bond networks. Because of the added constraint of hydrogen‐bond connectivity between the catalytic side chains, to find solutions, a wider range of interactions between these side chains and the transition state must be considered. Our new method starts from a ChemDraw‐like two‐dimensional representation of the transition state with hydrogen‐bond donors, acceptors, and covalent interaction sites indicated, and all placements of side‐chain functional groups that make the indicated interactions with the transition state, and are fully connected in a single hydrogen‐bond network are systematically enumerated. The RosettaMatch method can then be used to identify realizations of these fully‐connected active sites in protein scaffolds. The method generates many fully‐connected active site solutions for a set of model reactions that are promising starting points for the design of fully‐preorganized enzyme catalysts.     

Molecular architecture of cytochrome oxidase and its transition on treatment with alkali or sodium dodecyl sulfate.

In dimeric cytochrome oxidase [EC 1.9.3.1], one of the two heme a molecules of one monomeric unit has been proposed to be converted by the other unit, thus becoming latent in terms of catalytic functions (1). As the dimer was split into two monomers by treatment with alkali or sodium dodecyl sulfate (SDS), it was shown that the intensity of circular dichroism (CD) in the Soret region due to heme a decreased, probably reflecting release of the strain on the latent heme. On the other hand, the profile of magnetic circular dichroism (MCD) was nearly unchanged during this conversion, except for a weakening of the signal due to deprotonation of the heme during the alkali treatment. When the monomer was further dissociated into constituent subunits in strong alkali or at high concentrations of SDS, the CD spectrum disappeared almost completely, indicating loss of the asymmetric interactions of the chromophoric heme a with its immediate environments, consisting of the subunit assembly. The MCD pattern also suffered a small change as the dissociation proceeded, and a specific pattern appeared as the Schiff base was finally formed. The Schiff base formation of cytochrome oxidase in strong alkali proceeded in two steps whether the heme iron was in the oxidized or reduced state. As a consequence of the initial rapid reaction, the enzyme was suggested to have been disintegrated into constituent subunits with heme a being attached nonspecifically to either one, and structural characteristics dependent on the redox state were completely lost. The Arrehenius plot for this rapid change showed a break, indicating a transition in the structure of the cytochrome oxidase assembly, although no such phenomenon was observed during the slow reaction. Activation parameters in the rapid and slow reactions for the oxidized and reduced oxidase are given. Based on these findings, as well as other considerations, a molecular architecture of this enzyme is proposed; the role of heme a in anchoring four 14,000-dalton polypeptides into the minimal functional unit catalyzing the aerobic oxidation of ferrocytochrome c is emphasized.