Kinetic studies on the reaction mechanism of sarcosine oxidase.

A sarcosine oxidase (sarcosine: oxygen oxidoreductase (demethylating), EC 1.5.3.1) isolated from Corynebacterium sp. U-96 contains both covalently bound FAD and noncovalently bound FAD. The noncovalent FAD reacts with sarcosine, the covalent FAD with molecular oxygen (Jorns, M.S. (1985) Biochemistry 24, 3189-3194). To clarify the reaction mechanism of the enzyme, kinetic investigations were performed by the stopped-flow method as well as by analysis of the overall reaction. The absorption spectrum of the enzyme in the steady state was very similar to that of the oxidized enzyme, and no intermediate enzyme species, such as a semiquinoid flavin, was detected. The rate for anaerobic reduction of the noncovalently bound FAD and the covalently bound FAD by sarcosine were 31 and 6.7 s-1, respectively. The latter value was smaller than the value of respective Vmax/e0 obtained by the overall reaction kinetics (Vmax/e0: the maximum velocity per enzyme concentration). Both rate constants for oxidation of the two FADs by molecular oxygen were 100 s-1. A reaction scheme of sarcosine oxidase is proposed to account for the data obtained; 70% of the enzyme functions via a fully reduced enzyme, and 30% of the enzyme goes along a side-path, without forming the fully reduced enzyme. In addition, it is suggested that the reactivity of noncovalently bound FAD with sarcosine is affected by the oxidation-reduction state of the covalently bound FAD, in contrast to the reactivity of the covalently bound FAD with molecular oxygen, which is independent of the oxidation-reduction state of the noncovalently bound FAD.

Cysteine residues in the active site of Corynebacterium sarcosine oxidase.

Sarcosine oxidase from Corynebacterium sp. U-96 is inhibited by iodoacetamide (IAM) and the inhibition is prevented by the substrate analog, sodium acetate. To elucidate the mechanism of inhibition of the enzyme by IAM, we determined the amino acid sequences around the IAM-reactive cysteine residues, and the effects of the modification on the enzyme activity and the oxidation-reduction of the FAD moieties of the enzyme. The enzyme was specifically labeled with [14C]IAM, and the labeled subunit B was digested with trypsin and chymotrypsin. The HPLC profiles of the proteolytic digests showed mainly two radioactive peaks. The 14C-labeled peptides were purified, and their N-terminal sequences were determined to be Cys-Gly-Thr-Pro-Gly-Ala-Gly-Tyr (TC-1) and Ala-Gly-Ile-Ala-Cys-Xaa-Asp-Xaa-Val-Ala(-)- (TC-2). Peptide TC-2 contains a covalent FAD-binding sequence [Asx-His-Val-Ala; Shiga et al. (1983) Biochem. Int., 6, 737]. [14C]IAM-incorporation into the TC-1 sequence was strongly inhibited by sodium acetate. The N-terminal amino acid sequence of the CNBr fragment containing the TC-1 sequence (65 residues) was determined. According to the secondary structure predictions, Gly-Thr-Pro-Gly-Ala-Gly of the TC-1 sequence is located between the beta sheet and alpha helix of the sequence, indicating the presence of an AMP-binding site in the TC-1 region. The activity of the enzyme treated with IAM in the presence and absence of sodium acetate was not inhibited by sodium sulfite, which is known to react specifically with covalent FAD.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding reaction of hemin to globin.

Binding of hemin to globin was studied in the presence of 25 mM caffeine by measuring CD and optical absorption changes in the Soret region. CD and optical absorption spectra after mixing equimolar amounts of hemin and globin were the same as those of ferric hemoglobin. In contrast, addition of excess globin to hemin formed a complex that was distinguishable from ferric hemoglobin in terms of the CD and optical absorption spectra. By comparing the spectra of the complex with those of various hemoglobin derivatives, it was concluded that the complex was globin which carried a hemin exclusively on the alpha chain. This means that the alpha chain of the globin molecule has a greater affinity for hemin than the beta chain, as observed by other investigators using hemin-cyanide. The rate of binding of hemin to globin was estimated by the use of CD and optical absorption stopped-flow apparatus. The rate of hemin binding to the alpha chain of globin was obtained by mixing hemin and excess globin, and that to the beta chain was obtained by mixing equimolar concentrations of hemin and globin. The results showed that hemin was bound to the alpha chain in the globin molecule to form a transient intermediate, followed by its transformation into another intermediate, the transformation was the rate-limiting step, and the beta chain in the globin molecule had a greater affinity for hemin after hemin binding to the alpha chain than before.

Kinetic characterization of antibody-catalyzed insertion of a metal ion into porphyrin.

The insertion of a copper (II) ion into mesoporphyrin by a monoclonal catalytic antibody has been investigated kinetically by measuring the increase in Soret absorbance due to the production of copper (II)-mesoporphyrin. The initial rate of the reaction showed saturation kinetics as a function of the mesoporphyrin concentration, while it increased linearly with an increase in the copper (II) concentration. Based on observations, a scheme for the reaction was proposed: mesoporphyrin binds to the antibody to form a complex, and copper (II) binds to the complex to yield copper (II)-mesoporphyrin. Kinetic parameters for the respective steps were estimated, and the thermodynamic parameters were calculated. The binding of mesoporphyrin to the antibody was endothermic and entropically driven. This implies that hydrophobic interactions are an important factor in the binding. Free energy profiles for the antibody-catalyzed and uncatalyzed reactions were drawn by use of the obtained thermodynamic parameter values. The results demonstrate that the rate acceleration by, the antibody is ascribable to transition-state stabilization, and suggest that the structure of mesoporphyrin in the complex is more distorted than that of free mesoporphyrin.

Remarkable functional aspects of myoglobin induced by diazaheme prosthetic group.

The iron complex of beta,delta-diazamesoporphyrin III, a molecular hybrid of porphyrin and phthalocyanine, was incorporated into apomyoglobin to investigate novel biological aspects of myoglobin. The reconstituted ferric protein forms an internal hemichrome with the iron-bound distal histidine. The reduced ferrous protein has extraordinarily high affinities for O2 and CO. The ferrous myoglobin is capable of strong binding with pyridine, imidazole, cyanide, and azide, and reacts moderately with ammonia. The NO complex exhibited 5-coordinate to 6-coordinate transition over 150 min. The instability of 5-coordinate NO heme is consistent with a high affinity of imidazole to the ferrous heme. The kinetic analyses of the ferrous derivatives suggest the importance of the pi orbitals in neutral ligands as well as the negative charges in anionic ligands. A high affinity of imidazole to ferrous diazaheme accounts for the internal hemochrome formation in ferrous myoglobin containing phthalocyanines.

Interaction between alpha 1 and beta 1 subunits of human hemoglobin.

We prepared normal and modified alpha and beta globulin chains in which C-terminal residues were enzymatically removed. The CD spectra of the deoxy form of these chains and the reconstituted modified Hb's were measured in the Soret region. The CD spectra of the modified Hb's were markedly different from the arithmetic means of respective spectra of their constituent chains. This difference was ascribed to the interaction between alpha 1 and beta 1 subunits to make the alpha 1 beta 1 dimer. The peak wavelength of the difference CD spectra could be classified into two groups, one was 433 +/- 1 nm and the other 437 +/- 1 nm. A comparison of this classification with the previously identified quaternary structures revealed that the R and T structures showed a maximum of the difference CD spectra at 437 +/- 1 nm and 433 +/- 1 nm, respectively. These results indicated that the R and T structures differed in the interaction between alpha 1 and beta 1 subunits.

Reconstitution of human fetal hemoglobin from isolated alpha and gamma chains.

The reconstitution of hemoglobin F from isolated alpha and gamma chains was studied. An equimolar amounts of the alpha and gamma chains were mixed and incubated in 10 mM potassium phosphate buffer, pH 7.0, at 25 degrees C. Formation of hemoglobin F in the mixture was measured by separating hemoglobins on a cation exchange HPLC. Time courses of the formation of Hb F were independent of the protein concentration and could be analyzed on an exponential process with a first-order rate constant of (2.0 +/- 0.4) x 10(-3) h-1. Under the experimental conditions the isolated gamma chain existed as tetramer dominantly. These results suggest that the overall reaction of the reconstitution of hemoglobin F is limited by the dissociation step of the self-associated gamma chain.

Presence of AMP binding sequence in subunit B of Corynebacterium sarcosine oxidase.

Corynebacterium sarcosine oxidase is composed of A, B, C, and D subunits. To characterize these subunits, we analyzed their N-terminal sequences by automated Edman degradation. We identified 20 residues of subunit A, 58 of B, 31 of C, and 33 of D. There was no homology among these sequences according to secondary structure predictions and hydrophilicity profiles. But we found that subunit B contained a sequence homologous to that of the AMP-binding site of other flavoproteins.

Kinetic study on myoglobin refolding monitored by five optical probe stopped-flow methods.

The refolding kinetics of horse cyanometmyoglobin induced by concentration jump of urea was investigated by five optical probe stopped-flow methods: absorption at 422 nm, tryptophyl fluorescence at around 340 nm, circular dichroism (CD) at 222 nm, CD at 260 nm, and CD at 422 nm. In the refolding process, we detected three phases with rate constants of > 1 x 10(2) s-1, (4.5-9.3) s-1, and (2-5) x 10(-3) s-1. In the fastest phase, a substantial amount of secondary structure (approximately 40%) is formed within the dead time of the CD stopped-flow apparatus (10.7 ms). The kinetic intermediate populated in the fastest phase is shown to capture a hemindicyanide, suggesting that a "heme pocket precursor" recognized by hemindicyanide must be constructed within the dead time. In the middle phase, most of secondary and tertiary structures, especially around the captured hemindicyanide, have been constructed. In the slowest phase, we detected a minor structural rearrangement accompanying the ligand-exchange reaction in the fifth coordination of ferric iron. We present a possible model for the refolding process of myoglobin in the presence of the heme group.

Specific orientation of porphyrin at the binding site of catalytic antibody.

The catalytic antibody which catalyzes insertion of a cupric ion into mesoporphyrin bound ferric N-methyl mesoporhyrin and ferric mesoporhyrin to yield the respective complexes. The binding affinity of cyanide to the ferric iron in the complexes was compared with that of free ferric porphyrins. The results indicate that the one side of the porphyrin plane in the complex is thoroughly exposed to surrounding solvents and the other side interacts with the protein molecule. The cyanide binding suggests the specific orientation of distorted porphyrin at the binding site of the antibody.

Kinetics of formation of antibody-ferric porphyrin complex with peroxidase activity.

The antibody 2B4 combines with ferric mesoporphyrin to form an antibody-ferric mesoporphyrin complex which has a peroxidase activity. Formation of the complex was investigated by measuring the absorption in the Soret region after mixing the antibody and ferric mesoporphyrin. A rapid increase and a gradual decrease in the absorption were observed, and the respective first-order rate constants were obtained. From the dependence of values of the rate constants on the concentration of ferric mesoporphyrin, the complex formation was explained by a plausible mechanism, in which the antibody associated with ferric mesoporphyrin to form the first complex followed by a conformational change to the second complex. The first complex had almost the same peroxidase activity as that of the second complex. Our results suggests that the antibody acquires the peroxidase activity as soon as ferric mesoporphyrin is incorporated into its binding site, and that there will be no protein ligand to the iron center of ferric mesoporphyrin in the complex.

Reconstitution of myoglobin from apoprotein and heme, monitored by stopped-flow absorption, fluorescence and circular dichroism.

The reconstitution reaction of ferric cyanomyoglobin from apomyoglobin and hemin dicyanide was investigated with a stopped-flow apparatus by the use of five kinds of probes; (a) Soret absorption, (b) fluorescence quenching of tryptophan, (c) far-ultraviolet CD, (d) near-ultraviolet CD, and (e) Soret CD. After mixing of apomyoglobulin with equimolar amounts of hemin dicyanide, the Soret absorption band was shifted to longer wavelengths within 10 ms. The shifted band kept its shape for a few seconds, and then gradually shifted to shorter wavelengths. A rate constant of the slow reaction was 1.1 x 10(-2) s-1. Time courses of fluorescence quenching followed a second-order reaction with a rate constant of 9 x 10(7) M-1 s-1. Far-ultraviolet CD recovered to the level of native state within the response time of an apparatus (= 64 ms). Near-ultraviolet CD and Soret CD changed with first-order rate constants of 5-30 s-1 and 5 x 10(-3) s-1 respectively. On the basis of the kinetic results we propose the following reconstitution pathway of myoglobin. Apomyoglobin has essentially a highly folded structure similar to myoglobin, but there are some differences in the secondary structure between them. In the first step, heme enters the pocket-like site of apomyoglobin and interacts with surrounding hydrophobic residues in the pocket, and then the interaction may give a complete ordered structure to the protein. Second, the tertiary structure of the heme pocket is partly constructed. Third, the iron-proximal His bond occurs, followed by the attainment of the final conformation. This sequence of the events shows that the polypeptide chain is entirely folded before the completion of three-dimensional structure of the heme pocket. The reconstitution pathway is fairly different from that of the alpha subunit of hemoglobin reported by Leutzinger and Beychok [Proc. Natl Acad. Sci. USA (1981) 78, 780-784], which described how a drastic recovery in helicity was observed on the heme-binding, and that the recovery is introduced by the formation of the heme pocket structure. The difference in the results found for the alpha subunit and myoglobin suggests a difference in conformation: in apomyoglobin most of the helices are arranged and folded around a helix core to form a compact structure as a whole, while in apo-alpha subunit some helices are not folded around the helix core. Helix D, which is absent in the alpha subunit, may play an important role in folding of the helices.

Kinetics of the reconstitution of hemoglobin from semihemoglobins alpha and beta with heme.

Kinetics of the reconstitution of hemoglobin from semihemoglobins alpha and beta with hemin dicyanide have been investigated using three kinds of stopped-flow technique (Soret absorption, fluorescence quenching of tryptophan, and Soret CD). The semihemoglobins alpha and beta are occupied by heme in the alpha and beta chains, respectively, the other chain being heme-free. Based on the kinetic results, the following scheme for the reconstitution is proposed; First, hemin dicyanide enters the pocket-like site of the apo chains. Second, in semihemoglobin alpha, the CN-ligand in the fifth coordination position of iron is replaced by the imidazole ring of the proximal His immediately after the heme insertion. In contrast, semihemoglobin beta changes its conformation after the heme insertion, and this is followed by the ligand replacement. Finally, the partial structure changes induced by the ligand replacement propagate onto the whole molecule and the final conformation is attained. The results indicate that semihemoglobin alpha retains a more rigid and organized structure, and more closely approaches its final structure than does semihemoglobin beta.

The reaction of Aspergillus niger catalase with methyl hydroperoxide.

The formation of Compound I from Aspergillus niger catalase and methyl hydroperoxide (CH3OOH) has been investigated kinetically by means of rapid-scanning stopped-flow techniques. The spectral changes during the reaction showed distinct isobestic points. The second-order rate constant and the activation energy for the formation of Compound I were 6.4 x 10(3) M-1s-1 and 10.4 kcal.mol-1, respectively. After formation of Compound I, the absorbance at the Soret peak returned slowly to the level of ferric enzyme with a first-order rate constant of 1.7 x 10(-3) s-1. Spectrophotometric titration of the enzyme with CH3OOH indicates that 4 mol of peroxide react with 1 mol of enzyme to form 1 mol of Compound I. The amount of Compound I formed was proportional to the specific activity of the catalase. The irreversible inhibition of catalase by 3-amino-1,2,4-triazole (AT) was observed in the presence of CH3OOH or H2O2. The second-order rate constant of the catalase-AT formation in CH3OOH was 3.0 M-1 min-1 at 37 degrees C and pH 6.8 and the pKa value was estimated to be 6.10 from the pH profile of the rate constant of the AT-inhibition. These results indicate that A. niger catalase forms Compound I with the same properties as other catalases and peroxidases, but the velocity of the Compound I formation is lower than that of the others.

Delayed appearance of the catalytic activity by immunization of a rabbit compared with the hapten binding.

Polyclonal antibodies catalyzing the hydrolysis of carbonate ester were generated by immunizing a rabbit with hapten(4-nitrophenyl phosphate II) conjugated to keyhole limpet hemocyanin. The hydrolytic activity of IgG purified from antisera exhibited plateu one month later than the simple hapten-binding. The affinity of IgG with substrate increased even after the hapten-binding reached plateu. These suggest a strategy to generate good polyclonal catalytic antibodies and the day to fuse spleen cell with myeloma cell to get good monoclonal catalytic antibodies.

Chemical modification of a catalytic antibody that accelerates the hydrolysis of carbonate esters.

Catalytic antibody, 4A1, catalyzes the hydrolysis of p-nitrophenyl alkyl carbonate. To determine the amino acid residues related to the catalytic activity of the antibody, we studied the effect of Tyr-, Trp-, and Lys-selective reagents on the catalytic activity and determined the amino acid sequences around the modified amino acid residues. We found that the Tyr-selective reagent is the most effective one and the modification of one Tyr residue results in the complete loss of the catalytic activity. The modified Tyr residue is identified to be Tyr-32 in the CDR-1 of the L chain.

A catalytic antibody that accelerates the hydrolysis of carbonate esters. Prediction of the binding-site structure of the substrate.

Monoclonal antibodies catalyzing the hydrolysis of p-nitrophenyl alkyl carbonate were obtained using p-nitrophenyl phosphonate as hapten. One of the antibodies, 4A1, has a relatively high activity for the substrate having a bulky group. To determine the amino acid residues related to the binding of the bulky group, we determined the amino acid sequences of VL and VH regions of 4A1 by the cycle sequencing method, built the three-dimensional structure of the V regions, labeled 4A1 with [14C]phenyl glyoxal in the presence and absence of I-1 or I-13, and analyzed the labeled incubation mixture with SDS-PAGE. From these results, the possibility that Arg-H28 of the heavy chain is involved in binding the bulky group of the substrate is discussed.