Cyclic peptide formation catalyzed by an antibody ligase.

Cyclic hexapeptides represent a class of compounds with important, diverse biological activities. We report herein that the antibody 16G3 catalyzes the cyclization of d-Trp-Gly-Pal-Pro-Gly-Phe small middle dotp-nitrophenyl ester (8a) to give c-(d-Trp-Gly-Pal-Pro-Gly-l-Phe) (11a). The antibody does not, however, catalyze either epimerization or hydrolysis. The resulting rate enhancement of the cyclization by 16G3 (22-fold) was sufficient to form the desired product in greater than 90% yield. In absolute rate terms, the turnover of 16G3 is estimated to be 2 min(-1). The background rate of epimerization of 8a was reduced from 10 to 1% and hydrolysis from 50 to 4% in the presence of 16G3. As expected, the catalytic effects of 16G3 were blocked by the addition of an amount of the hapten equal to twice the antibody concentration. We also synthesized three diastereomers of 8a: the d-Trp(1)-d-Phe(6) (8b), l-Trp(1)-l-Phe(6) (8c), and l-Trp(1)-d-Phe(6) (8d) hexapeptides as well as d-Trp'-l-Trp(6) (12) and d-Phe'-l-Phe(6) (13). As expected, the rate enhancement by 16G3 was greatest for 8a, because the stereochemistry of Trp(1) and Phe(6) matches that of the corresponding residues on the hapten used to induce the biosynthesis of 16G3. A model of the variable domain of 16G3 was generated from the primary sequence using the antibody structural database to guide the model construction. The resulting model provided support for some previously proposed interpretations of the kinetic data, while providing valuable new insights for others.

Peptide synthesis catalyzed by an antibody containing a binding site for variable amino acids.

Monoclonal antibodies, induced with a phosphonate diester hapten, catalyzed the coupling of p-nitrophenyl esters of N-acetyl valine, leucine, and phenylalanine with tryptophan amide to form the corresponding dipeptides. All possible stereoisomeric combinations of the ester and amide substrates were coupled at comparable rates. The antibodies did not catalyze the hydrolysis of the dipeptide product nor hydrolysis or racemization of the activated esters. The yields of the dipeptides ranged from 44 to 94 percent. The antibodies were capable of multiple turnovers at rates that exceeded the rate of spontaneous ester hydrolysis. This achievement suggests routes toward creating a small number of antibody catalysts for polypeptide syntheses.

Mechanism of DNA replication fidelity for three mutants of DNA polymerase I: Klenow fragment KF(exo+), KF(polA5), and KF(exo-).

Inhibition of the pre-steady-state burst of nucleotide incorporation by a single incorrect nucleotide (nucleotide discrimination) was measured with the Klenow fragment of DNA polymerase I [KF(exo+)]. For the eight mispairs studied on three DNA sequences, only low levels of discrimination ranging from none to 23-fold were found. The kinetics of dNTP incorporation into the 9/20-mer at low nucleotide concentrations was also determined. A limit of greater than or equal to 250 s-1 was placed on the nucleotide off-rate from the KF(exo+)-9/20-dTTP complex in accord with nucleotide binding being at equilibrium in the overall kinetic sequence. The influence of the relatively short length of the 9/20-mer on the mechanism of DNA replication fidelity was determined by remeasuring important kinetic parameters on a 30/M13-mer with high homology to the 9/20-mer. Pre-steady-state data on the nucleotide turnover rates, the dATP(alpha S) elemental effect, and the burst of dAMP misincorporation into the 30/M13-mer demonstrated that the kinetics were not affected by the length of the DNA primer/template. The effects on fidelity of two site-specific mutations, KF(polA5) and KF(exo-), were also examined. KF(polA5) showed an increased rate of DNA dissociation and a decreased rate of polymerization resulting in less processive DNA synthesis. Nevertheless, with at least one misincorporation event, that of dAMP into the 9/20-mer, KF(polA5) displays an increased replication fidelity.(ABSTRACT TRUNCATED AT 250 WORDS)

Kinetic mechanism of DNA polymerase I (Klenow).

The minimal kinetic scheme for DNA polymerization catalyzed by the Klenow fragment of DNA polymerase I (KF) from Escherichia coli has been determined with short DNA oligomers of defined sequence. A key feature of this scheme is a minimal two-step sequence that interconverts the ternary KF.DNAn.dNTP and KF.DNAn+1.PPi complexes. The rate is not limited by the actual polymerization but by a separate step, possibly important in ensuring fidelity [Mizrahi, V., Henrie, R. N., Marlier, J. F., Johnson, K. A., & Benkovic, S. J. (1985) Biochemistry 24, 4010-4018]. Evidence for this sequence is supplied by the observation of biphasic kinetics in single-turnover pyrophosphorolysis experiments (the microscopic reverse of polymerization). Data analysis then provides an estimate of the internal equilibrium constant. The dissociations of DNA, dNTP, and PPi from the various binary and ternary complexes were measured by partitioning (isotope-trapping) experiments. The rate constant for DNA dissociation from KF is sequence dependent and is rate limiting during nonprocessive DNA synthesis. The combination of single-turnover (both directions) and isotope-trapping experiments provides sufficient information to permit a quantitative evaluation of the kinetic scheme for specific DNA sequences.

Mechanism of the idling-turnover reaction of the large (Klenow) fragment of Escherichia coli DNA polymerase I.

The mechanism of the idling-turnover reaction catalyzed by the large (Klenow) fragment of Escherichia coli DNA polymerase I has been investigated. The reaction cycle involved is one of excision/incorporation, in which the 3' deoxynucleotide residue of the primer DNA strand is partitioned into its 5'-mono- and 5'-triphosphate derivatives, respectively. Mechanistic studies suggest the 5'-monophosphate product is formed in the first step by simple 3'----5' exonucleolytic cleavage. Rapid polymerization follows with the concomitant release of inorganic pyrophosphate. In the second step, the 5'-triphosphate product is generated by a pyrophosphorolysis reaction, which, despite the low concentration of pyrophosphate that has accumulated, occurs at a rate that is comparable with that of the parallel 3'----5' hydrolysis reaction.

The effect of the 3',5' thiophosphoryl linkage on the exonuclease activities of T4 polymerase and the Klenow fragment.

The 3'----5' exonuclease activities of T4 DNA polymerase and the Klenow fragment of Polymerase I towards the phosphoryl and thiophosphoryl 3',5' linkage were examined under comparable conditions of idling-turnover, duplex hydrolysis and turnover during polymerization. With the T4 enzyme there is a negligible effect of thiosubstitution on these activities; with the Klenow fragment there is a greater than one hundred-fold reduction in rate with the thiolinkage for the exonuclease but not polymerization activities. This inability to hydrolyze rapidly the thiophosphoryl linkage extends to the hydrolytic activity of Exonuclease III. The quantitation of the exonuclease activities of these three proteins under various conditions should aid in the successful employment of thiophosphoryl nucleoside triphosphates for their incorporation into DNA.

Kinetic relationships between the various activities of the formyl-methenyl-methylenetetrahydrofolate synthetase.

The formyl-methenyl-methylenetetrahydrofolate synthetase from chicken liver catalyzes the formation of the 10-formyl- and 5,10-methenyltetrahydrofolate cofactors via three enzymatic activities. In this report we define the kinetic relationships between the activities of this trifunctional protein. An investigation of the time course for 10-formyl cofactor synthesis by computer modeling indicates that commencing with tetrahydropteroyltriglutamate, the activities of the synthetase/cyclohydrolase couple act as separate enzymic species. In contrast, 10-formyl cofactor formation from the 5,10-methylene cofactor utilizing the dehydrogenase/cyclohydrolase couple is described by a single or interactive site model that partitions the 5,10-methenyl intermediate primarily (85%) to the 10-formyl product. An unusual characteristic of the latter coupled activities is the negligible cyclohydrolase activity toward exogenous 5,10-methenyl cofactor, which serves as substrate in the individual activity assay. This is based on (1) competitive inhibition by 5,11-methenyltetrahydrohomofolate against the 5,10-methenyl derivative in the cyclohydrolase-catalyzed hydrolysis but the absence of such inhibition in the dehydrogenase/cyclohydrolase couple and (2) a pulse-chase experiment showing the failure of chase 5,10-methenyl cofactor to dilute the 10-formyl product derived from the coupled activities. The result of this coupling is to minimize the concentration of the 5,10-methenyl species, consistent with its noninvolvement in de novo purine biosynthesis.

L(-)-10-Formyltetrahydrofolate is the cofactor for glycinamide ribonucleotide transformylase from chicken liver.

It is shown that L(-)-10-formyltetrahydrofolate serves as the cofactor for glycinamide ribonucleotide transformylase from chicken liver. The utilization of L(-)-10-formyl-H4folate was not previously recognized, because L-(+)-10-formyl-H4folate is an excellent competitive inhibitor of the enzyme, Ki = 0.75 +/- 0.07 microM, and historically the transformylase assay was carried out with a mixture of diastereomers. The results are discussed in relation to the utilization of L(+)-5,10-methenyl-H4folate.

On the cofactor specificity of glycinamide ribonucleotide and 5-aminoimidazole-4-carboxamide ribonucleotide transformylase from chicken liver.

Tests of 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) and glycinamide ribonucleotide (GAR) transformylase cofactor specificity were conducted with 5-and/or 8-deazafolate analogues formylated at N-10. Several of these compounds were found to serve as cofactors for both the enzymes. The finding that 10-formyl-8-deazafolate can be used by AICAR transformylase eliminates those mechanisms requiring cyclization to a methenyl derivative prior to carbon unit transfer for this transformylase. Surprisingly, a similar analogue, 10-formyl-5,8-deazafolate, is very effective as a cofactor for GAR transformylase in the presence or absence of the trifunctional protein which is required for 5,10-methenyl-H4-folate activity with this transformylase. This finding suggests that the trifunctional protein modulates GAR transformylase cofactor specificity by supplying the active cofactor as the N10-formyl species, possibly through a transport process that avoids its dissociation into solution.

Investigation of the pre-steady-state kinetics of fructose bisphosphatase by employment of an indicator method.

The pre-steady-state kinetics for the hydrolysis of fructose 1,6-bisphosphate by rabbit liver fructose bis-phosphatase have been investigated by stopped-flow kinetics utilizing an acid-base indicator method that permits the continuous monitoring of the inorganic phosphate product. The reaction sequence is characterized by two successive first-order steps followed by establishment of the steady-state rate. The first exponential process results from a conformational change in the protein that is dye sensitive owing to a perturbation of an acidic residue on the protein. A second process reflects the rapid initial turnover of all four subunits of the enzyme with the concomitant release of inorganic phosphate followed by the rate-limiting step of the catalytic cycle. This latter step may involve a product release (fructose 6-phosphate) or a second conformational change. The catalytic cycle ends with decay of the enzyme to its initial unreactive resting state.

Binding and kinetic data for rabbit liver fructose-1,6-bisphosphatase with Zn2+ as cofactor.

Atomic absorption determinations of zinc content were employed to demonstrate the technique to obtain zinc-free rabbit liver fructose-1,6-bisphosphatase (D-fructose-1,6-bisphosphate 1-phosphohydrolase, EC 3.1.3.11). Reactivation of the apoenzyme by Zn(2+) is rapid (within 1 min) and restores up to 96% of the initial specific activity. Gel filtration measurements showed that the enzyme contains four binding sites for zinc per molecule, one per subunit. The dissociation constants for the initial two binding sites are less than 0.1 muM. In the presence of a substrate analog, (alpha + beta) methyl D-fructofuranoside 1,6-bisphosphate, at a level where two analog molecules are bound per phosphatase molecule, a total of eight Zn(2+) ions bind at 8 muM Zn(2+), revealing the presence of additional binding sites, including the catalytic one. The activity in the presence of Zn(2+) is maximal at ca. 8 muM Zn(2+), which corresponds to saturation of the four subunit sites plus the catalytic sites in the presence of substrate. At metal ion concentrations less than 10 muM, the order of activation is Zn(2+) > Mn(2+) > Mg(2+). In kinetic assays with two metal cofactors the effect of Zn(2+) at concentrations less than 10 muM on either the Mg(2+) or the Mn(2+) assays is inhibitory owing to the apparent formation of mixed (two different elements) metal ion-enzyme complexes possessing a catalytic activity that is measureable but lower than anticipated if the catalysis by the various metal ions is simply additive. Hence the activation by EDTA of the Mg(2+) and Mn(2+) assays is explicable in terms of Zn(2+) removal, thus eliminating mixed metal species. Collectively these observations suggest that fructose-1,6-bisphosphatase may function in vivo as a Zn(2+) metalloprotein.

Stereochemistry of methylene transfer involving 5,10-methylenetetrahydrofolate.

The stereochemistry of the transfer catalyzed by rabbit liver serine transhydroxymethylase (EC 2.1.2.1) of the prochiral hydroxymethyl group from serine to tetrahydrofolate to form 5,10-methylenetetrahydrofolate was studied. Initial kinetic studies on labeled 5,10-methylenetetrahydrofolate showed that nonenzymatic racemization of the prochiral methylene center was buffer dependent and was slow under the conditions employed. Specifically tritiated (3R)- and (3S)-serines were employed to study the transfer reaction. Reactions were carried out under various conditions and the stereochemistry of the methylene carbon of the 5,10-methylenetetrahydrofolate produced was determined. The enzyme was shown to be partially stereospecific for this transfer reaction, proceeding with a loss of about 50% of the stereochemical purity of the transferred carbon center. Possible mechanistic interpretations of this finding are discussed.