Comparative affinity labeling with reactive UDP-glucose analogues: possible locations of five lysyl residues around the substrate bound to potato tuber UDP-glucose pyrophosphorylase.

By using two reactive analogues of UDP-Glc, uridine di- and triphosphopyridoxals, we have recently probed the substrate-binding site in potato tuber UDP-Glc pyrophosphorylase [EC 2.7.7.9]. In this work, pyridoxal diphospho-alpha-D-glucose was used for the same purpose. This compound is also a reactive UDP-Glc analogue but having its reactive group on the opposite side of the pyrophosphate linkage to those of the above two compounds. The enzyme was rapidly inactivated when incubated with the compound at very low concentrations followed by reduction with sodium borohydride. The inactivation was almost completely prevented by UDP-Glc and UTP. Complete inactivation correspond to the incorporation of 1.0 mol of the reagent per mol of enzyme monomer. The label was found to be distributed in five lysyl residues (Lys-263, Lys-329, Lys-367, Lys-409, and Lys-40. All of these results were similar to those obtained previously with the other compounds, suggesting the presence of a cluster of five lysyl residues at or near the substrate-binding site of this enzyme. However, the incorporations of labels into each lysyl residue differed depending on the compounds used. The substrate retarded the incorporations in different manners. Based on the combined results of the present and previous studies, a hypothetical model is presented for the possible locations of the five lysyl residues around the substrate bound to the enzyme. This model is consistent with the kinetic properties of mutant enzymes in which the five lysyl residues were individually replaced by glutamine via site-directed mutagenesis.     

Low modularity of aminoacyl-tRNA substrates in polymerization by the ribosome

Aminoacyl-transfer RNAs contain four standardized units: amino acids, an invariant 3′-terminal CCA, trinucleotide anticodons and tRNA bodies. The degree of interchangeability of the three variable modules is poorly understood, despite its role in evolution and the engineering of translation to incorporate unnatural amino acids. Here, a purified translation system is used to investigate effects of various module swaps on the efficiency of multiple ribosomal incorporations of unnatural aminoacyl-tRNA substrates per peptide product. The yields of products containing three to five adjacent l-amino acids with unnatural side chains are low and cannot be improved by optimization or explained simply by any single factor tested. Though combinations of modules that allow quantitative single unnatural incorporations are found readily, finding combinations that enable efficient synthesis of products containing multiple unnatural amino acids is challenging. This implies that assaying multiple, as opposed to single, incorporations per product is a more stringent assay of substrate activity. The unpredictability of most results illustrates the multifactorial nature of substrate recognition and the value of synthetic biology for testing our understanding of translation. Data indicate that the degree of interchangeability of the modules of aminoacyl-tRNAs is low.     

Development of peptide substrates for trypsin based on monomer/excimer fluorescence of pyrene

An assay using fluorogenic peptides based on the monomer/excimer fluorescence features of pyrene was developed to measure the proteolytic activity of trypsin, a serine protease. Two pyrene moieties were incorporated into the respective N- and C-terminus of the peptides as (pyrene)-C-Xaa-C-(pyrene), where Xaa represents amino acid residues of 5-, 6-, 7-, or 8-mer containing the cleavage site of trypsin. The proteolytic cleavage of the substrates led to an increase in monomer fluorescence and a decrease in excimer fluorescence of pyrene. Kinetic parameters (k(cat) and K(m)) for the enzymatic hydrolysis of the substrates were successfully determined. The parameters are dependent on the chain length of the substrate and optimal catalytic activity was obtained with substrates that consisted of 9 or 10 amino acid residues. The present assay system is sensitive and the preparation of the substrate is very simple. We suggest that this method may be suitable for high-throughput screening and also applicable to the characterization of other proteases.     

The reciprocal exclusion by L-dopa (L-3,4-dihydroxyphenylalanine) and L-tyrosine of their incorporation as single units into a soluble rat brain protein.

Several compounds, structurally and metabolically related to phenylalanine and tyrosine, were tested for their effects on the incorporations of phenylalanine and tyrosine as single units into a protein of the soluble subcellular fraction of rat brain. Of the compounds tested, only L-dopa (L-3,4-dihydroxyphenylalanine) inhibited these incorporations. Further, L-dopa was incorporated into a protein of the same fraction in such a way that it excluded the incorporation of tyrosine as a single unit. Conversely, tyrosine inhibited and excluded the incorporation of L-dopa. The incorporation of L-dopa required ATP (apparent Km = 0.23mM), KCl (apparent Km = 20mM) and MgCl2 (optimal concentration range, 5-16mM). These requirements were similar to those previously determined for the incorporation of tyrosine and phenylalanine. The inactivation rate of the enzymic systems for L-tyrosine and L-dopa incorporations, when kept at 37 degrees C, was the same for both amino acids (half-life = 80 min). It is suggested that the acceptor for the incorporation of dopa is the same as that for the incorporation of tyrosine.     

Characterization of TAT-mediated transport of detachable kinase substrates

The conjugation of peptides derived from the HIV TAT protein to membrane-impermeant molecules has gained wide acceptance as a means for intracellular delivery. Numerous studies have addressed the mechanism of uptake and kinetics of TAT translocation, but the cytosolic concentrations and bioavailability of the transported cargo have not been well-characterized. The current paper utilizes a microanalytical assay to perform quantitative single-cell measurements of the concentration and accessibility of peptide-based substrates for protein kinase B (PKB) and Ca(2+)/calmodulin-activated kinase II. The substrate peptide and TAT were conjugated through a releasable linker, either a disulfide or photolabile bond. Free substrate peptide concentrations of approximately 10(-20)-10(-18) moles were attainable in a cell when substrates were delivered utilizing these conjugates. The substrate peptides delivered as a disulfide conjugate were often present in the cytosol as several oxidized forms. Brief exposure of cells loaded with the photolabile conjugates to UVA light released free substrate peptide into the cytosol. Substrate peptide delivered by either conjugate was accessible to cytosolic kinase as demonstrated by the efficient phosphorylation of the peptide when the appropriate kinase was active. After incubation of the conjugated substrate with cells, free, kinase-accessible substrate was detectable in less than 30 min. Release of the majority of loaded substrate peptide from sequestered organelles occurred within 1 h. The utility of the photocleavable conjugates was demonstrated by measuring the activation of PKB in 3T3 cells after addition of varying concentrations of platelet-derived growth factor.     

Kinetics and substrate specificity of membrane-reconstituted peptide transporter DtpT of Lactococcus lactis

The peptide transport protein DtpT of Lactococcus lactis was purified and reconstituted into detergent-destabilized liposomes. The kinetics and substrate specificity of the transporter in the proteoliposomal system were determined, using Pro-[(14)C]Ala as a reporter peptide in the presence of various peptides or peptide mimetics. The DtpT protein appears to be specific for di- and tripeptides, with the highest affinities for peptides with at least one hydrophobic residue. The effect of the hydrophobicity, size, or charge of the amino acid was different for the amino- and carboxyl-terminal positions of dipeptides. Free amino acids, omega-amino fatty acid compounds, or peptides with more than three amino acid residues do not interact with DtpT. For high-affinity interaction with DtpT, the peptides need to have free amino and carboxyl termini, amino acids in the L configuration, and trans-peptide bonds. Comparison of the specificity of DtpT with that of the eukaryotic homologues PepT(1) and PepT(2) shows that the bacterial transporter is more restrictive in its substrate recognition.     

The N-hydroxysuccinimide ester of Boc-[S-(3-nitro-2-pyridinesulfenyl)]-cysteine: a heterobifunctional cross-linking agent

Synthetic cysteine-containing peptides were unidirectionally conjugated to albumin via disulfide bonds using the S-(3-nitro-2-pyridinesulfenyl) derivative of cysteine. This method employs the N-hydroxysuccinimide ester of Boc-[S-(3-nitro-2-pyridinesulfenyl)]-cysteine, a protected amino acid derivative used in peptide synthesis, as a heterobifunctional cross-linking agent. The disulfide bonds in the conjugates are formed by the reaction of free thiols with S-(3-nitro-2-pyridinesulfenyl) groups. Bovine albumin was conjugated in this manner to several synthetic peptides derived from human fibrin. Amino acid analysis of these conjugates demonstrated incorporations of from 6 to 11 peptide molecules per molecule of protein.     

Detection of femtomole quantities of proteases by high-performance liquid chromatography

Small amounts (femtomoles) of proteases, as might be present in cell extracts or secretions, were detected using reverse-phase high-performance liquid chromatography. Carboxymethylated lysozyme and cytochrome c were incubated with trypsin and chymotrypsin. Peptide peaks were present in the column elution profiles (as detected by absorbance, 206 nm) from incubations with as little as 0.1 fmol of chymotrypsin and 5 fmol of trypsin. In addition, the disappearance of the substrate peak or the increase in peptide peaks could be quantitated by integrating the areas under the peaks. In this way estimates of relative enzyme concentrations or duration of incubation can be determined. However, when [14C]lysozyme was used as a substrate and the radioactivity of collected peaks was measured, the assay was less sensitive than that using uv absorbance. This finding probably is related to the selective radiolabeling of the substrate, in contrast to uv detection, which should detect all the peptides. The technique reported in this paper should prove to be a sensitive indicator of proteolytic activity in cell or tissue preparations where the use of synthetic ester or amide substrates might lead to erroneous conclusions regarding the nature of the enzymatic activity present. Furthermore, by the collection of the peptides generated, one would have the ability to determine amino acid compositions or sequences and thus ascertain the specificity of enzymatic cleavage.     

Pre-steady-state kinetic studies of the fidelity of human DNA polymerase mu

DNA polymerase mu (Polmu), an X-family DNA polymerase, is preferentially expressed in secondary lymphoid tissues with yet unknown physiological functions. In this study, Polmu was overexpressed in Escherichia coli and purified to homogeneity. The purified enzyme had a lifetime of <20 min at 37 degrees C, but was stable for over 3 h at 25 degrees C in an optimized reaction buffer. The fidelity of human Polmu was thus determined using pre-steady-state kinetic analysis of the incorporation of single nucleotides into undamaged DNA 21/41-mer substrates at 25 degrees C. Single-turnover saturation kinetics for all 16 possible deoxynucleotide (dNTP) incorporations and for four matched ribonucleotide (rNTP) incorporations were measured under conditions where Polmu was in molar excess over DNA. The polymerization rate (k(p)), binding affinity (K(d)), and substrate specificity (k(p)/K(d)) are 0.006-0.076 s(-1), 0.35-1.8 microM, and (8-64) x10(-3) microM(-1) s(-1), respectively, for matched incoming dNTPs, (2-30) x 10(-5) s(-1), 7.3-135 microM, and (4-61) x 10(-7) microM(-1) s(-1), respectively, for mismatched incoming dNTPs, and (2-73) x 10(-4) s(-1), 45-302 microM, and (7-1300) x 10(-7) microM(-1) s(-1), respectively, for matched incoming rNTPs. The overall fidelity of Polmu was estimated to be in the range of 10(-3)-10(-5) for both dNTP and rNTP incorporations and was sequence-independent. The sugar selectivity, defined as the substrate specificity ratio of a matched dNTP versus a matched rNTP, was measured to be in the range of 492-10959. In addition to a slow and distributive DNA polymerase activity, Polmu was identified to possess a weak strand-displacement activity. The potential biological roles of Polmu are discussed.     

Bimodal regulatory effect of melittin and phospholipase A2-activating protein on human type II secretory phospholipase A2

Melittin and phospholipase A2-activating protein (PLAP) are known as efficient activators of secretory phospholipase A2(sPLA2) types I, II, and III when phospholipid liposomes are used as substrate. The present study demonstrates that both peptides can either inhibit or activate sPLA2 depending on the peptide/phospholipid ratio when erythrocyte membranes serve as a biologically relevant substrate. Low concentrations of melittin and PLAP were observed to inhibit sPLA2-triggered release of fatty acids from erythrocyte membranes. The inhibition was reversed at melittin concentrations above 1 microM. PLAP-induced inhibition of sPLA2 persisted steadily throughout the used concentration range (0-150 nM). The two peptides induced a dose-dependent activation of sPLA2 at low concentrations, followed by inhibition when model membranes were used as substrate. This opposite modulatory effect on biological membranes and model membranes is discussed with respect to different mechanisms the interaction of the regulatory peptides with the enzyme molecules and the substrate vesicles.     

Enantioselective ester hydrolysis catalyzed by beta-cyclodextrin conjugated with beta-hairpin peptides

Designed cyclodextrin-peptide conjugates, which have one or two beta-hairpin peptides, have been synthesized as catalysts for ester hydrolysis. One or two beta-hairpin peptides were located at the primary hydroxyl group side of beta-cyclodextrin so as to arrange two histidine residues that act as a general acid and a general base catalysts and provide the substrate recognition subsite. Kinetic studies revealed that the two-beta-hairpin peptide was more effective than that of the one-beta-hairpin peptide for substrate recognition.     

Peptides that bind the HIV-1 integrase and modulate its enzymatic activity--kinetic studies and mode of action

Several peptides that specifically bind the HIV-1 integrase (IN) and either inhibit or stimulate its enzymatic activity were developed in our laboratories. Kinetic studies using 3'-end processing and strand-transfer assays were performed to study the mode of action of these peptides. The effects of the various peptides on the interaction between IN and its substrate DNA were also studied by fluorescence anisotropy. On the basis of our results, we divided these IN-interacting peptides into three groups: (a) IN-inhibitory peptides, whose binding to IN decrease its affinity for the substrate DNA - these peptides increased the K(m) of the IN-DNA interaction, and were thus inhibitory; (b) peptides that slightly increased the K(m) of the IN-DNA interaction, but in addition modified the V(max) and K(cat) values of the IN, and thus stimulated or inhibited IN activity, respectively; and (c) peptides that bound IN but had no effect on its enzymatic activity. We elucidated the approximate binding sites of the peptides in the structure of IN, providing structural insights into their mechanism of action. The IN-stimulating peptide bound IN in several specific sites that did not bind any of the inhibitory peptides. This may account for its unique activity.     

Apparent transinhibition of peptide uptake in the scutellum of barley grain

The uptake of glycylsarcosine (Gly-Sar) into scutella separated from germinating grains of barley ( Hordeum vulgare L. cv. Himalaya) is inhibited by other peptides; in most cases the inhibition is not purely competitive but of a mixed type (simultaneous increase in the apparent K_m and decrease in V_max) (Sopanen, T. 1979. FEBS Lett. 108: 447–450). The aim of the present experiments was to elucidate the mechanism of the mixed inhibition by studying how peptides already taken up into the cells affect the uptake of Gly-Sar.
When scutella were preincubated in the presence of various peptides, 11 of the 13 peptides tested inhibited the subsequent uptake of Gly-Sar by 10 to 45%. The inhibition, studied in detail with leucylleucine and prolylproline, was due to a decrease in V_max. The two peptides having no effect were glycylglycine and D-alanyl-L-alanine which are the only peptides known to date acting as purely competitive inhibitors when present together with the substrate Gly-Sar.
Preincubation with leucine, proline and alanine was not inhibitory, although preincubation with the corresponding dipeptides was. This result, together with the demonstration of intact leucylleucine in the scutella after preincubation with leucylleucine, indicates that the inhibition was caused by the intact peptides.
The results support the notion that in the mixed type inhibition the increase in the apparent K_m is due to competition for the carrier at the outside of the membrane, while the decrease in V_max is due to peptides taken up and binding to the carrier at the inside of the membrane.     

Biosynthesis of the dimethylbenzene moiety of riboflavin and dimethylbenzimidazole: evidence for the involvement of C-1 of a pentose as a precursor.

The relative incorporations of specially labeled pyruvate, lactate, erythritol, D-erythrose, D-ribose, and D-glucose precursors into the dimethylbenzene carbon atoms of the 5,6-dimethylbenzimidazole unit of vitamin B12 by Propionibacterium shermanii have been determined. The incorporation data provide information regarding the putative four-carbon biosynthetic unit which is involved in the formation of 6,7-dimethyl-8-ribityllumazine and which is the source of the eight dimethylbenzene carbon atoms of both 5,6-dimethylbenzimidazole and riboflavin. The relative incorporations of the labeled lactate and pyruvate precursors are not consistent with either acetoin or 2,3-butanedione functioning as the four-carbon biosynthetic unit. The relative incorporations of the labeled hexose, pentose, and tetrose precursors indicate that the observed incorporation of C-1 of the pentose into the dimethylbenzene carbon atoms does not involve metabolism to a tetrose intermediate, but occurs more directly. It is concluded that the C-1 position of a pentose precursor is involved in the formation of the putative four-carbon biosynthetic unit.     

In vivo N-glycosylation and fate of Asn-X-Ser/Thr tripeptides

The minimum primary structural requirement for a tripeptide to serve as a substrate for oligosaccharyl transferase is the sequence -Asn-X-Ser/Thr-. In the present study the activities of three structurally different tripeptides containing acceptor sequences for oligosaccharyl transferase were compared in three systems: Xenopus oocytes, in which they were introduced into the cytoplasm by microinjection, cultured mammalian cells, and isolated rat liver microsomes. In the last two systems, the peptides were added exogenously to the culture or to the incubation medium, respectively. On the basis of lectin column and paper chromatographic analysis it was established that the microinjected acceptor tripeptides were glycosylated in Xenopus oocytes. However, lectin column analysis and retention of sensitivity to endoglycosidase H revealed that none of the three glycopeptides was processed to complex oligosaccharide chains and none was subsequently secreted. Rather, over a 24-h period the glycopeptides were degraded. Chloroquine was found to block this degradation process, but even under these conditions, the glycopeptides were not secreted into the medium. In the isolated microsomes the glycosylation of the acceptor tripeptides was time-dependent and the tripeptide with an iodotyrosine residue in the X position was found to be a poor substrate. When added to cultured mammalian cells, all three of the tripeptides were taken up, glycosylated, and subsequently secreted. These results are discussed in the context of the wide differences in glycosylation of the three peptides and their lack of secretion after glycosylation in Xenopus oocytes.     

Photoaffinity labelling of cholinesterases. Discrimination between active and peripheral sites.

Two para-dialkylaminobenzenediazonium salts, the dimethylamino (A) and dibutylamino (B) derivatives, are presented as structural probes for acetylcholinesterase and butyrylcholinesterase. While being reversible competitive inhibitors in the dark, A and B behave, upon irradiation and through the formation of arylcation species, as irreversible labels of ammonium-binding sites of both enzymes. The observed variations of the different inactivation rate constants point to a different structural environment for acetylcholinesterase-binding and butyrylcholinesterase-binding sites. Moreover, in the case of acetylcholinesterase, protection experiments with specific ligands (edrophonium and propidium) showed that the dimethylamino salt A exclusively labels the hydrolytic anionic site, whereas the dibutylamino salt B also labels the peripheral site. Specificities and stoechiometries of the incorporations were determined and, in the case of acetylcholinesterase, the irradiated protein was submitted to chemical degradation. Peptide maps were obtained by gel-permeation chromatography and HPLC, giving access to labelled peptides which belong either to the active or to the peripheral site.     

An Improved Screening Method for Inhibitors of Nucleic Acid Synthesis

A screening method for the antibiotics capable of inhibiting synthesis of nucleic acid in bacterial cells or mammalian tumor cells was investigated. The DNA and RNA syntheses in Bacillus subtilis 168 thymine^?, indole^? were studied by the assay of incorporations of ³H-thymine and ¹⁴C-uracil into the cells, respectively. With known antibiotics against nucleic acid synthesis, the adequacy of the method was examined, and the result proved that this method is more sensitive and specific than the conventional assay methods.

It was found as a new fact that cellocidin is a potent and specific inhibitor to the thymine incorporation into DNA.

By an almost similar procedure, an inhibitory effect of several antibiotics on the incorporations of ³H-thymidine and ¹⁴C-uridme into Ehrlich ascites carcinoma cells was also studied.     

Inhibitory effects of 3'deoxycytidine 5'-triphosphate and 3'-deoxyuridine 5'-triphosphate on DNA-dependent RNA polymerases I and II purified from Dictyostelium discoideum cells.

3'-Deoxycytidine 5'-triphosphate and 3'-deoxyuridine 5'-triphosphate were synthesized starting from cordycepin in good yield. The inhibitory effects of these nucleotides were examined in comparison with that of cordycepin 5'-triphosphate (3'-dATP) using purified DNA-dependent RNA polymerases I and II from Dictyostelium discoideum cells. Both nucleotide analogues strongly and competitively inhibited the incorporations of CTP and UTP into RNA by the RNA polymerases. The Km and Ki values for CTP and 3'-dCTP were 6.3 micro M and 3.0 micro M, respectively, and those for UTP and 3'-dUTP were 6.3 micro M and 2.0 micro M, respectively. These two analogues will be useful in studies at the molecular level on the relationship of template and substrate in RNA synthesis with chromatin, isolated nuclei or permeable cells, because they do not have any effect on poly (rA) synthesis.     

Substrate specificity and kinetic mechanism of human placental insulin receptor/kinase

The insulin receptor has been shown to be a protein kinase which phosphorylates its substrates on tyrosine residues. To examine the acceptor specificity of affinity-purified insulin receptor/kinase, hydroxyamino acid containing analogues of the synthetic peptide substrate Arg-Arg-Leu-Ile-Glu-Asp-Ala-Glu-Tyr-Ala-Ala-Arg-Gly were prepared. Substitution of serine, threonine, or D-tyrosine for L-tyrosine completely ablated the acceptor activity of the synthetic peptides. These peptides, along with a phenylalanine-containing analogue, did serve as competitive inhibitors of the insulin receptor/kinase with apparent Ki values in the range of 2-4 mM. These data suggest that the insulin receptor/kinase is specific for tyrosine residues in its acceptor substrate and imply that serine phosphate or threonine phosphate present in receptor is due to phosphorylation by other protein kinases. The kinetics of the phosphorylation of the L-tyrosine-containing peptide were examined by using prephosphorylated insulin receptor/kinase. Prephosphorylation of the receptor was necessary to maximally activate the kinase and to linearize the initial velocity of the peptide phosphorylation reaction. The data obtained rule out a ping-pong mechanism and are consistent with a random-order rapid-equilibrium mechanism for the phosphorylation of this peptide substrate. Additional experiments demonstrated that the autophosphorylated insulin receptor was not able to transfer the preincorporated phosphate to the synthetic peptide substrate. Thus, the insulin receptor/kinase catalyzes the reaction via a mechanism that does not involve transfer of phosphate from a phosphotyrosine-containing enzyme intermediate.