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Results for “Substrate Cycling”

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PubMed1979

Nuclear protein kinase activities during the cell cycle of HeLa S3 cells.

To ascertain the activity and substrate specificity of nuclear protein kinases during various stages of the cell cycle of HeLa S3 cells, a nuclear phospho-protein-enriched sample was extracted from synchronised cells and assayed in vitro in the presence of homologous substrates. The nuclear protein kinases increased in activity during S and G2 phase to a level that was twice that of kinases from early S phase cells. The activity was reduced during mitosis but increased again in G1 phase. When the phosphoproteins were separated into five fractions by cellulose-phosphate chromatography each fraction, though not homogenous, exhibited differences in activity. Variations in the activity of the protein kinase fractions were observed during the cell cycle, similar to those observed for the unfractionated kinases. Sodium dodecyl sulfate polyacrylamide gel electrophoretic analysis of the proteins phosphorylated by each of the five kinase fractions demonstrated a substrate specificity. The fractions also exhibited some cell cycle stage-specific preference for substrates; kinases from G1 cells phosphorylated mainly high molecular weight polypeptides, whereas lower molecular weight species were phosphorylated by kinases from the S, G2 and mitotic stages of the cell cycle. Inhibition of DNA and histone synthesis by cytosine arabinoside had no effect on the activity or substrate specificity of S phase kinases. Some kinase fractions phosphorylated histones as well as non-histone chromosomal proteins and this phosphorylation was also cell cycle stage dependent. The presence of histones in the in vitro assay influenced the ability of some fractions to phosphorylate particular non-histone polypeptides; non-histone proteins also appeared to affect the in vitro phosphorylation of histones.

Cell Cycle↗

PubMed2005

On the mechanism of isomerization of all-trans-retinol esters to 11-cis-retinol in retinal pigment epithelial cells: 11-fluoro-all-trans-retinol as substrate/inhibitor in the visual cycle.

The synthesis of 11-fluoro-all-trans-retinol (11-F-tROL), which is shown to be an excellent substrate for processing by visual cycle enzymes, is described. It is isomerized to its 11-cis congener subsequent to its esterification by lecithin retinol acyl transferase (LRAT) approximately as well as is vitamin A itself. The enzymatic turnover of 11-F-tROL is unaccompanied by enzyme inhibition. The previously reported lack of isomerization of this substrate had been suggested as evidence for a carbonium mechanism in the critical enzymatic isomerization pathway in vision. The mechanism of this process remains unknown.

Esters↗

PubMed2002

Phosphorylation of the septin cdc3 in g1 by the cdc28 kinase is essential for efficient septin ring disassembly.

The septins constitute a family of filament-forming proteins ubiquitous in eukaryotic species. We demonstrate here that the Saccharomyces cerevisiae septin, Cdc3, is a substrate of the cell cycle regulatory cyclin-dependent kinase (Cdk), Cdc28. Two serines near the C-terminus of Cdc3 are phosphorylated in a Cdc28-dependent manner. Analysis of a mutant allele that cannot be phosphorylated at these sites revealed an effect of Cdc28 phosphorylation of Cdc3 at the time of budding. Immunofluorescence analysis of wild-type and mutant Cdc3 indicated that prevention of phosphorylation at Cdc28-dependent sites impairs the disassembly of the old septin ring, which is inherited at mitosis but which usually disappears immediately prior to assembly of a new ring. Furthermore, immuno-fluorescence analysis of septin ring dynamics in a G1 cyclin (Cln) mutant suggests that G1 cyclin function is required for efficient ring disassembly. Thus, phosphorylation of Cdc3 by the Cdc28 kinase at the end of G1 may facilitate initiation of a new cell cycle by promoting disassembly of the obsolete septin ring from the previous cell cycle.

Amino Acid Sequence↗

PubMed1999

The reaction mechanism of ribonuclease II and its interaction with nucleic acid secondary structures.

Ribonuclease II is a processive 3'- to 5'-exoribonuclease in Escherichia coli with two binding sites: a catalytic site associated with the first few 3'-nucleotides and an anchor site binding nucleotides approximately 15 to 25 from the 3'-end. When RNase II degrades single-stranded helical poly(C), the enzyme-substrate complex dissociates at discrete intervals of 12 nucleotides. RNase II stalled at the last rC of single-stranded 3'-(rC)(n)(dC)(m) oligonucleotides. The more residues released, the faster the stalled complex dissociated and the less it inhibited RNase II activity, i.e. the enzyme-substrate association weakened progressively. Using phosphodiesterase I (PDE I) as a probe, a method was developed to identify cytidine residues in (32)P-oligonucleotides interacting with a protein. PAGE bands corresponding to nucleotides 1-6 from the 3'-end were consistent with interaction at the catalytic site, and following a gap, bands approximately 15 to 25 from the 3'-end, with anchor site association. Both 3' and 5' binding were necessary to maintain the complex. Of most significance, the original anchor site nucleotides remained fixed at the anchor site while the 3'-end was pulled, or threaded, through the catalytic site, i.e. the substrate did not 'slide' through the enzyme. DNA oligonucleotides with double-stranded stem-loops were good competitive inhibitors of RNase II. A 3'-single-stranded arm was essential, while optimal binding required both 5'- and 3'-arms. PDE I probing indicated that the nucleotides at the anchor site were specified by the spatial distance from the catalytic site, and on only one of the duplex strands. When degradation of a structured RNA paused or stopped, the RNase II-product commenced cycles of dissociation-reassociation. Duplex strand binding by RNase II made complex DNA or RNA structures accessible to degradation by other nucleases and further verified the PDE I footprinting method.

Base Sequence↗

PubMed1998

Direct binding of CDC20 protein family members activates the anaphase-promoting complex in mitosis and G1.

Activation of the anaphase-promoting complex (APC) is required for anaphase initiation and for exit from mitosis. We show that APC is activated during mitosis and G1 by two regulatory factors, hCDC20 and hCDH1. These proteins directly bind to APC and activate its cyclin ubiquitination activity. hCDC20 confers a strict destruction-box (D-box) dependence on APC, while hCDH1 shows a much more relaxed specificity for the D-box. In HeLa cells, the protein levels of hCDC20 as well as its binding to APC peak in mitosis and decrease drastically at early G1. Thus, hCDC20 is the mitotic activator of APC and directs the degradation of substrates containing the D-box. The hCDH1 protein level remains constant during the cell cycle and may target specific substrates lacking the D-box in G1, such as polo-like kinase, for ubiquitination.

Anaphase-Promoting Complex-Cyclosome↗

PubMed2001

Hyperammonemia in urea cycle disorders: role of the nephrologist.

Hyperammonemia associated with inherited disorders of amino acid and organic acid metabolism is usually manifested by irritability, somnolence, vomiting, seizures, and coma. Although the majority of these patients present in the newborn period, they may also present in childhood, adolescence, and adulthood with failure to thrive, persistent vomiting, developmental delay, or behavioral changes. Persistent hyperammonemia, if not treated rapidly, may cause irreversible neuronal damage. After the diagnosis of hyperammonemia is established in an acutely ill patient, certain diagnostic tests should be performed to differentiate between urea cycle defects and other causes of hyperammonemic encephalopathy. In a patient with a presumed inherited metabolic disorder, the aim of therapy should be to normalize blood ammonia levels. Recent experience has provided treatment guidelines that include minimizing endogenous ammonia production and protein catabolism, restricting nitrogen intake, administering substrates of the urea cycle, administering compounds that facilitate the removal of ammonia through alternative pathways, and, in severe cases, dialysis therapy. Initiation of dialysis in the encephalopathic patient with hyperammonemia is indicated if the ammonia blood level is greater than three to four times the upper limit of normal. Hemodialysis is the most effective treatment for rapidly reducing blood ammonia levels. Continuous hemofiltration and peritoneal dialysis are also effective modalities for reducing blood ammonia levels. An improved understanding of the metabolism of ammonia and neurological consequences of hyperammonemia will assist the nephrologist in providing optimal care for this high-risk patient population.

Algorithms↗

PubMed1986

Non-steady-state kinetics of brain glutamate decarboxylase resulting from interconversion of the apo- and holoenzyme.

In addition to its primary reaction, brain glutamate decarboxylase (L-glutamate 1-carboxy-lyase, EC 4.1.1.15) catalyses an alternative transamination reaction that leads to the production of apoenzyme. Apoenzyme can be converted to holoenzyme by reaction with pyridoxal 5'-phosphate, thereby completing a cyclic interconversion of the apo- and holoenzyme. The effect of the cycle on the kinetic behavior of the enzyme was investigated with the aid of a kinetic model that combines a steady-state description of the primary reaction and a non-steady-state description of the cycle. In the presence of saturating levels of the cofactor, pyridoxal 5'-phosphate, the cycle had little effect on the kinetics of slowly transaminated substrates such as glutamate. However, the kinetic behavior of aspartate, a rapidly transaminated substrate, was strongly affected by the cycle. With aspartate, a large proportion of apoenzyme was produced, resulting in non-linear decarboxylation time courses. Estimates of the steady-state kinetic parameters for aspartate (Km, Ki, Vmax) and the apparent type of inhibition were found to depend strongly on the assay time and procedure. Similar dependencies were found for the aspartate analogues, methyl alpha-DL-aspartate, cysteine sulfinate and beta-alanine, suggesting that they also undergo rapid transamination. The kinetic model accurately predicted holoenzyme levels and accurately described the decarboxylation time courses for glutamate, aspartate and mixtures of these substrates.

Animals↗

PubMed2006

Glucose and lactate are equally effective in energizing activity-dependent synaptic vesicle turnover in purified cortical neurons.

This study examines the role of glucose and lactate as energy substrates to sustain synaptic vesicle cycling. Synaptic vesicle turnover was assessed in a quantitative manner by fluorescence microscopy in primary cultures of mouse cortical neurons. An electrode-equipped perfusion chamber was used to stimulate cells both by electrical field and potassium depolarization during image acquisition. An image analysis procedure was elaborated to select in an unbiased manner synaptic boutons loaded with the fluorescent dye N-(3-triethylammoniumpropyl)-4-(4-(dibutylamino)styryl)pyridinium dibromide (FM1-43). Whereas a minority of the sites fully released their dye content following electrical stimulation, others needed subsequent K(+) depolarization to achieve full release. This functional heterogeneity was not significantly altered by the nature of metabolic substrates. Repetitive stimulation sequences of FM1-43 uptake and release were then performed in the absence of any metabolic substrate and showed that the number of active sites dramatically decreased after the first cycle of loading/unloading. The presence of 1 mM glucose or lactate was sufficient to sustain synaptic vesicle cycling under these conditions. Moreover, both substrates were equivalent for recovery of function after a phase of decreased metabolic substrate availability. Thus, lactate appears to be equivalent to glucose for sustaining synaptic vesicle turnover in cultured cortical neurons during activity.

Animals↗

PubMed1985

Cytochrome P450: substrate and prosthetic-group free radicals generated during the enzymatic cycle.

During the enzymatic cycle of the cytochromes P450, dioxygen binds to the ferrous haemprotein when the resting ferric haemprotein has undergone a one-electron oxidation after substrate binding. A further one-electron reduction generates an intermediate that is isoelectronic with a peroxide dianion coordinated to a ferric iron. Heterolytic cleavage of the omicron--omicron bond generates water and a species which is formally an oxene (oxygen atom) coordinated by iron(III). However, on the basis of model reactions and by analogy to the catalases and peroxidases, this active oxidizing intermediate is formulated as an oxo-FeIV porphyrin pi-cation radical. The radical is stabilized by delocalization on the porphyrin macrocycle and the high oxidation state is achieved by oxidizing both the metal and the porphyrin ring of the haemprotein. Hydrogen atom abstraction from a saturated hydrocarbon substrate generates a substrate free radical, constrained by the protein binding site, and the equivalent of a hydroxyl radical bound to iron(III). Coupling of the 'hydroxy' and substrate radicals generates hydroxylated product and resting protein. For olefins an initial electron transfer to oxidized haemprotein gives a substrate cation radical. Further reaction of this radical can give the epoxide, the principal product; an aldehyde or ketone by rearrangement; or an alkylated haemprotein resulting in suicide inhibition.

Catalase↗

PubMed1996

Studies on the in vitro phosphorylation of HSSB-p34 and -p107 by cyclin-dependent kinases. Cyclin-substrate interactions dictate the efficiency of phosphorylation.

Cyclin-dependent kinases (Cdks) are required for cell cycle progression. Two potentially significant Cdk substrates in human cells are the human single-stranded binding protein (HSSB or RPA), which plays an essential role in DNA replication, repair, and recombination, and the tumor suppressor p107 which acts to negatively regulate cell growth. In this report we describe the in vitro phosphorylation of these two proteins by Cdks in an attempt to understand how cyclin-substrate interactions direct phosphorylation efficiencies. We show that cyclin A-Cdk2 efficiently phosphorylates the p34 subunit of HSSB (HSSB-p34) alone or as a part of the heterotrimeric complex. In contrast, cyclin E-Cdk2 that is active in phosphorylating histone H1, does not support the phosphorylation of the p34 subunit of HSSB. We provide evidence that this differential phosphorylation results from a specific interaction between HSSB-p34 and cyclin A, but not cyclin E. Thus the observed cell cycle-dependent phosphorylation of HSSB-p34 at the G1 to S transition is most likely catalyzed by cyclin A-Cdk2 initiated by the direct interaction between cyclin A and the HSSB-p34 subunit. These studies are consistent with our previous observation that p107, which directly binds cyclin A, is efficiently phosphorylated by cyclin A-Cdk2 but not cyclin B-associated kinases. Here we further demonstrate that cyclin A only complexes with p107 in its unphosphorylated form. These data suggest a catalytic mechanism by which Cdk acts: substrate targeting by a cyclin-substrate interaction followed by dissociation of the Cdk upon phosphate incorporation allowing the Cdk to become available for the next cycle of phosphorylation.

Base Sequence↗

PubMed2006

The role of the phospho-CDK2/cyclin A recruitment site in substrate recognition.

Phospho-CDK2/cyclin A, a kinase that is active in cell cycle S phase, contains an RXL substrate recognition site that is over 40 A from the catalytic site. The role of this recruitment site, which enhances substrate affinity and catalytic efficiency, has been investigated using peptides derived from the natural substrates, namely CDC6 and p107, and a bispeptide inhibitor in which the gamma-phosphate of ATP is covalently attached by a linker to the CDC6 substrate peptide. X-ray studies with a 30-residue CDC6 peptide in complex with pCDK2/cyclin A showed binding of a dodecamer peptide at the recruitment site and a heptapeptide at the catalytic site, but no density for the linking 11 residues. Kinetic studies established that the CDC6 peptide had an 18-fold lower Km compared with heptapeptide substrate and that this effect required the recruitment peptide to be covalently linked to the substrate peptide. X-ray studies with the CDC6 bispeptide showed binding of the dodecamer at the recruitment site and the modified ATP in two alternative conformations at the catalytic site. The CDC6 bispeptide was a potent inhibitor competitive with both ATP and peptide substrate of pCDK2/cyclin A activity against a heptapeptide substrate (Ki = 0.83 nm) but less effective against RXL-containing substrates. We discuss how localization at the recruitment site (KD 0.4 microm) leads to increased catalytic efficiency and the design of a potent inhibitor. The notion of a flexible linker between the sites, which must have more than a minimal number of residues, provides an explanation for recognition and discrimination against different substrates.

Adenosine Triphosphate↗

PubMed2005

Genome-wide surveys for phosphorylation-dependent substrates of SCF ubiquitin ligases.

The SCF (Skp1-Cullin-F-box) family of ubiquitin ligases target numerous substrates for ubiquitin-dependent proteolysis, including cell cycle regulators, transcription factors, and signal transducers. Substrates are recruited to an invariant core SCF complex through one of a large family of substrate-specific adapter subunits called F-box proteins, each of which binds multiple specific substrates, often in a phosphorylation-dependent manner. The identification of substrates for SCF complexes has proven difficult, especially given the requirement of often complex phosphorylation events for substrate recognition. The archetype for such interactions is the binding of the yeast F-box protein Cdc4 to its various substrates by means of multiple motifs that weakly match an optimal consensus called the Cdc4 phosphodegron (CPD), which is phosphorylated by cyclin-dependent kinases (CDKs) and possibly other kinases. Provided phosphodegron recognition motifs and/or the targeting kinases for SCF substrates are delineated, it is possible to use genome-wide methods to identify new substrates. Here we describe two methods for the systematic retrieval of SCF substrates based on membrane arrays of synthetic phosphopeptides and on genome-wide kinase substrate profiles. In the first approach, which identifies substrates with strong matches to the CPD, a search of the predicted yeast proteome with the optimal CPD motif identified approximately 1100 matches. A phosphopeptide membrane array corresponding to each of these sequences is then probed with recombinant Cdc4, thereby identifying potential substrates. In the second approach, which identifies substrates that lack strong CPD motifs, a genome-wide set of recombinant CDK substrates is phosphorylated and directly assayed for binding to Cdc4. The proteins corresponding to these hits from each approach can then be subjected to the more stringent criteria of phosphorylation-dependent binding to Cdc4, ubiquitination by SCF(Cdc4)in vitro, and Cdc4-dependent protein instability in vivo. Both methods have identified novel substrates of Cdc4 and may, in principle, be used to identify numerous new substrates of other SCF and SCF-like complexes from yeast to humans.

Amino Acid Sequence↗

PubMed2001

Regulation of skeletal muscle amino acid metabolism during exercise.

The contribution of amino acid oxidation to total energy expenditure is negligible during short-term intense exercise and accounts for 3-6% of the total adenosine triphosphate supplied during prolonged exercise in humans. While not quantitatively important in terms of energy supply, the intermediary metabolism of several amino acids-notably glutamate, alanine, and the branched-chain amino acids-affects other metabolites, including the intermediates within the tricarboxylic acid (TCA) cycle. Glutamate appears to be a key substrate for the rapid increase in muscle TCA cycle intermediates (TCAI) that occurs at the onset of moderate to intense exercise, due to a rightward shift of the reaction catalyzed by alanine aminotransferase (glutamate + pyruvate <==> alanine + 2-oxoglutarate). The pool of muscle TCAI declines during prolonged exercise, and this has been attributed to an increase in leucine oxidation that relies on one of the TCAI. However, this mechanism does not appear to be quantitatively important due of the relatively low maximal activity of branched-chain oxoacid dehydrogenase, the key enzyme involved. It has been suggested that an increase in TCAI is necessary to attain high rates of aerobic energy production and that a decline in TCAI may be a causative factor in local muscle fatigue. These topics remain controversial, but recent evidence suggests that changes in TCAI during exercise are unrelated to oxidative energy provision in skeletal muscle.

Amino Acids↗

PubMed1995

Fermentative and aerobic metabolism in Rhizobium etli.

Strains of Rhizobium etli, Rhizobium meliloti, and Rhizobium tropici decreased their capacity to grow after successive subcultures in minimal medium, with a pattern characteristic for each species. During the growth of R. etli CE 3 in minimal medium (MM), a fermentation-like response was apparent: the O2 content was reduced and, simultaneously, organic acids and amino acids were excreted and poly-beta-hydroxybutyrate (PHB) was accumulated. Some of the organic acids excreted into the medium were tricarboxylic acid (TCA) cycle intermediates, and, concomitantly, the activities of several TCA cycle and auxiliary enzymes decreased substantially or became undetectable. Optimal and sustained growth and a low PHB content were found in R. etli CE 3 when it was grown in MM inoculated at a low cell density with O2 maintained at 20% or with the addition of supplements that have an effect on the supply of substrates for the TCA cycle. In the presence of supplements such as biotin or thiamine, no amino acids were excreted and the organic acids already excreted into the medium were later reutilized. Levels of enzyme activities in cells from supplemented cultures indicated that carbon flux through the TCA cycle was maintained, which did not happen in MM. It is proposed that the fermentative state in Rhizobium species is triggered by a cell density signal that results in the regulation of some of the enzymes responsible for the flux of carbon through the TCA cycle and that this in turn determines how much carbon is available for the synthesis and accumulation of PHB. The fermentative state of free-living Rhizobium species may be closely related to the metabolism that these bacteria express during symbiosis.

Aerobiosis↗

PubMed1994

Metabolism of malate in bovine adrenocortical mitochondria studied by 13C-NMR spectroscopy.

13C-NMR spectroscopy was used to study the metabolism of [13C]malate in bovine coupled adrenocortical mitochondria. The most apparent difference between the mitochondria from steroidogenic tissues and mitochondria from other tissues is the presence, in addition to the normal respiratory chain, of a second electron-transport system responsible for steroid hydroxylation. [13C]malate was synthesized from [13C]succinate by isolated adrenocortical mitochondria. The basic functional suspension consisted of oxygenated mitochondria to which were added ADP, inorganic phosphate (Pi) and [13C]malate, both in the absence or presence of the steroid substrate, deoxycorticosterone. These mitochondria synthesized [13C]citrate and [13C]pyruvate from [13C]malate. The 13C labeling of these two metabolites demonstrated an important role of the malic enzyme and the kinetics depended on the presence of the steroid substrate; the citric acid cycle was stopped during the hydroxylation pathway. The addition of cyanide, a strong inhibitor of the respiratory chain, confirmed an increased malic enzyme activity when hydroxylation occurred, since pyruvate was trapped by formation of a cyanohydrin. The relative enzymic activities of malic enzyme and isocitrate dehydrogenase were compared, both in the absence or presence of the steroid substrate, by supplementing the basic suspension with unlabeled exogenous metabolites, such as pyruvate or oxaloacetate.

Adrenal Cortex↗

PubMedDate not supplied

[Study of conditions for cleaving bovine leukemia virus RNA in vitro using ribozymes directed against long terminal repeats].

Ribozyme has been constructed by the oligonucleotide synthesis technique that is capable of splitting bovine leukemia virus (BLV) RNA-substrate in the R-region (358th nucleotide). Ribozyme has been shown to efficiently split the RNA containing R-region of the virus. The efficiency of ribozyme function depends on conditions of the reaction reaching its maximum at 25 degrees C and pH 7.3-7.6. The efficiency of splitting is increased by multiple heating-cooling cycles of the substrate-ribozyme mixture.

Base Sequence↗

PubMed1997

Mapping of the plasminogen binding site of streptokinase with short synthetic peptides.

Although several recent studies employing various truncated fragments of streptokinase (SK) have demonstrated that the high-affinity interactions of this protein with human plasminogen (HPG) to form activator complex (SK-HPG) are located in the central region of SK, the exact location and nature of such HPG interacting site(s) is still unclear. In order to locate the "core" HPG binding ability in SK, we focused on the primary structure of a tryptic fragment of SK derived from the central region (SK143-293) that could bind as well as activate HPG, albeit at reduced levels in comparison to the activity of the native, full-length protein. Because this fragment was refractory to further controlled proteolysis, we took recourse to a synthetic peptide approach wherein the HPG interacting properties of 16 overlapping 20-mer peptides derived from this region of SK were examined systematically. Only four peptides from this set, viz., SK234-253, SK254-273, SK274-293, and SK263-282, together representing the contiguous sequence SK234-293, displayed HPG binding ability. This was established by a specific HPG-binding ELISA as well as by dot blot assay using 125I-labeled HPG. These results showed that the minimal sequence with HPG binding function resided between residues 234 and 293. None of the synthetic SK peptides was found to activate HPG, either individually or in combination, but, in competition experiments where each of the peptides was added prior to complex formation between SK and HPG, three of the HPG binding peptides (SK234-253, SK254-273, and SK274-293) inhibited strongly the generation of a functional activator complex by SK and HPG. This indicated that residues 234-293 in SK participate directly in intermolecular contact formation with HPG during the formation of the 1:1 SK-HPG complex. Two of the three peptides (SK234-253 and SK274-293), apart from interfering in SK-HPG complex formation, also showed inhibition of the amidolytic activity of free HPN by increasing the K(m) by approximately fivefold. A similar increase in K(m) for amidolysis by HPN as a result of complexation with SK has been interpreted previously to arise from the steric hinderance at or near the active site due to the binding of SK in this region. Thus, our results suggest that SK234-253 and SK274-293 also, like SK, bound close to the active site of HPN, an event that was reflected in the observed alteration in its substrate accessibility. By contrast, whereas the intervening peptide (SK254-273) could not inhibit amidolysis by free HPN, it showed a marked inhibition of the activation of "substrate" PG (human or bovine plasminogen) by activator complex, indicating that this particular region is intimately involved in interaction of the SK-HPG activator complex with substrate plasminogen during the catalytic cycle. This finding provides a rational explanation for one of the most intriguing aspects of SK action, i.e., the ability of the SK-HPG complex to catalyze selectively the activation of substrate molecules of PG to PN, whereas free HPN alone cannot do so. Taken together, the results presented in this paper strongly support a model of SK action in which the segment 234-293 of SK, by virtue of the epitopes present in residues 234-253 and 274-293, binds close to the active center of HPN (or, a cryptic active site, in the case of HPG) during the intermolecular association of the two proteins to form the equimolar activator complex; the segment SK254-273 present in the center of the core region then imparts an ability to the activator complex to interact selectively with substrate PG molecules during each PG activation cycle.

Amidohydrolases↗

PubMed1983

Analysis of cyclic enzyme reaction schemes by the graph-theoretic method.

The development of the graph-theoretic method is proposed particularly for the analysis of closed cycles of elementary stages in enzyme reaction schemes. Some simplifications of the graph structure may be based on the application of Kirchhoff's laws to enzyme reaction graphs in the steady-state. The importance of the cyclic processes for enzyme regulations and a principle non-equilibrium of this phenomenon are emphasized. As an example of the regulatory role of cycles "the liberation" from substrate inhibition by substrate analogues is considered. The modification of the graph-theoretic method in the pre-steady-state kinetics for arbitrary initial conditions (for pre-mixing procedures) is also discussed. The necessary and sufficient conditions for damped oscillations in the pre-steady state are formulated which are the equality conditions for some of the rate constants along the cycle (both for reversible and irreversible stages).

Enzyme Inhibitors↗