Acceptor substrate inhibits transketolase competitively with respect to donor substrate

Two substrates of the transketolase reaction are known to bind with the enzyme according to a ping-pong mechanism [1]. It is shown in this work that high concentrations of ribose-5-phosphate (acceptor substrate) compete with xylulose-5-phosphate (donor substrate), suppressing the transketolase activity (Ki = 3.8 mM). However, interacting with the donor-substrate binding site on the protein molecule, the acceptor substrate, unlike the donor substrate, does not cause any change in the active site of the enzyme. The data are interesting in terms of studying the regulatory mechanism of the transketolase activity and the structure of the enzyme-substrate complex.     

GroEL/S substrate specificity based on substrate unfolding propensity

Phage P22 wild-type (WT) coat protein does not require GroEL/S to fold but temperature-sensitive-folding (tsf) coat proteins need the chaperone complex for correct folding. WT coat protein and all variants absolutely require P22 scaffolding protein, an assembly chaperone, to assemble into precursor structures termed procapsids. Previously, we showed that a global suppressor (su) substitution, T1661, which rescues several tsf coat protein variants, functioned by inducing GroEL/S. This led to an increased formation of tsf:T1661 coat protein:GroEL complexes compared with the tsf parents. The increased concentration of complexes resulted in more assembly-competent coat proteins because of a shift in the chaperone-driven kinetic partitioning between aggregation-prone intermediates toward correct folding and assembly. We have now investigated the folding and assembly of coat protein variants that carry a different global su substitution, F170L. By monitoring levels of phage production in the presence of a dysfunctional GroEL we found that tsf:F170L proteins demonstrate a less stringent requirement for GroEL. Tsf:F170L proteins also did not cause induction of the chaperones. Circular dichroism and tryptophan fluorescence indicate that the native state of the tsf: F170L coat proteins is restored to WT-like values. In addition, native acrylamide gel electrophoresis shows a stabilized native state for tsf:F170L coat proteins. The F170L su substitution also increases procapsid production compared with their tsf parents. We propose that the F170L su substitution has a decreased requirement for the chaperones GroEL and GroES as a result of restoring the tsf coat proteins to a WT-like state. Our data also suggest that GroEL/S can be induced by increasing the population of unfolding intermediates.     

Optimal substrate shape for vesicle adhesion on a curved substrate

When pulling a vesicle adhered on a substrate, both the force-displacement profile and the maximum force at pull-off are sensitively dependent upon the substrate shape. Here we consider the adhesion between a two-dimensional vesicle and a rigid substrate via long-range molecular interactions. For a given contact area, the theoretical pull-off force of the vesicle is obtained by multiplying the theoretical strength of adhesion and the contact area. It is shown that one may design an optimal substrate shape to achieve the theoretical pull-off force.     

Regulator and substrate

Like other organisms, plants rely on autophagy to recycle intracellular components needed for development, new growth and survival during nutrient stress. This ‘self eating’ is a catabolic process by which unwanted cytoplasmic materials and dysfunctional organelles are sequestered into vesicles and subsequently delivered to the vacuole for breakdown. The process is tightly regulated by the autophagy-related 1(ATG1)-ATG13 kinase complex which is controlled by multiple nutrient-responsive upstream regulators that integrate nutrient demand with availability. To further appreciate how autophagy is controlled in plants, we recently examined the functions of the ATG1-ATG13 complex in Arabidopsis thaliana. Our data revealed a dual role for the ATG1-ATG13 complex, first as a regulator of plant autophagy, and second as a substrate of this recycling process.     

Inhibition-threshold substrate concentrations

A proposed substrate inhibition model (M. C. Tseng and M. Wayman, Can. J. Microbiol., 21 , 994 (1975)), ((1)) ((2)) derived from yeast growth rates has been applied to data for bacterial growth: Pseudomonas methanica grown on methanol and Arthrobacter AK19 grown on n-butanol. The model represents the experimental data very well.     

Effects of substrate and substrate analogues on the trinitrophenylation of myosin

The effects of ATP, ATP analogues, Mg²⁺ and actin on the trinitrophenylation of myosin and on the enzymic properties of trinitrophenylated samples were studied.

1. 1. Trinitrophenylation of myosin was inhibited by the presence of ATP and its analogues during the treatment in the order ADP > ATP > pyrophosphate > AMP.

2. 2. The alteration of the enzymic properties due to trinitrophenylation of myosin was prevented by the presence of ATP or ADP and somewhat less by that of pyrophosphate and AMP during trinitrophenylation, but only if Mg²⁺ was also present.

3. 3. Neither the degree of trinitrophenylation nor the enzymic properties of the trinitrophenylated myosin were influenced by the presence of actin during the treatment of myosin.

A survey of furin substrate specificity using substrate phage display.

The substrate specificity of furin, a mammalian enzyme involved in the cleavage of many constitutively expressed protein precursors, was studied using substrate phage display. In this method, a multitude of substrate sequences are displayed as fusion proteins on filamentous phage particles and ones that are cleaved can be purified by affinity chromatography. The cleaved phage are propagated and submitted to additional rounds of protease selection to further enrich for good substrates. DNA sequencing of the cleaved phage is used to identify the substrate sequence. After 6 rounds of sorting a substrate phage library comprising 5 randomized amino acids (xxxxx), virtually all clones had an RxxR motif and many had Lys, Arg, or Pro before the second Arg. Nine of the selected sequences were assayed using a substrate-alkaline phosphatase fusion protein system. All were cleaved after the RxxR, and some substrates with Pro or Thr in P2 were also found to be cleaved as efficiently as RxKR or RxRR. To further elaborate surrounding determinants, we constructed 2 secondary libraries (xxRx(K/R)Rx and xxRxPRx). Although no consensus developed for the latter library, many of the sequences in the the former library had the 7-residue motif (L/P)RRF(K/R)RP, suggesting that the furin recognition sequence may extend over more than 4 residues. These studies further clarify the substrate specificity of furin and suggest the substrate phage method may be useful for identifying consensus substrate motifs in other protein processing enzymes.     

Reversible inhibition in bimolecular rapid-equilibrium random-order enzyme systems. The effect of substrate–substrate and inhibitor–substrate interactions

A model is presented that accounts for all types of reversible inhibition by a single inhibitor molecule in bimolecular rapid-equilibrium random-order enzyme systems. The characterization of inhibition mechanisms by graphical methods is examined, and a system of nomenclature is suggested.     

I Siah substrate!

Proteins are targeted to the E3 RING ubiquitin ligase Siah through a PxAxVxP degron motif. In this issue of Structure, House et al. (2006) present the structural basis by which Siah recognizes its degron with high affinity and specificity.     

Novel cell-penetrating calpain substrate

The calpain enzymes play important roles in numerous processes in the cell. In vivo analysis of calpain activity might be useful for clarification of their role in different diseases. Our early results suggested that a peptide substrate, Dabcyl-TPLKSPPPSPR- EDANS, based on the calpain cleavage sequences is suitable for developing a new cell-penetrating calpain substrate. This conjugate with the Dabcyl and EDANS fluorophores as a FRET pair is specific for calpain even in cell lysate, but unfortunately has poor cell uptake. Therefore, we have modified this sequence by C-terminal elongation with heptaarginine unit possessing cell-penetrating activity. In order to preserve the necessary distance between the two FRET partners, we inserted a Glu residue between the substrate and heptaarginine parts of the peptide. Thus, the cell-penetrating substrate Dabcyl-TPLKSPPPSPRE( EDANS)R 7 was synthesized. This peptide not only retained the substrate property, but was a better substrate of Calpain B enzyme. The cell uptake of the substrate conjugate was studied by fluorescence microscopy and flow cytometry. The results showed that the conjugate enters COS-7 cells more efficiently than the peptide substrate without heptaarginine. The uptake occurs already at low concentration and the compound is distributed homogeneously inside cells. These observations might indicate that this new cell-penetrating substrate could be useful for determining calpain activity in cell lysate or in intact cells of various origins.     

A substrate for telomerase

Recent data indicates that controlled in vivo synthesis of telomeric DNA is a ‘ménage à trois’, in which sister chromatid termini paired by telomere end-binding protein constitute a core substrate for a telomerase dimer. Such an arrangement could serve to fine tune synthesis of telomeric DNA and might ensure similar telomerase processivity for paired sister chromatid termini, possibly to secure the maintenance of individual telomere lengths in daughter cells. It also suggests that the bona fide end-capping protein, which is likely to regulate telomerase by restricting access to chromosome termini, has escaped detection in man.     

Role of enzyme-peptide substrate backbone hydrogen bonding in determining protein kinase substrate specificities

As part of a search for peptides that have specificity for selected protein kinases, the possibility that adenosine cyclic 3',5'-phosphate dependent protein kinase (A-kinase) recognizes the hydrogen-bonding potential of its peptide substrates was investigated. A-Kinase catalyzes the phosphorylation of five N alpha-methylated and four depsipeptide derivatives of Leu-Arg-Arg-Ala-Ser-Leu-Gly (peptide 1) at rates that differ by at least 7 orders of magnitude. These peptide 1 analogues each lack the ability to donate a hydrogen bond at selected positions in the peptide chain. If a particular amide hydrogen of a peptide amide is involved in hydrogen bonding, which is important for enzyme recognition, the prediction is that peptides which contain an ester or a N-methylated bond at that position in peptide 1 will be comparatively poor substrates. In contrast, if a depsipeptide has a reactivity comparable to that of peptide 1 but the analogous N-methylated peptide has a poor reactivity with A-kinase, the result might indicate that the N-methyl group causes unfavorable steric effects. The depsipeptide that lacks a Leu6 amide proton is a good substrate for A-kinase, but the corresponding N-methylated peptide is phosphorylated far less efficiently. This result and others presented in this paper suggest that although enzyme-substrate hydrogen bonding may play some role in A-kinase catalysis of phosphoryl group transfer, other explanations are necessary to account for the relative reactivities of N alpha-methylated and depsi-containing peptide 1 analogues.(ABSTRACT TRUNCATED AT 250 WORDS)     

The study of substrate specificity of a new peptide substrate of endothelin-converting enzyme

A new hexapeptide CMC-Ala-Gly-Gly-Trp-Phe-Arg was used as a substrate for assay of endothelin-converting (ECE; EC 3.4.24.71) and angiotensin-converting (ACE; EC 3.4.15.1) enzymes and of neutral endopeptidase (NEP; EC 3.4.24.11). The specific inhibitors lisinopril (for ACE) and thiorphan (for NEP) were used for discrimination between activities of these enzymes.