Rate Of Substrate Cleavage Research Articles

Aldol Cleavage in Water and the Power of Citrate Lyase as a Catalyst.

Citrate lyase allows Klebsiella aerogenes to grow anaerobically on citrate as the sole carbon source. Arrhenius analysis of experiments at high temperatures indicates that citrate is cleaved nonenzymatically to acetate and oxaloacetate with a t1/2 of 6.9 million years in neutral solution at 25 °C, while malate cleavage occurs even more slowly (t1/2 = 280 million years). However, t1/2 is only 10 days for the nonenzymatic cleavage of 4-hydroxy-2-ketoglutarate, indicating that the introduction of an α-keto group enhances the rate of aldol cleavage of malate by a factor of 1010. The aldol cleavages of citrate and malate, like the decarboxylation of malonate (t1/2 = 180 years), are associated with a near-zero entropy of activation, and their extreme differences in rate reflect differences between their heats of activation. Citrate lyase enhances the rate of substrate cleavage 6 × 1015-fold, comparable in magnitude with the rate enhancement produced by OMP decarboxylase, although these enzymes are strikingly different in their mechanisms of action.

Clinical Evaluation of Pathognomonic Salivary Protease Fingerprinting for Oral Disease Diagnosis.

Dental decay (Caries) and periodontal disease are globally prevalent diseases with significant clinical need for improved diagnosis. As mediators of dental disease-specific extracellular matrix degradation, proteases are promising analytes. We hypothesized that dysregulation of active proteases can be functionally linked to oral disease status and may be used for diagnosis. To address this, we examined a total of 52 patients with varying oral disease states, including healthy controls. Whole mouth saliva samples and caries biopsies were collected and subjected to analysis. Overall proteolytic and substrate specific activities were assessed using five multiplexed, fluorogenic peptides. Peptide cleavage was further described by inhibitors targeting matrix metalloproteases (MMPs) and cysteine, serine, calpain proteases (CSC). Proteolytic fingerprints, supported by supervised machine-learning analysis, were delineated by total proteolytic activity (PepE) and substrate preference combined with inhibition profiles. Caries and peridontitis showed increased enzymatic activities of MMPs with common (PepA) and divergent substrate cleavage patterns (PepE), suggesting different MMP contribution in particular disease states. Overall, sensitivity and specificity values of 84.6% and 90.0%, respectively, were attained. Thus, a combined analysis of protease derived individual and arrayed substrate cleavage rates in conjunction with inhibitor profiles may represent a sensitive and specific tool for oral disease detection.

Cleavage of peptidic inhibitors by target protease is caused by peptide conformational transition

Some peptide sequences can behave as either substrates or inhibitors of serine proteases. Working with a cyclic peptidic inhibitor of the serine protease urokinase-type plasminogen activator (uPA), we have now demonstrated a new mechanism for an inhibitor-to-substrate switch. The peptide, CSWRGLENHAAC (upain-2), is a competitive inhibitor of human uPA, but is also slowly converted to a substrate in which the bond between Arg4 and Gly5 (the P1-P1′ bond) is cleaved. Substituting the P2 residue Trp3 to an Ala or substituting the P1 Arg4 residue with 4-guanidino-phenylalanine strongly increased the substrate cleavage rate. We studied the structural basis for the inhibitor-to-substrate switch by determining the crystal structures of the various peptide variants in complex with the catalytic domain of uPA. While the slowly cleaved peptides bound clearly in inhibitory mode, with the oxyanion hole blocked by the side chain of the P3′ residue Glu7, peptides behaving essentially as substrates with a much accelerated rate of cleavage was observed to be bound to the enzyme in substrate mode. Our analysis reveals that the inhibitor-to-substrate switch was associated with a 7 Å translocation of the P2 residue, and we conclude that the inhibitor-to-substrate switch of upain-2 is a result of a major conformational change in the enzyme-bound state of the peptide. This conclusion is in contrast to findings with so-called standard mechanism inhibitors in which the inhibitor-to-substrate switch is linked to minor conformational changes in the backbone of the inhibitory peptide stretch.

Modulation of Ribozyme and Deoxyribozyme Activities Using Tetraalkylammonium Ions.

Nucleic acid enzymes require specific metal ions to be catalytically active. The functions of the metal ions having structural and catalytic roles are affected by competing cations. Large-sized tetraalkylammonium ions have a propensity to preferentially bind to single strands of RNA and DNA. Here, the large cations are used in the reactions of lead-dependent ribozyme and 17E deoxyribozyme that require divalent metal ions to cleave a nucleic acid substrate. Kinetic analysis shows that tetraalkylammonium ions influence the rate of substrate cleavage, and the effects are different depending on the nucleic acid enzymes and metal ions used. Importantly, the large cations used here increase the dependence of cleavage rates on metal ion concentration and enhance the ability of the enzyme to monitor changes in metal ion concentrations. The same effect is also observed for the metal ion concentration dependence of the thermal stability of RNA and DNA structures, indicating that the large cations affect the binding of structural metal ions. The use of large tetraalkylammonium ions provides new ways to study the importance of metal ions to nucleic acid enzymes, and also to modulate the functionality of nucleic acid enzymes.

Profiling of metalloprotease activities in cerebrospinal fluids of patients with neoplastic meningitis

BackgroundNeoplastic invasion into leptomeninges and subarachnoid space, resulting in neoplastic meningitis (NM) is a fatal complication of advanced solid and hematological neoplasms. Identification of malignant involvement of the cerebrospinal fluid (CSF) early in the disease course has crucial prognostic and therapeutic implications, but remains challenging. As indicators of extracellular matrix (ECM) degradation and breakdown of the blood–brain-barrier, Matrix Metalloproteases (MMPs) and A Disintegrin and Metalloproteases (ADAMs) are potential analytes for cerebral pathophysiology and metastatic dissemination of tumor cells into the CSF.MethodsWe compared protease activities in CSF samples from patients with NM and control individuals using FRET-based metalloprotease substrates with distinct enzyme selectivity profiles in a real-time, multiplex approach termed “proteolytic activity matrix assay” (PrAMA). Protease activity dynamics can be tracked by fluorescence changes over time. By simultaneously monitoring a panel of 5 FRET-substrate cleavages, a proteolytic signature can be identified and analyzed to infer the activities of multiple specific proteases. Distinct patterns of substrate cleavage comparing disease vs. control samples allow rapid, reproducible and sensitive discrimination even in small volumes of CSF.ResultsIndividual substrate cleavage rates were linked to distinct proteases, and PrAMA computational inference implied increased activities of MMP-9, ADAM8 and ADAM17 (4–5-fold on average) in CSF samples from NM patients that were inhibitable by the metalloprotease inhibitor batimastat (BB-94). The activities of these proteases correlated with blood–brain barrier impairment. Notably, CSF cell counts were not found to directly reflect the protease activities observed in CSF samples from NM patients; this may explain the frequent clinical observation of negative cytology in NM patients.ConclusionPrAMA analysis of CSF samples is a potential diagnostic method for sensitive detection of NM and may be suitable for the clinical routine.

Mechanism of Ribonuclease III Catalytic Regulation by Serine Phosphorylation

Ribonuclease III (RNase III) is a conserved, gene-regulatory bacterial endonuclease that cleaves double-helical structures in diverse coding and noncoding RNAs. RNase III is subject to multiple levels of control, reflective of its global regulatory functions. Escherichia coli (Ec) RNase III catalytic activity is known to increase during bacteriophage T7 infection, reflecting the expression of the phage-encoded protein kinase, T7PK. However, the mechanism of catalytic enhancement is unknown. This study shows that Ec-RNase III is phosphorylated on serine in vitro by purified T7PK, and identifies the targets as Ser33 and Ser34 in the N-terminal catalytic domain. Kinetic experiments reveal a 5-fold increase in kcat and a 1.4-fold decrease in Km following phosphorylation, providing a 7.4–fold increase in catalytic efficiency. Phosphorylation does not change the rate of substrate cleavage under single-turnover conditions, indicating that phosphorylation enhances product release, which also is the rate-limiting step in the steady-state. Molecular dynamics simulations provide a mechanism for facilitated product release, in which the Ser33 phosphomonoester forms a salt bridge with the Arg95 guanidinium group, thereby weakening RNase III engagement of product. The simulations also show why glutamic acid substitution at either serine does not confer enhancement, thus underscoring the specific requirement for a phosphomonoester.

Reversal of Heparin-Induced Anticoagulation By Andexanet Alfa, a Universal Antidote for Factor Xa Inhibitors

Background: Unfractionated heparin is used in the management of venous thromboembolism, stroke prevention in atrial fibrillation as well as in cardiac surgeries (e.g., valve replacement and other procedures requiring cardiopulmonary bypass). Bleeding is the major complication that may result from these therapies. Although protamine sulfate can be used to neutralize heparin, its administration can cause severe hypotensive and anaphylactic reactions. Andexanet alfa (AnXa) is a recombinant modified human fXa under development for the reversal of both direct and antithrombin III (ATIII)-dependent indirect fXa inhibitors. We previously reported nonclinical and Phase 2 clinical data in healthy subjects with enoxaparin, a low molecular weight heparin (LMWH). Here we report new in vitro data demonstrating that AnXa can also effectively reverse anticoagulation of unfractionated heparin.Methods: Inhibition of human fXa or thrombin (IIa) by ATIII in the presence of heparin was studied in an enzymatic assay in buffered solution. The reaction mixture contained fXa or IIa (20 nM), ATIII (200 nM), different amounts of unfractionated heparin and AnXa. At different time points, a small aliquot of the reaction mixture was taken and quenched into a 96-well assay plate containing protamine (50 µg/mL) and a chromogenic substrate (100 µM) for fXa (Spectrozyme-Xa) or IIa (S2238). Residual fXa or IIa activity was measured in a plate reader by monitoring the initial rate of substrate cleavage at 405 nm. Reversal of heparin anti-fXa and anti-IIa activities by AnXa in human plasma was evaluated using modified anti-fXa and anti-IIa chromogenic assays. Reversal of heparin-induced clotting prolongation of human plasma was measured by a 96-well format turbidity assay using an aPTT reagent and Ca2+. The reversal effect of AnXa on heparin anticoagulation and clot formation was further characterized by thromboelastography (TEG) in human plasma or whole blood. Reversal of heparin was compared to enoxaparin. Protamine sulfate was included as a control. Di-arginine piperazine (PER977), a positively charged small molecule, was also tested for comparison.Results: AnXa dose-dependently reversed the anti-fXa activity of heparin in the enzymatic assay and in human plasma. Interestingly, AnXa was also able to reverse the heparin anti-IIa activity in the same assays. In the enzymatic assay with IIa and ATIII, heparin accelerated the reaction of IIa inhibition by ~1000-fold. AnXa dose-dependently reversed the IIa inhibition to its basal level seen without heparin. The reversal effect of AnXa on IIa inhibition could be blocked by addition of a small molecule direct fXa inhibitor (e.g. rivaroxaban) in the same enzymatic assay. This suggests that interaction of AnXa with the primary binding site on the surface of heparin-activated ATIII (i.e., the reactive center loop (RCL)) might play a major role in the anti-IIa reversal as binding to the RCL was the minimal requirement for the inhibition of both fXa and IIa by ATIII. In human plasma, AnXa reversed the anti-IIa activity of heparin (0.8 IU/mL) with an estimated EC50 comparable to anti-fXa reversal (anti-fXa:126 nM; anti-IIa: 131nM). These results indicate that AnXa was able to compete with not only fXa, but also IIa, for binding to heparinized-ATIII and reverse both the anti-fXa and anti-IIa activities of heparin. In addition, AnXa dose-dependently and completely reversed prolongation of clotting by heparin (0.8 IU/mL) in human plasma as measured by the turbidity assay as well as parameters of heparin (1.0 IU/mL) anticoagulation as measured by TEG in either plasma or whole blood. As expected, protamine sulfate (5-10 µg/mL) neutralized heparin (1.0 IU/mL) anticoagulation in plasma in the TEG assay. At higher concentrations, protamine prevented clot formation, consistent with protamine's known anticoagulant effect when overdosed. No reversal activity was observed by PER977 in the same TEG assays using either plasma or whole blood.Conclusions: The current and previously reported data demonstrate that AnXa could be a universal fXa inhibitor antidote to reverse a broad range of newer direct oral fXa inhibitors, ATIII-dependent indirect inhibitors, such as fondaparinux and enoxaparin, as well as unfractionated heparin. The mechanism for reversal of ATIII-dependent inhibitors by AnXa is distinct from other positively charged molecules that bind directly to heparin. DisclosuresLu:Portola Pharmaceuticals, Inc.: Employment. Lin:Portola Pharmaceuticals, Inc.: Employment. Curnutte:Sea Lane Biotechnologies: Consultancy; 3-V Biosciences: Equity Ownership; Portola Pharmaceuticals, Inc.: Employment. Conley:Portola Pharmaceuticals, Inc.: Employment.

Effects of background anionic compounds on the activity of the hammerhead ribozyme in Mg(2+)-unsaturated solutions.

Cellular ribozymes exhibit catalytic activity in media containing large numbers of anionic compounds and macromolecules. In this study, the RNA cleavage activity of the hammerhead ribozyme induced by Mg(2+) was investigated using the solutions containing background nucleic acids, small phosphate and carboxylic acid compounds, and neutral polymers. Analysis of the substrate cleavage kinetics showed that the anionic compounds do not affect the ribozyme activity in Mg(2+)-saturated solutions and there is almost no effect of the anion-Mg(2+) complexes formed. On the other hand, the rate of substrate cleavage in Mg(2+)-unsaturated solutions was reduced under conditions of a high background of anionic compounds found in cells. The extent of the reduction was more with a greater net negative charge, caused by decreased amounts of Mg(2+) that could be used for the ribozyme reaction. It was remarkable that background DNA and RNA molecules having phosphodiester bonds reduced the cleavage rate as much as adenosine monophosphates having a charge of -2 when the effects of the same amount of phosphate groups were compared. Greater reductions in rates than those expected from the molecular charge were also observed in the background of fatty acids that form micelles. An addition of poly(ethylene glycol) to the solutions partially restored the ribozyme activity, suggesting a possible role of macromolecular crowding in counteracting the inhibitory effects of background anions on the ribozyme reaction. The results have biological and practical implications with respect to the effects of molecular environment on the efficiency of ion binding to RNA.

Development of a chimeric hemicellulase to enhance the xylose production and thermotolerance

Xylan is an abundant plant cell wall polysaccharide and its reduction to xylose units for subsequent biotechnological applications requires a combination of distinct hemicellulases and auxiliary enzymes, mainly endo-xylanases and ß-xylosidases. In the present work, a bifunctional enzyme consisting of a GH11 endo-1,4-β-xylanase fused to a GH43 β-xylosidase, both from Bacillus subtilis, was designed taking into account the quaternary arrangement and accessibility to the substrate. The parental enzymes and the resulting chimera were successfully expressed in Escherichia coli, purified and characterized. Interestingly, the substrate cleavage rate was altered by the molecular fusion improving at least 3-fold the xylose production using specific substrates as beechwood xylan and hemicelluloses from pretreated biomass. Moreover, the chimeric enzyme showed higher thermotolerance with a positive shift of the optimum temperature from 35 to 50°C for xylosidase activity. This improvement in the thermal stability was also observed by circular dichroism unfolding studies, which seems to be related to a gain of stability of the β-xylosidase domain. These results demonstrate the superior functional and stability properties of the chimeric enzyme in comparison to individual parental domains, suggesting the molecular fusion as a promising strategy for enhancing enzyme cocktails aiming at lignocellulose hydrolysis.

Karakteristik Trypsin Inhibitor dan Penjajagan Sebagai Komponen Makanan Fungsional Penderita Diabetes (IIDM)

Trypsin inhibitors (TI) are substances which, when added to a mixture of a trypsin and a subtrate, bind to the enzyme and render it to decrease in the rate of substrate cleavage. These inhibitors are nonglycosylated, water-soluble (albumin) that account for about 0,2-2 % of the total soluble protein of the legume seeds. Two major families of trypsin inhibitors have been described in legumes: the Bowmen-Brix-type (BBI) and the Kunitz-type inhibitors (KTI). They are distinct families of proteins, as evidenced by their molecular weights, compositions, and amino acid sequences. Because of their unique pharmacological properties, these inhibitors hold considerable promise in clinical applications in their field of medicine. At least one inhibitor in soybeans, the BM, has been shown to have clear anticarcinogenic activity in both in vitro and in vivo carcinogenic Trypsin inhbitors (TI) are substances which, when added to a mixture of a trypsin and a substrate, bind to the enzyme and render it to decrease in the rate of substrate cleavage. These inhibitors are nonglycosylated, water-soluble (albumin) that account for about 0,2 –2 % of the total soluble protein of the legume seeds. Two major families of trypsin inhibitors have been described in legumes: the Bowmen-Birk-type (BBI) and the Kunitz-type inhibitors (K7'I). They are distinct families of proteins, as evidenced by their molecular weights, compositions, and amino acid sequences. Because of their unique pharmacological assay systems. increasing need and awareness for functional food has motivated food scientists and industries to search functional food components and ingredients for certain target group, including functional food for diabetes. Soy TI may enhance the production of more trypsin and probably insulin as well. The dietary 77evokes pancreatic enzyme secretion by forming inactive trypsinT1 complex. As the level of trypsin goes below a threshold level, the pancreas is induced to produce more enzymes. The mediating agent between the enzymes and the pancreas is cholecystokinin (CCK), which is released from the jejunul endocrine cells when the level of trypsin in the intestine becomes depleted. CCK is intestinal hormone which stimulate insulin secretion. Ti regenerated 13-cells which indicate the beneficial effect of TI on the insulin production of the pancreas. These novel findings provide evidence to support the potential utility of TI in the treatment of type 2 diabetes (11DM/ Insulin-Independent Diabetic Mellitus). However, TI are also known as anti nutrient substances and to cause pancreatic hypertrophy.

Identification of Serpin Determinants of Specificity and Selectivity for Furin Inhibition through Studies of α1PDX (α1-Protease Inhibitor Portland)-Serpin B8 and Furin Active-site Loop Chimeras

α1-Protease inhibitor Portland (α1PDX) is an engineered serpin family inhibitor of the proprotein convertase (PC), furin, that exhibits high specificity but limited selectivity for inhibiting furin over other PC family proteases. Here, we characterize serpin B8, a natural inhibitor of furin, together with α1PDX-serpin B8 and furin-PC chimeras to identify determinants of serpin specificity and selectivity for furin inhibition. Replacing reactive center loop (RCL) sequences of α1PDX with those of serpin B8 demonstrated that both the P4-P1 RXXR recognition sequence as well as the P1'-P5' sequence are critical determinants of serpin specificity for furin. Alignments of PC catalytic domains revealed four variable active-site loops whose role in furin reactivity with serpin B8 was tested by engineering furin-PC loop chimeras. The furin(298-300) loop but not the other loops differentially affected furin reactivity with serpin B8 and α1PDX in a manner that depended on the serpin RCL-primed sequence. Modeling of the serpin B8-furin Michaelis complex identified serpin exosites in strand 3C close to the 298-300 loop whose substitution in α1PDX differentially affected furin reactivity depending on the furin loop and serpin RCL-primed sequences. These studies demonstrate that RCL-primed residues, strand 3C exosites, and the furin(298-300) loop are critical determinants of serpin reactivity with furin, which may be exploited in the design of specific and selective α1PDX inhibitors of PCs.

Interactions of Heparin and a Covalently Linked Antithrombin Heparin Complex with the Components of the Fibrinolytic Pathway.

Abstract 2211 Introduction:Unfractionated heparin (UFH) is used for the prophylaxis and treatment of thromboembolic diseases. UFH catalyzes inhibition by antithrombin (AT) of the serine proteases in the coagulation cascade. Additionally, UFH has been shown to interact with components of the fibrinolytic pathway in vitro. However UFH has several limitations which impact its utility as a therapeutic agent. Our lab has developed a novel covalent antithrombin-heparin complex (ATH) which inhibits most serine proteases of the coagulation pathway significantly faster when compared to non covalent mixtures of AT and UFH. However, the interactions of ATH with the components of the fibrinolytic pathway have not been studied before. Thus, the present study investigates possible serpin-heparin interactions of AT + UFH vs ATH within the fibrinolytic pathway. Methods:Discontinuous second order rate constant assays under pseudo-first order conditions were carried out to obtain second order rate constant (k2) values for the inhibition of plasmin by AT+UFH versus ATH. Briefly, at specific time intervals 20 nM plasmin was inhibited by 200 nM AT + 0–5000 nM UFH or by 200 nM ATH in the presence of 2.5 mM Ca2+. Reactions were neutralized by the simultaneous addition of a solution containing polybrene and plasmin substrate S-2366™ in buffer. Residual plasmin activity was measured and the final k2 values calculated. For experiments involving tPA, wells containing 40nM tPA and increasing concentrations of AT, UFH or ATH, at mole ratios ranging from 0 to 20:1, were incubated for 15 min. Reactions with tPA were neutralized by simultaneous addition of a solution containing either polybrene and tPA substrate, S-2288™ in buffer, (ATH and UFH) or only the substrate S-2288™ in buffer (AT). Enzyme activity was then determined by measuring rate of substrate cleavage (Vmax). Results:When plasmin was inhibited by AT in the absence of UFH, k2 values of 2.82×105 +/− 4.46×104 M−1 min−1 were observed. The k2 values increased with addition of successively higher concentrations of UFH up to a plateau with maximal k2 of 5.74×106 +/− 2.78×105 M−1 min−1 at a UFH concentration of 3000nM. For inhibition of plasmin by ATH, k2 values of 6.39 × 106 +/− 5.88 × 105 M−1 min−1 were observed. Inhibition of plasmin by ATH was not significantly different when compared to the highest k2 values obtained with UFH. (p=0.36) No statistically significant difference in tPA enzyme activity was observed when Vmax values for tPA alone were compared with those in the presence of AT, UFH or ATH. (p=0.932, p=0.085, p=0.31 respectively) Significance:The characteristic shape of the curve obtained from the k2vs. UFH plot suggests that the mechanism responsible for inhibition of plasmin by AT+UFH involves conformational activation of the serpin. The k2 values in this study for inhibition of plasmin by both AT+UFH and ATH were three orders of magnitude lower than k2 values for inhibition of thrombin or factor Xa. Furthermore these results suggest that tPA is not inhibited by AT + UFH or ATH, and is not influenced by the presence of UFH alone. Cumulatively, this indicates that the fibrinolytic pathway is minimally impacted by AT + UFH or ATH, allowing maximal antithrombotic potential to be achieved during anticoagulation. Overall, the favourable anticoagulant properties of ATH combined with the findings of this study strengthens the utility of the covalent conjugate over conventional UFH for the treatment of thromboembolic disorders. Disclosures:No relevant conflicts of interest to declare.

Protein Kinase C recognition sites in the cytoplasmic domain of Endothelin Converting Enzyme-1c

Endothelin Converting Enzyme-1 (ECE-1) is essential for the production of the potent vasoconstrictor Endothelin-1 (ET-1). The activation of Protein Kinase C (PKC) by phorbol 12-myristate 13-acetate (PMA) can increase ECE-1 phosphorylation, which in turn promotes ECE-1c trafficking to the cell surface where ET-1 production occurs. This study has identified the specific residues in the N-terminal cytoplasmic tail of ECE-1c isoform that are phosphorylated upon the activation of PKC. Levels of phosphorylation are expressed as a % phosphorylation in untreated CHO-K1 cells. We transfected CHO-K1 cells with wild type and mutant forms of ECE-1c (Ala4-ECE-1c, Ala35ECE-1c and Ala4/35ECE-1c) to confirm the involvement of Thr4 and Ser35 residues in PMA induced phosphorylation of ECE-1c. Phosphorylation of wild type ECE-1c increased in response to PMA treatment (150±13%, unpaired t-test, P<0.05, significantly different compared to untreated control). The two single mutants and one combined mutant significantly reduced the PMA induced phosphorylation (103–117±6–13%; unpaired t-test; n=8; P<0.05 significantly different compared to untreated control). The mutations had no effect on the basal ECE-1c phosphorylation. In addition, they had no effect on the catalytic activity as evidenced by the similar rate of substrate cleavage compared to wild type. This study is the first to confirm the residues phosphorylated upon the activation of PKC by PMA. The results complete a gap in our understanding of the mechanism(s) behind PKC induced trafficking of ECE-1.

General Acid–Base Catalysis Mediated by Nucleobases in the Hairpin Ribozyme

The catalytic mechanism by which the hairpin ribozyme accelerates cleavage or ligation of the phosphodiester backbone of RNA has been incompletely understood. There is experimental evidence for an important role for an adenine (A38) and a guanine (G8), and it has been proposed that these act in general acid-base catalysis. In this work we show that a large reduction in cleavage rate on substitution of A38 by purine (A38P) can be reversed by replacement of the 5'-oxygen atom at the scissile phosphate by sulfur (5'-PS), which is a much better leaving group. This is consistent with A38 acting as the general acid in the unmodified ribozyme. The rate of cleavage of the 5'-PS substrate by the A38P ribozyme increases with pH log-linearly, indicative of a requirement for a deprotonated base with a relatively high pK(a). On substitution of G8 by diaminopurine, the 5'-PS substrate cleavage rate at first increases with pH and then remains at a plateau, exhibiting an apparent pK(a) consistent with this nucleotide acting in general base catalysis. Alternative explanations for the pH dependence of hairpin ribozyme reactivity are discussed, from which we conclude that general acid-base catalysis by A38 and G8 is the simplest and most probable explanation consistent with all the experimental data.

Identifi cation of protease exosite-interacting peptides that enhance substrate cleavage kinetics

Many peptidases are thought to require non-active site interaction surfaces, or exosites, to recognize and cleave physiological substrates with high specificity and catalytic efficiency. However, the existence and function of protease exosites remain obscure owing to a lack of effective methods to identify and characterize exosite-interacting substrates. To address this need, we modified the cellular libraries of peptide substrates (CLiPS) methodology to enable the discovery of exosite-interacting peptide ligands. Invariant cleavage motifs recognized by the active sites of thrombin and caspase-7 were displayed on the outer surface of bacteria adjacent to a candidate exosite-interacting peptide. Exosite peptide libraries were then screened for ligands that accelerate cleavage of the active site recognition motif using two-color flow cytometry. Exosite CLiPS (eCLiPS) identified exosite-binding peptides for thrombin that were highly similar to a critical exosite interaction motif in the thrombin substrate, protease-activated receptor 1. Protease activity probes incorporating exosite-binding peptides were cleaved ten-fold faster than substrates without exosite ligands, increasing their sensitivity to thrombin activity in vitro. For comparison, screening with caspase-7 yielded peptides that modestly enhanced (two-fold) substrate cleavage rates. The eCLiPS method provides a new tool to profile the ligand specificity of protease exosites and to develop improved substrates.

MIA-QSPR and effect of variable selection on the modeling of kinetic parameters related to activities of modified peptides against dengue type 2

Multivariate image analysis applied to quantitative structure–property relationship (MIA-QSPR) has shown to be a useful tool to model the biochemical properties of a series of drug-like compounds. However, drawing and alignment of two-dimensional structures (the images) are usually performed manually, resulting in a few imperfections. Selection of descriptors, which are in fact pixels of images, can minimize such effects; also, it enables selection of those variables which indeed explains the variance in the activities block. Therefore, in order to obtain more parsimonious, predictive models, interval PLS (iPLS), genetic algorithm (GA), and ordered predictors selection (OPS) were applied to select appropriate MIA descriptors to model kinetic constants, namely substrate cleavage rate ( k cat) and Michaelis ( K m) constants, which correlate to the bioactivities of peptides against Dengue type 2 (DEN-2). The models built were used to predict k cat and K m of new proposed peptides, which are miscellany of substructures of the most promising peptides experimentally tested elsewhere.

Association of Botulinum Neurotoxin Serotype A Light Chain with Plasma Membrane-bound SNAP-25

The Clostridium botulinum neurotoxins (BoNTs) cleave SNARE proteins, which inhibit binding and thus fusion of neurotransmitter vesicles to the plasma membrane of peripheral neurons. BoNTs comprise an N-terminal light chain (LC) and C-terminal heavy chain, which are linked by a disulfide bond. There are seven serotypes (A-G) of BoNTs based upon immunological neutralization. Although the binding and entry of BoNT/A into neurons has been subjected to considerable investigation, the intracellular events that allow BoNT/A to efficiently cleave SNAP-25 within neurons is less well understood. Earlier studies showed that intracellular LC/A bound to the plasma membrane of neurons. In this study, intracellular LC/A is shown to directly bind SNAP-25 on the plasma membrane. Solid phase binding showed that the N-terminal residues of LC/A bound residues 80-110 of SNAP-25, which was also observed in cultured neurons. Association of the N-terminal 8 amino acids of LC/A and residues 80-110 of SNAP-25 also enhanced substrate cleavage. These findings explain how LC/A associates with SNAP-25 on the plasma membrane and provide a basis for LC/A cleavage of SNAP-25 within the SNARE complex.

Non-Catalytic Domains of ADAMTS13 Can Redirect the Substrate Specificity of ADAMTS5

AbstractAbstract 2211The von Willebrand factor (VWF) cleaving protease, ADAMTS13, and the aggrecanase, ADAMTS5, have a modular structure that includes metalloprotease (M), disintegrin-like (D), thrombospondin-1 (T), cysteine-rich (C), and spacer (S) domains. Both enzymes utilize some combination of DTCS domains to bind substrates and facilitate proteolysis, thereby maintaining the homeostatic balance between the synthesis and degradation of their substrates. We constructed chimeric metalloproteinases and substrates to examine the activity of ADAMTS13 and ADAMTS5 towards their respective physiological cleavage sites at VWF Tyr1605-Met1606 and aggrecan interglobular domain (IGD) Glu373-Ala374 (as shown in table). Cleavage rates were determined by ELISA, and C-terminal products were sequenced to confirm specificity. ADAMTS13 truncated after the S domain (MDTCS13) cleaved recombinant VWF Asp1596-Arg1668 (VWF73) much more rapidly than did constructs MDT13/CS5 and MD13/TCS5, in which distal ADAMTS13 domains were replaced by those of ADAMTS5. Similarly, replacement of the C-terminal 52 residues of VWF73 by aggrecan IGD residues Glu394-Gly458 (VWF/IGD) markedly impaired cleavage by MDTCS13, MDT13/CS5, and MD13/TCS5.Therefore, optimal cleavage of VWF73 depends on interactions between ADAMTS13 TCS domains and C-terminal sites of VWF73. In contrast, MDTCS5 was inactive toward VWF73 or VWF/IGD, whereas MD5/TCS13 efficiently cleaved VWF73 (at Glu1615-Ile1616) but not VWF/IGD. Thus, the TCS domains of ADAMTS13 interact with the Lys1617-Arg1668 segment of VWF73. In the context of ADAMTS13, this interaction accelerates the physiological cleavage of VWF. In the context of the chimeric MD5/TCS13, this interaction allows the ADAMTS5 active site to recognize and cleave a new site in VWF73, which is otherwise resistant to ADAMTS5. As expected, MDTCS5 readily cleaved recombinant IGD residues Thr331-Gly458 (IGD). Replacing the C-terminal 65 residues of IGD with VWF Lys1617-Arg1668 (IGD/VWF) minimally altered the rate of cleavage by MDTCS5, and replacement of the ADAMTS5 TCS domains by those of ADAMTS13 (MD5/TCS13) had little effect on the cleavage of either IGD or IGD/VWF. MDTCS5 and MD5/TCS13 also cleaved the same Glu373-Ala374 site in purified aggrecan with similar efficiency (not shown in table), indicating that recognition of the major cleavage site in the IGD domain does not depend strongly on specific TCS domains. In contrast, the other major site of aggrecan proteolysis by MDTCS5, at Glu1480-Ala1481, was completely resistant to MD5/TCS13, indicating that the TCS domains of ADAMTS13 cannot substitute for those of ADAMTS5. These results show that non-catalytic domains, particularly TCS domains, are principal modifiers of physiological substrate recognition and cleavage by ADAMTS5 and ADAMTS13, and these domains may have a similar function in other members of the ADAMTS family.TableEfficiency of substrate cleavageEnzymeVWF73 (kcat/Km)VWF/IGD (kcat/Km)IGD/VWF (kcat/Km)IGD (kcat/Km)Aggrecan E1480-A1481MDTCS1344 ± 43.4 ± 0.2N/AN/AN/AMDT13/CS516 ± 0.31.1 ± 0.1N/AN/AN/AMD13/TCS52.8 ± 1.10.92±0.1N/AN/AN/AMD5/TCS1312.7 ± 1.00.7 ± 0.186 ± 932 ± 3N/AMDTCS5N/AN/A47 ± 357 ± 3+Values (mean ± SD) for kcat/Km (×105 M-1s-1) were calculated from the initial rate of substrate cleavage determined by ELISA of products. Cleavage of aggrecan at the Glu1480-Ala1481 bond was analyzed by Western blotting with a site-specific antibody. N/A (no activity) indicates no significant cleavage identified by Western blotting or ELISA. Disclosures:No relevant conflicts of interest to declare.

Mechanism of Aldolase Control of Sorting Nexin 9 Function in Endocytosis

Sorting nexin 9 (SNX9) functions in a complex with the GTPase dynamin-2 at clathrin-coated pits, where it provokes fission of vesicles to complete endocytosis. Here the SNX9.dynamin-2 complex binds to clathrin and adapter protein complex 2 (AP-2) that line these pits, and this occurs through interactions of the low complexity domain (LC4) of SNX9 with AP-2. Intriguingly, localization of the SNX9.dynamin-2 complex to clathrin-coated pits is blocked by interactions with the abundant glycolytic enzyme aldolase, which also binds to the LC4 domain of SNX9. The crystal structure of the LC4 motif of human SNX9 in complex with aldolase explains the biochemistry and biology of this interaction, where SNX9 binds near the active site of aldolase via residues 165-171 that are also required for the interactions of SNX9 with AP-2. Accordingly, SNX9 binding to aldolase is structurally precluded by the binding of substrate to the active site. Interactions of SNX9 with aldolase are far more extensive and differ from those of the actin-nucleating factor WASP with aldolase, indicating considerable plasticity in mechanisms that direct the functions of the aldolase as a scaffold protein.

Activation of ExoU Phospholipase Activity Requires Specific C-Terminal Regions

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that utilizes a type III secretion system to subvert host innate immunity. Of the 4 known effector proteins injected into eukaryotic cells, ExoS and ExoU are cytotoxic. The cytotoxic phenotype of ExoU depends on the enzymatic activity of the patatin-like phospholipase A(2) domain localized to the N-terminal half of the protein. Amino acid residues located within the C-terminal region of ExoU are postulated to be required for trafficking or localization to the plasma membrane of eukaryotic cells. This report describes the characterization of a transposon-based linker insertion library in ExoU. Utilizing an unbiased screening approach and sensitive methods for measuring enzymatic activity, we identified regions of ExoU that are critical for activation of the phospholipase activity by the only known cofactor, SOD1. Insertions at D572 and L618 reduced the rate of substrate cleavage. Enzymatic activity could be restored to almost parental levels when SOD1 concentrations were increased, suggesting that the linker insertion disrupted the interaction between ExoU and SOD1. An enzyme-linked immunosorbent assay (ELISA)-based binding test was developed to measure ExoU-SOD1 binding. These experiments suggest that ExoU activation by SOD1 is hampered by linker insertion. ExoU derivatives harboring minimal phospholipase activity retained biological activity in tissue culture assays. These proteins affected primarily cellular architecture in a manner similar to that of ExoT. Our studies suggest that conformational changes in ExoU are facilitated by SOD1. Importantly, the level of phospholipase activity influences the biological outcome of ExoU intoxication.