Substrate specificity and novel selective inhibitors of TNF-alpha converting enzyme (TACE) from two-dimensional substrate mapping

We report a systematic analysis of the P1' and P2' substrate specificity of TNF-alpha converting enzyme (TACE) using a peptide library and a novel analytical method, and we use the substrate specificity information to design novel reverse hydroxamate inhibitors. Initial truncation studies, using the amino acid sequence around the cleavage site in precursor-TNF-alpha, showed that good turnover was obtained with the peptide DNP-LAQAVRSS-NH2. Based on this result, 1000 different peptide substrates of the form Biotin-LAQA-P1'-P2'-SSK(DNP)-NH2 were prepared, with 50 different natural and unnatural amino acids at P1' in combination with 20 different amino acids at P2'. The peptides were pooled, treated with purified microsomal TACE, and the reaction mixtures were passed over a streptavidin affinity column to remove unreacted substrate and the N-terminal biotinylated product. C-terminal cleavage products not binding to streptavidin were subjected to liquid chromatography/mass spectrometry analysis where individual products were identified and semiquantitated. 25 of the substrates were resynthesized as discrete peptides and assayed with recombinant TACE. The experiments show that recombinant TACE prefers lipophilic amino acids at the P1' position, such as phenylglycine, homophenylalanine, leucine and valine. At the P2' position, TACE can accommodate basic amino acids, such as arginine and lysine, as well as certain non-basic amino acids such as citrulline, methionine sulfoxide and threonine. These substrate preferences were used in the design of novel reverse hydroxamate TACE inhibitors with phenethyl and 5-methyl-thiophene-methyl side-chains at P1', and threonine and nitro-arginine at P2'.     

Random peptide synthesis using immobilized enzymes in high concentrations of organic solvents

Trypsin, leucine aminopeptidase, and carboxypeptidase B were separately immobilized on controlled pore glass and reacted with a dipeptide substrate in high concentrations of either acetone or 1-propanol. Hydrolytic activity was demonstrated and evidence for the possible synthesis of peptide polymer is presented. Directed synthesis using amino acids and blocked amino acids as substrates was not successful.     

Clone,Purification and Characterization of Thermostable Aminopeptidase ST1737 from Sulfolobus tokodaii

The aminopeptidase gene from thermophilic archaea Sulfolobustokodaii was cloned and expressed in Escherichia coli BL21 codon-plus(DE3). To overexpress the aminopeptidase, the vector pET32a was constructed, in which the target gene was fused with the genes of histidine-tag and thioredoxin(Trx). The expressed protein was purified using Ni²⁺-column affinity chromatography and ion exchange chromatography and cleft with enterokinase(EK) to obtain the purified aminopeptidase(ST1737). The biochemical and enzymic properties of the expressed ST1737 were characterized. The results show that its optimal pH and temperature are 8 and 80 ℃, respectively. The half-life of ST1737(0.2 mg/mL) is about 85 h at 90 ℃, indicating that the enzyme exhibits an excellent thermostability. The activity of ST1737 could still maintain over 85% after its treatment at 25 ℃ in different buffers with a pH range of from 6.0 to 10.5 for 24 h, demonstrating that ST1737 is stable in neutral or slight alkali environment. The enzyme shows a high activity for the substrates, such as unmodified peptide Asp-Ala, while the pNPC₈ shows an optimal esterase substrate specificity. These results indicate that the enzyme is a bifunctional enzyme, and different from the aminopeptidase reported before.     

Approach to studying proteinase specificity by continuous-flow fast atom bombardment mass spectrometry and high-performance liquid chromatography combined with photodiode-array ultraviolet detection.

Fast atom bombardment mass spectrometry (FAB-MS) and high-performance liquid chromatography using a photodiode-array ultraviolet detector were applied to study a dynorphin-converting endopeptidase from the human pituitary gland. The specificity of the enzyme was tested towards various opioid peptides derived from the prodynorphin precursor, i.e. dynorphin A, dynorphin B and alpha-neoendorphin. Peptide fragments were analysed directly by continuous-flow FAB-MS and those containing aromatic amino acids were detected independently by the photodiode-array ultraviolet detector. The results obtained suggest a similar processing of these structure-related substrates and it appears that the enzyme recognizes the dibasic stretch in their sequence. It is also clear from this study that the combination of the above techniques provides a powerful tool for studies of enzymatic conversion among the prodynorphin-derived peptides and it should be applicable to studies of similar mechanisms in other peptide systems.     

Immobilized Leucine Aminopeptidase Applications in Protein Chemistry

Abstract

Leucine aminopeptidase (EC 3.4.1.1) has been covalentiy bound to porous glass through an azo linkage. For the hydrolysis of leucine p-nitroanilide at pH 7.3 and 25°, K_m(app) for the immobilized enzyme is higher than that of the soluble enzyme: 1.30 ± 0.2 and 0.53 ± 0.03 mM, respectively. However, at saturating levels of substrate the immobilized derivative and free enzyme have similar activities; k. values for the bound and free enzymes are 46 ± 5 and 46 ± 2 sec^?1, respectively. In addition, the pH and temperature dependences of the two enzyme forms are quite similar. These data suggest that the environment and conformation of the enzyme are not significantly changed after coupling. The apparent decrease in the substrate binding ability could be explained by a decrease in the effective diffusion coefficient of the substrate.

The insoluble enzyme is also active against peptide substrates. After treatment to remove contaminating proteases, immobilized leucine aminopeptidase was used successfully in sequencing experiments. The bound enzyme should be useful in total hydrolysis of peptides and proteins. The aminoethylated derivatives of the A- and B-chains of insulin were hydrolyzed essentially to completion. βLactoglobulin was hydrolyzed to the extent of 93% with immobilized leucine aminopeptidase and immobilized pronase.     

Purification of substance P endopeptidase activity in the rat ventral tegemental area with the Akta-Purifier chromatographic system

The new chromatographic system Akta-Purifier 10 (Amersham-Pharmacia Biotech), scaled for preparative HPLC, was used for the purification of Substance P (SP) endopeptidase activity in the ventral tegemental area (VTA) of the rat brain. SP endopeptidase previously identified and purified from human cerebrospinal fluid has been found to degrade the neuroactive peptide SP in a specific pattern. In this study we have recovered SP endopeptidase from the rat VTA following a purification scheme involving homogenization (ultrasonication) and extraction of the excised tissue, size-exclusion chromatography (Superdex 75 HR), and ion-exchange chromatography (Resource Q). In this way we were able to achieve a purification factor of almost 7,500, based on specific activity. The obtained SP endopeptidase activity, was then subjected to characterization with regard to inhibition profile. The enzyme activity was monitored by following the conversion of SP to its N-terminal fragment SP(1-7) using a radioimmunoassay, specific for the heptapeptide product. On basis of inhibition profile it was possible to discern two different SP endopeptidase-like activities, one sensitive toward the protease inhibitor phosphoramidon (preparation A), and another non-sensitive to phosphoramidon or captopril (preparation B). The molecular masses of preparations A and B, as derived from sodium dodecyl sulfate-polyacrylamide gel electrophoresis, were found to be 90,000 and 76,000, respectively. Our data suggest that the purified phosphoramidon sensitive endopeptidase activity may be an enzyme that plays a major role in the conversion of SP to its bioactive fragment SP(1-7) in the rat VTA. This is likely to be identical to the previously known neutral endopeptidase (EC 3.4.24.11). However, this study also demonstrates the existence of a distinct endopeptidase activity with properties in agreement with rat spinal cord SP endopeptidase. In the context of previously shown altered levels of SP(1-7) in the VTA during morphine withdrawal both purified enzyme activities may turn out to be responsible.     

Automated phenylthiocarbamyl amino acid analysis of carboxypeptidase/aminopeptidase digests and acid hydrolysates

A fully automated exopeptidase digestion procedure for the partial determination of N- and C-terminal peptide/protein sequence is described. The digestion of various substrates with aminopeptidase M, carboxypeptidase A, P or Y was accomplished with the Varian 9090 autosampler's robotic automix routines. The released free amino acids, in addition to free amino acids from acid hydrolysates, were derivatized with phenylisothiocyanate in an automated fashion and subsequently chromatographed on a C18 column for separation and quantitation. The advantages of automating this precolumn phenylisothiocyanate derivatization are the virtual elimination of sample manipulation errors and very reproducible data due to the precise control of the reaction conditions both of which, facilitate the interpretation of the exopeptidase reaction kinetic data.     

Tryptophan aminopeptidase activity of several indole prenyltransferases from Aspergillus fumigatus

Recently, five indole prenyltransferases from Aspergillus fumigatus have been proven biochemically to be responsible for prenylations of diverse substrates. In this study, we show peptidase activities of 7-DMATS, FgaPT1, CdpNPT, and FtmPT1, with preference for linear peptides containing a tryptophanyl moiety at the N terminus. Testing of 31 peptides revealed that these enzymes shared similar substrate specificity and accepted H-L-Trp-L-Ala-OH and H-L-Trp-Gly-OH as best substrates for aminopeptidase activity. By using H-L-Trp-Gly-OH as substrate, Km values at 350, 380, 300, and 420 microM and enzymatic rate constants kcat/Km at 0.51, 0.24, 0.53, and 0.14 mM(-1)s(-1) were determined for 7-DMATS, FgaPT1, CdpNPT, and FtmPT1, respectively. In contrast to prenyltransferase activities, the aminopeptidase activities were strongly or completely inhibited by EDTA. Mn2+ increased the aminopeptidase activities of FtmPT1 and CdpNPT up to 4- and 6-fold, respectively. To the best of our knowledge, this is the first report on the catalytic promiscuity of prenyltransferases.     

Micellar electrokinetic chromatography and laser induced fluorescence detection of botulinum neurotoxin type A activity using a dual-labelled substrate

The activity of Botulinum neurotoxin type A (BoNT A) can be measured by monitoring the toxin's endopeptidase reaction with its peptide substrate. In this report, a sensitive and simple capillary electrophoresis (CE) method for analysing BoNT A activity was developed using a peptide substrate labelled with Fluorescein isothiocynate (FITC) at the N-terminal and biotin at the C-terminal. This dual labelling enables not only highly sensitive laser induced fluorescence (LIF) detection of the reaction product, but also good analytical separation of the product from the peptide substrate by Micellar Electrokinetic Chromatography (MEKC). The separation between the product peak and the substrate peak was approximately 5 min using the dual-labelled substrate, while just about 1 min using the FITC-labelled substrate without biotinylation. Using the current assay method, BoNT A with concentration as low as 0.1 ng ml^?1 (3.6 U mL^?1 in mouse LD₅₀) in water was detected with a S:N ratio of 3 (RSD <19%) and a linear range of four orders of magnitude. With CE's advantages of very small sample volume needed, this method may find particular applications as in assays of BoNT A activity in water samples and kinetic analyses of toxin activity.     

Purification,Characterization and N‐terminal Sequence Analysis of Betel Leaf (Piper betle) Invertase

The present study is the first report describing the purification, enzymatic properties and N‐terminal amino acid sequence of a native invertase in betel leaf. The invertase was purified as a monomeric glycoprotein of molecular mass (Mr) 68 kDa. The enzyme was capable to attack β‐fructofuranoside linkages from the fructose end of sucrose, raffinose and stachyose indicating it as an authentic β‐D‐fructofuranosidase with high specificity for sucrose (Km 4.83 mM). The maximum activity was detected at pH 5.2 and 37 °C. Glucose and fructose showed typical inhibitory effect on the enzyme activity where as lectin was found to be effective activators of the enzyme. Significant inhibition by heavy metal ion Hg²⁺ and sulfhydryl group modifying agents suggesting that free sulfhydryl group containing amino acid, cysteine is necessary for the catalytic activity of the invertase. A BLAST search of the N‐terminal amino acid sequence of betel leaf invertase showed significant homology with the homologous invertases in database.     

Proline-Specific Extracellular Aminopeptidase Purified from <Emphasis Type="Italic">Streptomyces lavendulae</Emphasis>

Aminopeptidases catalyze the cleavage of specific amino acids from the amino terminus of protein or peptide substrates. A proline-specific aminopeptidase was purified to homogeneity from the culture-free extract of Streptomyces lavendulae ATCC 14162 in sequential steps comprising ammonium sulfate precipitation, ultra-filtration, and column chromatography on Q-sepharose and Sephadex G-100. The purified protein showed approximately 60 kDa in SDS-PAGE and was optimally active at pH 6.5 and 40 °C. Kinetic studies showed a K _m and V _max of 0.23 mM and 0.087 μmol/min, respectively, using Pro-p-NA, the substrate with maximum specificity. Enzyme activity was inhibited by PMSF and ions like Zn²⁺, Co²⁺, and Ni²⁺. However, unlike other aminopeptidases, the activity was enhanced in the presence of DTT, 1,10-phenanthroline, EDTA, amastatin, and bestatin. Ions like Ca²⁺, Mg²⁺, and Mn²⁺ also enhanced the activity.     

靛红类双功能抑制剂: 调控SARS-3CL蛋白酶聚集状态与活性

1-(2-萘甲基)靛红-5-甲酰胺类化合物通过与底物口袋结合来抑制SARS-3CL 蛋白酶的活性, 而SARS-3CL蛋白酶自身的N端8 肽是作用于蛋白二聚界面的抑制剂. 本文设计同时占据SARS-3CL蛋白酶底物口袋和二聚界面的双功能抑制剂, 通过固相多肽合成方法制备由1-(2-萘甲基)靛红-5-甲酸和N端8肽组成的化合物, 得到不同长度连接链的6 个目标产物. 用显色底物方法测定化合物对SARS-3CL蛋白酶的抑制活性,其中化合物3的活性最高, IC₅₀值(半抑制率)为3.8 μmol·L^-1, 连接偶数甘氨酸的活性明显要好于连接奇数甘氨酸的化合物. 用超速离心沉降速率方法研究了化合物3对SARS-3CL蛋白酶聚集状态与活性的调控作用, 其同时具有诱导与抑制二聚的双重能力, 综合调控结果是抑制SARS-3CL蛋白酶的二聚. 这项研究给应用合成的化合物研究酶活性调节机制提供了一个示例.     

A New Aminopeptidase from the Keratin-Degrading Strain Streptomyces fradiae var. k11

An aminopeptidase gene fragment was isolated from a keratin-degrading strain, Streptomyces fradiae var. k11, by PCR amplification using a degenerate primer set designed based on the partial amino acid sequence of the native enzyme. The gene, designated sfap, encoded a polypeptide of 461 amino acids comprised of three domains: a signal peptide, a mature region, and a C-terminal propeptide. The aminopeptidase, SFAP, had highest amino acid sequence identity (79%) with a putative aminopeptidase from Streptomyces griseus subsp. griseus NBRC 13350. The gene with and without C-terminal propeptide was successfully overexpressed in Escherichia coli BL21 (DE3), and the gene without C-terminal propeptide encoded a functional enzyme. Purified recombinant SFAP exhibited optimal activity at pH 8.0 and 60 °C, and retained >60% peak activity over a broad range of temperature. The enzyme was thermal and pH stable, and showed metalloprotease characteristics, which was inhibited by EDTA but activated by Ca²⁺ and Co²⁺. This is the first study to report the gene cloning and expression of a leucine aminopeptidase from S. fradiae.     

Structural Elucidation of the Bispecificity of A Domains as a Basis for Activating Non‐natural Amino Acids

Many biologically active peptide secondary metabolites of bacteria are produced by modular enzyme complexes, the non‐ribosomal peptide synthetases. Substrate selection occurs through an adenylation (A) domain, which activates the cognate amino acid with high fidelity. The recently discovered A domain of an Anabaenopeptin synthetase from Planktothrix agardhii (ApnA A₁) is capable of activating two chemically distinct amino acids (Arg and Tyr). Crystal structures of the A domain reveal how both substrates fit into to binding pocket of the enzyme. Analysis of the binding pocket led to the identification of three residues that are critical for substrate recognition. Systematic mutagenesis of these residues created A domains that were monospecific, or changed the substrate specificity to tryptophan. The non‐natural amino acid 4‐azidophenylalanine is also efficiently activated by a mutant A domain, thus enabling the production of diversified non‐ribosomal peptides for bioorthogonal labeling.     

A Bottom‐Up Proteomic Approach to Identify Substrate Specificity of Outer‐Membrane Protease OmpT

Identifying peptide substrates that are efficiently cleaved by proteases gives insights into substrate recognition and specificity, guides development of inhibitors, and improves assay sensitivity. Peptide arrays and SAMDI mass spectrometry were used to identify a tetrapeptide substrate exhibiting high activity for the bacterial outer‐membrane protease (OmpT). Analysis of protease activity for the preferred residues at the cleavage site (P1, P1′) and nearest‐neighbor positions (P2, P2′) and their positional interdependence revealed FRRV as the optimal peptide with the highest OmpT activity. Substituting FRRV into a fragment of LL37, a natural substrate of OmpT, led to a greater than 400‐fold improvement in OmpT catalytic efficiency, with a k _cat/K _m value of 6.1×10⁶ L mol⁻¹ s⁻¹. Wild‐type and mutant OmpT displayed significant differences in their substrate specificities, demonstrating that even modest mutants may not be suitable substitutes for the native enzyme.     

An electrophoretic method for the detection of chymotrypsin and trypsin activity directly in whole blood

In biomedical research and clinical diagnostics, it is a major challenge to measure disease‐related degradative enzyme activity directly in whole blood. Present techniques for assaying degradative enzyme activity require sample preparation, which makes the assays time‐consuming and costly. This study now describes a simple and rapid electrophoretic method that allows detection of degradative enzyme activity directly in whole blood using charge‐changing fluorescent peptide substrates. Charge‐changing substrates eliminate the need for sample preparation by producing positively charged cleavage fragments that can be readily separated from the oppositely charged fluorescent substrate and blood components by electrophoresis. Two peptide substrates have been developed for pancreatic α‐chymotrypsin and trypsin. For the first substrate, a detection limit of 3 ng for both α‐chymotrypsin and trypsin was achieved in whole rat blood using a 4% agarose gel. This substrate had minimal cross‐reactivity with the trypsin‐like proteases thrombin, plasmin, and kallikrein. For the second substrate (trypsin‐specific), a detection limit of about 10–20 pg was achieved using thinner higher resolution 20 and 25% polyacrylamide gels. Thus, the new charge changing peptide substrates enable a simple electrophoretic assay format for the measurement of degradative enzyme activity, which is an important step toward the development of novel point‐of‐care diagnostics.     

Investigations on the enzyme specificity of clostripain: a new efficient biocatalyst for the synthesis of peptide isosteres

To explore the ability of the cysteine protease clostripain as a biocatalyst for the synthesis of peptide isosteres, the S'-subsite specificity of this enzyme toward unnatural substrates was investigated. First, the function of clostripain for acylating aliphatic noncyclic and cyclic amines varying in chain length and ring size was analyzed using a standard acyl donor. Additionally, this series was expanded by use of aromatic amines, amino alcohols, derivatives of non-alpha-amino carboxylic acids, and symmetric and asymmetric diamines, respectively. The results obtained give a detailed picture of the unique reactivity of clostripain toward synthetic substrates, allowing insights into the basic enzyme-substrate interactions. Furthermore, the data provide a guideline for the use of clostripain as a biocatalyst for synthesis of peptide isosteres. The study was completed by the utilization of a model substrate mimetic enabling clostripain to react with noncoded and non-amino acid-derived amines as well as nonspecific acyl moieties. The results of this study indicate that this approach may extend the application range of clostripain as a biocatalyst outside of peptide synthesis.     

Controlled peptide solvation in portion-mixing libraries of FRET peptides: improved specificity determination for Dengue 2 virus NS2B-NS3 protease and human cathepsin S

The solubility of peptides in aqueous buffers used for the enzyme assays is a common limitation for all peptide libraries. In principle, the more water-soluble peptides are, the more susceptible they will be to peptidase hydrolysis. We have demonstrated that this bias can be circumvented in a portion-mixing fluorescence resonance energy transfer (FRET) peptide library by introducing k (lysine in the D-form) in both termini of the peptides. This more solvated library and another one without the k were assayed using trypsin and chymotrypsin as standard peptidases with high selectivity for R and K and for hydrophobic F and Y, respectively. Significantly improved consistency of the information on substrate profiles was obtained from the solvated library. The influence of improved solvation on substrate specificity determination was successfully demonstrated by the difference in specificity observed between the two libraries employing the human cathepsin S (accepts acidic, basic, or neutral amino acids at P1 position) and Dengue 2 virus NS2B-NS3 protease (high specificity to the pair of basic amino acids K-R, R-R, or Q-R/K at P2-P1 positions). In conclusion, hydration of the peptides has a major influence on protease processing, and this bias can be reduced in bound peptide libraries, improving reliability.     

Peptide hydrolysis by the binuclear zinc enzyme aminopeptidase from Aeromonas proteolytica: a density functional theory study

Aminopeptidase from Aeromonas proteolytica (AAP) is a binuclear zinc enzyme that catalyzes the cleavage of the N-terminal amino acid residue of peptides and proteins. In this study, we used density functional methods to investigate the reaction mechanism of this enzyme. A model of the active site was constructed on the basis of the X-ray crystal structure of the native enzyme, and a model dipeptide was used as a substrate. It was concluded that the hydroxide is capable of performing a nucleophilic attack at the peptide carbonyl from its bridging position without the need to first become terminal. The two zinc ions are shown to have quite different roles. Zn2 binds the amino group of the substrate, thereby orienting it toward the nucleophile, while Zn1 stabilizes the alkoxide ion of the tetrahedral intermediate, thereby lowering the barrier for the nucleophilic attack. The rate-limiting step is suggested to be the protonation of the nitrogen of the former peptide bond, which eventually leads to the cleavage of the C-N bond.