Enzyme nomenclature. Recommendations 1984. Supplement 2: corrections and additions

Purification and characterization of a fungal aspartic peptidase from Trichoderma reesei and its application for food and animal feed protein hydrolyses

BACKGROUND

Various neutral and alkaline peptidases are commercially available for use in protein hydrolysis under neutral to alkaline conditions. However, the hydrolysis of proteins under acidic conditions by applying fungal aspartic peptidases (FAPs) has not been investigated in depth so far. The aim of this study, thus, was to purify a FAP from the commercial enzyme preparation, ROHALASE® BXL, determine its biochemical characteristics, and investigate its application for the hydrolysis of food and animal feed proteins under acidic conditions.

RESULTS

A Trichoderma reesei derived FAP, with an apparent molecular mass of 45.8 kDa (sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SDS-PAGE) was purified 13.8-fold with a yield of 37% from ROHALASE® BXL. The FAP was identified as an aspartate protease (UniProt ID: G0R8T0) by inhibition and nano-LC-ESI-MS/MS studies. The FAP showed the highest activity at 50°C and pH 4.0. Monovalent cations, organic solvents, and reducing agents were tolerated well by the FAP. The FAP underwent an apparent competitive product inhibition by soy protein hydrolysate and whey protein hydrolysate with apparent K_i -values of 1.75 and 30.2 mg*mL^-1 , respectively. The FAP showed promising results in food (soy protein isolate and whey protein isolate) and animal feed protein hydrolyses. For the latter, an increase in the soluble protein content of 109% was noted after 30 min.

CONCLUSION

Our results demonstrate the applicability of fungal aspartic endopeptidases in the food and animal feed industry. Efficient protein hydrolysis of industrially relevant substrates such as acidic whey or animal feed proteins could be conducted by applying fungal aspartic peptidases. © 2022 Society of Chemical Industry.

In silico Identification and Characterization of Protein-Ligand Binding Sites

Protein-ligand binding site prediction methods aim to predict, from amino acid sequence, protein-ligand interactions, putative ligands, and ligand binding site residues using either sequence information, structural information, or a combination of both. In silico characterization of protein-ligand interactions has become extremely important to help determine a protein's functionality, as in vivo-based functional elucidation is unable to keep pace with the current growth of sequence databases. Additionally, in vitro biochemical functional elucidation is time-consuming, costly, and may not be feasible for large-scale analysis, such as drug discovery. Thus, in silico prediction of protein-ligand interactions must be utilized to aid in functional elucidation. Here, we briefly discuss protein function prediction, prediction of protein-ligand interactions, the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated EvaluatiOn (CAMEO) competitions, along with their role in shaping the field. We also discuss, in detail, our cutting-edge web-server method, FunFOLD for the structurally informed prediction of protein-ligand interactions. Furthermore, we provide a step-by-step guide on using the FunFOLD web server and FunFOLD3 downloadable application, along with some real world examples, where the FunFOLD methods have been used to aid functional elucidation.

A hybrid clustering of protein binding sites

The Protein Data Bank contains the description of approximately 27 000 protein-ligand binding sites. Most of the ligands at these sites are biologically active small molecules, affecting the biological function of the protein. The classification of their binding sites may lead to relevant results in drug discovery and design. Clusters of similar binding sites were created here by a hybrid, sequence and spatial structure-based approach, using the OPTICS clustering algorithm. A dissimilarity measure was defined: a distance function on the amino acid sequences of the binding sites. All the binding sites were clustered in the Protein Data Bank according to this distance function, and it was found that the clusters characterized well the Enzyme Commission numbers of the entries. The results, carefully color coded by the Enzyme Commission numbers of the proteins, containing the 20 967 binding sites clustered, are available as html files in three parts at http://pitgroup.org/seqclust/.

Characterization and localization of mitochondrial oligopeptidase (MOP) (EC 3.4.24.16) activity in the human cervical adenocarcinoma cell line HeLa

In this study we describe the partial purification and characterization of the HeLa cell oligopeptidase M or endopeptidase 3.4.24.16. The HeLa enzyme was isolated initially by its ability to hydrolyse a nonapeptide substrate (P9) which was cognate to the N-terminal cleavage site of preproTGF alpha. The enzyme was shown to be a metalloprotease as it was inhibited by Zn(2+)-chelating agents and DTT, and had an approximate molecular weight of 55-63 kD determined by gel filtration. Neurotensin, dynorphin A1-17 and GnRH1-9 were rapidly degraded by the enzyme while GnRH1-10 and somatostatin were not. Neurotensin was cleaved at the Pro10-Tyr11 bond, leading to the formation of neurotensin (1-10) and neurotensin (11-13). The K(m) for neurotensin cleavage was 7 microM and the Ki for the specific 24.16 dipeptide inhibitor (Pro-ile) was 140 microM which were similar to those observed from the human brain enzyme [Vincent et al. (1996): Brain Res 709:51-58]. Through the use of specific antibodies, the purified HeLa enzyme was shown to be oligopeptidase M. This enzyme and its closely related family member thimet oligopeptidase were shown to co-elute during the isolation procedure but were finally separated using a MonoQ column. Oligopeptidase M is located mainly in mitochondria though it was detected on the plasma membrane in an inactive form. The results obtained demonstrate the first recorded instance of this enzyme in human tissue cultured cells, and raise the issue of its function therein.

Human xenobiotic metabolizing esterases in liver and blood

Esterases in human liver microsomes hydrolysed fluazifop-butyl (Vmax 9.8 +/- 1.6 mumol/min/g tissue), paraoxon (Vmax 47.4 +/- 7.5 nmol/min/g tissue) and phenylacetate (Vmax 57 +/- 8 mumol/min/g tissue), whereas esterases found in the human liver cytosol hydrolysed fluazifop-butyl (Vmax 10.0 +/- 0.5 mumol/min/g tissue) and phenylacetate (Vmax 37 +/- 2.9 mumol/min/g tissue) but not paraoxon. Human plasma esterase hydrolysed fluazifop-butyl (Vmax 0.09 +/- 0.006 mumol/min/mL), paraoxon (Vmax 210 +/- 14 nmol/min/mL) and phenylacetate (Vmax 250 +/- 17 mumol/min/mL). Inhibitory studies using paraoxon, bis-nitrophenol phosphate and mercuric chloride indicated fluazifop-butyl hydrolysis involved carboxylesterase in liver microsomes and cytosol, and cholinesterase and carboxylesterase in plasma. Phenylacetate hydrolysis involved arylesterase in plasma, both arylesterase and carboxylesterase in liver microsomes and carboxylesterase in liver cytosol. Plasma hydrolysis is less important and overall esterase activity is lower in humans than in the rat which is therefore a poor model.

Molecular weight and substrate characteristics of human serum arylesterase following purification by immuno-affinity chromatography

Human serum arylesterase (EC 3.1.1.2) was purified over 400-fold with a recovery of 61-78% by single-step immuno-affinity chromatography using a monoclonal antibody, 12-1H8, as the adsorbent. The resultant preparation behaved as one component on SDS-PAGE with an apparent M(r) of 46,000, indicating its high homogeneity. Molecular weight was determined as 380,000 Da by HPLC on TSK-gel G-3000SW. The arylesterase molecule would thus appear to be comprised of octameric subunits. The purified protein hydrolyzed paraoxon. The present study suggests that a separate classification of EC 3.1.8.1 for its paraoxon hydrolyzing activity may not be appropriate to differentiate from arylesterase activity. In addition, the substrate for arylesterase is discussed in terms of its chemical structure.

Heat inactivation of paraoxonase and arylesterase activities in human and rabbit serum

The heat inactivation of esterases in human and rabbit serum was followed at 50 and 55 degrees C by measuring the decrease of activity with paraoxon, phenylacetate and beta-naphthylacetate as substrates. The rate of inactivation measured with the three substrates was slightly, but significantly different, indicating that the substrates are hydrolysed by different enzymes.

Peripheral esterases in the rat: effects of classical inducers

Liver microsomal paraoxonase, aryl esterase and fluazifop butyl esterase (carboxylesterase) were induced by pretreatment of rat with phenobarbitone but not by beta-naphthoflavone or clofibric acid. In the extrahepatic tissues lung cytosolicfluazifop butyl and phenylacetate esterase were induced.

Rat kidney endopeptidase 24.16. Purification, physico-chemical characteristics and differential specificity towards opiates, tachykinins and neurotensin-related peptides

Endopeptidase 24.16 was purified from rat kidney homogenate on the basis of its ability to generate the biologically inactive degradation products neurotensin (1-10) and neurotensin (11-13). On SDS gels of the proteins pooled after the last purification step, the enzyme appeared homogeneous and behaved as a 70-kDa monomer. The peptidase was not sensitive to specific inhibitors of aminopeptidases, pyroglutamyl aminopeptidase I, endopeptidase 24.11, endopeptidase 24.15, proline endopeptidase and angiotensin-converting enzyme but was potently inhibited by several metal chelators such as o-phenanthroline and EDTA and was blocked by divalent cations. The specificity of endopeptidase 24.16 towards peptides of the tachykinin, opioid and neurotensin families was examined by competition experiments of tritiated neurotensin hydrolysis as well as HPLC analysis. These results indicated that endopeptidase 24.16 could discriminate between peptides belonging to the same family. Neurotensin, Lys8-Asn9-neurotensin(8-13) and xenopsin were efficiently hydrolysed while neuromedin N and kinetensin underwent little if any proteolysis by the peptidase. Analogously, substance P and dynorphins (1-7) and (1-8) were readily proteolysed by endopeptidase 24.16 while neurokinin A, amphibian tachykinins and leucine or methionine enkephalins totally resisted degradation. By Triton X-114 phase separation, 15-20% of endopeptidase 24.16 partitioned in the detergent phase, indicating that renal endopeptidase 24.16 might exist in a genuine membrane-bound form. The equipotent solubilization of the enzyme by seven detergents of various critical miscellar concentrations confirmed the occurrence of a membrane-bound counterpart of endopeptidase 24.16. Furthermore, the absence of release elicited by phosphatidylinositol-specific phospholipase C suggested that the enzyme was not attached by a glycosyl-phosphatidylinositol anchor in the membrane of renal microvilli. Finally, endopeptidase 24.16 could not be released from these membranes upon trypsinolysis.

Nature and role of xenobiotic metabolizing esterases in rat liver, lung, skin and blood

In the present study, the distribution and nature of esterases in the rat which hydrolysed fluazifop-butyl, carbaryl, paraoxon and phenylacetate were investigated. Vmax and Km values for the hydrolysis reactions were determined. Fluazifop-butyl was hydrolysed to fluazifop by rat liver (Vmax mumol/min/g microsomes 6.2 +/- 0.4; cytosol 6.84 +/- 0.85), lung (Vmax microsomes 0.38 +/- 0.1; cytosol 1.5 +/- 0.32) and skin (Vmax microsomes 0.02 +/- 0.0015; cytosol 0.4 +/- 0.06) and by plasma (Vmax mumol/min/mL 5.8 +/- 0.48) and red blood cells (Vmax 0.03 +/- 0.015). Significant inhibition by paraoxon and bismitrophenol phosphate indicated the involvement of carboxylesterases. Carbaryl was hydrolysed by liver, lung and skin at a lower rate by microsomal fractions (Vmax nmol/min/g 2.1 +/- 0.25, 1.6 +/- 0.25, 0.2 +/- 0.035, respectively) compared to cytosolic fractions (Vmax 6.7 +/- 0.75, 1.4 +/- 0.36, 0.5 +/- 0.12) and plasma (Vmax nmol/min/mL 3.0 +/- 0.25). Hydrolysis involved carboxylesterases. Paraoxon was hydrolysed by paraoxonases/arylesterases only in the plasma (Vmax nmol/min/mL 246 +/- 12) and microsomal fractions from liver (Vmax 330 nmol/min/g +/- 25) and lung (Vmax 2 +/- 0.25). Phenylacetate was hydrolysed by both microsomal and cytosolic fractions from all tissues studied. Hydrolysis involved arylesterases in the microsomes and carboxylesterases in the cytosol. Extrahepatic hydrolysis may be important following some routes of exposure to xenobiotic esters.

Purification of rabbit and human serum paraoxonase

Rabbit serum paraoxonase/arylesterase has been purified to homogeneity by Cibacron Blue-agarose chromatography, gel filtration, DEAE-Trisacryl M chromatography, and preparative SDS gel electrophoresis. Renaturation (Copeland et al., 1982) and activity staining of the enzyme resolved by SDS gel electrophoresis allowed for identification and purification of paraoxonase. Two bands of active enzyme were purified by this procedure (35,000 and 38,000). Enzyme electroeluted from the preparative gels was reanalyzed by analytical SDS gel electrophoresis, and two higher molecular weight bands (43,000 and 48,000) were observed in addition to the original bands. This suggested that repeat electrophoresis resulted in an unfolding or other modification and slower migration of some of the purified protein. The lower mobility bands stained weakly for paraoxonase activity in preparative gels. Bands of each molecular weight species were electroblotted onto PVDF membranes and sequenced. The gas-phase sequence analysis showed that both the active bands and apparent molecular weight bands had identical amino-terminal sequences. Amino acid analysis of the four electrophoretic components from PVDF membranes also indicated compositional similarity. The amino-terminal sequences are typical of the leader sequences of secreted proteins. Human serum paraoxonase was purified by a similar procedure, and ten residues of the amino terminus were sequenced by gas-phase procedures. One amino acid difference between the first ten residues of human and rabbit was observed.

Immunoautoradiographic localisation of enkephalinase (EC 3.4.24.11) in rat gastrointestinal tract

Enkephalinase (EC 3.4.24.11, membrane metalloendopeptidase) is a zinc peptidase expressed by neurons and a variety of epithelial cells, and responsible for the inactivation of enkephalins in brain. Its functions in the gastrointestinal (GI) tract are less well understood although enkephalinase inhibitors were reported to induce a constellation of antisecretory and motor responses. Its localisation in various segments of the rat GI tract was established autoradiographically using a 125I-labelled monoclonal antibody. All along the GI tract, the highest immunoreactivity was found in mucosal layers e.g., in intestinal villi, basal epithelial layers of the oesophagus or gastric cardia, muscularis mucosae of the stomach and large intestine. The immunoreactivity was also high in the stomach submucosae and moderate in the muscularis propria of the caecum. A faint patchy immunoreactivity was also observed in several other layers. This distribution suggests that the membrane peptidase is expressed by enterocytes and a variety of other cells. Its high expression in mucosal layers is consistent with its participation in protein digestion and also in the inactivation of endogenous peptides, particularly the enkephalins, acting at this level to control secretory mechanisms and hydroelectrolytic fluxes. Its presence in submucosal layers may account for some naloxone-reversible motor responses elicited by enkephalinase inhibitors.

Tissue distribution of neutral endopeptidase 24.11 ('enkephalinase') activity in guinea pig trachea

The distribution of neutral endopeptidase 24.11 (NEP; 'enkephalinase') activity was studied on tissue sections of the guinea pig trachea using a histochemical method based on the catalytic activity of the enzyme. The specificity for NEP of the histochemical reaction was verified by application of an array of peptidase inhibitors. NEP activity was most prominent on the respiratory epithelium, but occurred also in submucous glands, connective tissue of the lamina propria, perichondrium and chondrocytes. The findings suggest that NEP in the trachea is involved in various functions, cleavage of neurally released peptides being only one of them.

A novel potential metallopeptidase derived from the enkephalinase gene by alternative splicing

Amplification of rat intestine mRNAs was performed by the reverse transcriptase-polymerase chain reaction (RT-PCR) using various oligonucleotide primers mainly corresponding to the translated region of the enkephalinase (EC 3.4.24.11, membrane metalloendopeptidase, MME I) gene. In addition to the expected transcript, a shorter one was identified and its sequence indicated that it corresponds to an alternatively spliced mRNA from which exons 5-18 of MME I are deleted. It encodes a deduced 255 amino acid protein, MME II, instead of the 742 amino acid sequence of enkephalinase. The deduced structure of MME II is consistent with its being a membrane-bound, zinc-containing glycoprotein with a modified peptidase activity. MME II mRNA is also expressed, together with MME I mRNA, in brain and thyroid in a tissue-specific manner.

Enkephalinase (EC 3.4.24.11) inhibitors: protection of endogenous ANF against inactivation and potential therapeutic applications

Atrial natriuretic factor (ANF) is a cardiac hormone exerting potent cardiovascular and renal effects but its poor intestinal absorption and rapid inactivation have prevented so far its therapeutic utilisation. However inhibition of endogenous ANF metabolism progressively emerges as a novel therapeutic approach in cardiovascular and renal disorders. The critical role played by enkephalinase (membrane metalloendopeptidase, EC 3.4.24.11) in ANF inactivation was deduced from the effects of inhibitors. These compounds not only protect partially exogenous ANF from hydrolysis by some tissue preparations in vitro but also, in vivo, they increase the half-life of the exogenous hormone in plasma and, even more markedly, its recovery in intact form in kidney, a major target organ. In addition, enkephalinase inhibitors increase by two- to three-fold the circulating level of endogenous ANF, even when the latter is already markedly elevated, such as in patients with chronic heart failure. Finally, enkephalinase inhibitors induce a series of ANF-like responses such as natriuresis, diuresis or increase in cGMP excretion which are attributable to the hormone. These pharmacological observations, as well as preliminary clinical trials, suggest that enkephalinase inhibitors may represent a novel class of therapeutic agents with potential applications in congestive heart failure, essential hypertension and various sodium-retaining states.