Asparagine Peptide Research Articles

APLpred: A machine learning-based tool for accurate prediction and characterization of asparagine peptide lyases using sequence-derived optimal features

Asparagine peptide lyase (APL) is among the seven groups of proteases, also known as proteolytic enzymes, which are classified according to their catalytic residue. APLs are synthesized as precursors or propeptides that undergo self-cleavage through autoproteolytic reaction. At present, APLs are grouped into 10 families belonging to six different clans of proteases. Recognizing their critical roles in many biological processes including virus maturation, and virulence, accurate identification and characterization of APLs is indispensable. Experimental identification and characterization of APLs is laborious and time-consuming. Here, we developed APLpred, a novel support vector machine (SVM) based predictor that can predict APLs from the primary sequences. APLpred was developed using Boruta-based optimal features derived from seven encodings and subsequently trained using five machine learning algorithms. After evaluating each model on an independent dataset, we selected APLpred (an SVM-based model) due to its consistent performance during cross-validation and independent evaluation. We anticipate APLpred will be an effective tool for identifying APLs. This could aid in designing inhibitors against these enzymes and exploring their functions. The APLpred web server is freely available at https://procarb.org/APLpred/.

Bacterial and Fungal Proteolytic Enzymes: Production, Catalysis and Potential Applications.

Submerged and solid-state bioprocesses have been extensively explored worldwide and employed in a number of important studies dealing with microbial cultivation for the production of enzymes. The development of these production technologies has facilitated the generation of new enzyme-based products with applications in pharmaceuticals, food, bioactive peptides, and basic research studies, among others. The applicability of microorganisms in biotechnology is potentiated because of their various advantages, including large-scale production, short time of cultivation, and ease of handling. Currently, several studies are being conducted to search for new microbial peptidases with peculiar biochemical properties for industrial applications. Bioprospecting, being an important prerequisite for research and biotechnological development, is based on exploring the microbial diversity for enzyme production. Limited information is available on the production of specific proteolytic enzymes from bacterial and fungal species, especially on the subgroups threonine and glutamic peptidases, and the seventh catalytic type, nonhydrolytic asparagine peptide lyase. This gap in information motivated the present study about these unique biocatalysts. In this study, the biochemical and biotechnological aspects of the seven catalytic types of proteolytic enzymes, namely aspartyl, cysteine, serine, metallo, glutamic, and threonine peptidase, and asparagine peptide lyase, are summarized, with an emphasis on new studies, production, catalysis, and application of these enzymes.

Yeast Methionine Aminopeptidase I: ALTERATION OF SUBSTRATE SPECIFICITY BY SITE-DIRECTED MUTAGENESIS

In eukaryotes, two isozymes (I and II) of methionine aminopeptidase (MetAP) catalyze the removal of the initiator methionine if the penultimate residue has a small radius of gyration (glycine, alanine, serine, threonine, proline, valine, and cysteine). Using site-directed mutagenesis, recombinant yeast MetAP I derivatives that are able to cleave N-terminal methionine from substrates that have larger penultimate residues have been expressed. A Met to Ala change at 329 (Met206 in Escherichia coli enzyme) produces an average catalytic efficiency 1.5-fold higher than the native enzyme on normal substrates and cleaves substrates containing penultimate asparagine, glutamine, isoleucine, leucine, methionine, and phenylalanine. Interestingly, the native enzyme also has significant activity with the asparagine peptide not previously identified as a substrate. Mutation of Gln356 (Gln233 in E. coli MetAP) to alanine results in a catalytic efficiency about one-third that of native with normal substrates but which can cleave methionine from substrates with penultimate histidine, asparagine, glutamine, leucine, methionine, phenylalanine, and tryptophan. Mutation of Ser195 to alanine had no effect on substrate specificity. None of the altered enzymes produced cleaved substrates with a fully charged residue (lysine, arginine, aspartic acid, or glutamic acid) or tyrosine in the penultimate position.

Identity of structure of ovine and bovine ACTH: Correction of revised structure of the ovine hormone

FEBS LettersVolume 45, Issue 1-2 p. 172-174 Full-length articleFree Access Identity of structure of ovine and bovine ACTH: Correction of revised structure of the ovine hormone A. Jöhl, A. Jöhl Research Department, Pharmaceuticals Division, Ciba-Geigy Limited, 4002 Basle, SwitzerlandSearch for more papers by this authorB. Riniker, B. Riniker Research Department, Pharmaceuticals Division, Ciba-Geigy Limited, 4002 Basle, SwitzerlandSearch for more papers by this authorL. Schenkel-Hulliger, L. Schenkel-Hulliger Research Department, Pharmaceuticals Division, Ciba-Geigy Limited, 4002 Basle, SwitzerlandSearch for more papers by this author A. Jöhl, A. Jöhl Research Department, Pharmaceuticals Division, Ciba-Geigy Limited, 4002 Basle, SwitzerlandSearch for more papers by this authorB. Riniker, B. Riniker Research Department, Pharmaceuticals Division, Ciba-Geigy Limited, 4002 Basle, SwitzerlandSearch for more papers by this authorL. Schenkel-Hulliger, L. Schenkel-Hulliger Research Department, Pharmaceuticals Division, Ciba-Geigy Limited, 4002 Basle, SwitzerlandSearch for more papers by this author First published: September 01, 1974 https://doi.org/10.1016/0014-5793(74)80838-0Citations: 17AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL No abstract is available for this article. References 1 R.G. Shepherd, S.D. Willson, K.S. Howard, P.H. Bell, D.S. Davies, S.B. Davis, E.A. Eigner, N.E. Shakespeare, J. Amer. Chem. Soc., 78, (1956), 5067– 2 C.H. Li, I.I. Geschwind, R.D. Cole, I.D. Raacke, J.I. Harris, J.S. Dixon, Nature, 176, (1955), 687– 3 J. Leonis, C.H. Li, D. Chung, J. Amer. Chem. Soc., 81, (1959), 419– 4 C.H. Li, J.S. Dixon, D. Chung, J. Amer. Chem. Soc., 80, (1958), 2587– 5 C.H. Li, J.S. Dixon, D. Chung, Biochim. Biophys. Acta, 46, (1961), 324– 6 T.H. Lee, A.B. Lerner, V. Buettner-Janusch, J. Biol. Chem., 236, (1961), 2970– 7 B. Riniker, P. Sieber, W. Rittel, H. Zuber, Nature New Biol., 235, (1972), 114– 8 L. Gráf, S. Bajusz, A. Patthy, E. Barát, G. Cseh, Acta Biochim. Biophys. Acad. Sci. Hung., 6, (1971), 415– 9 C.H. Li, Biochem. Biophys. Res. Commun., 49, (1972), 835– 10 C.H. Li, I.I. Geschwind, J.S. Dixon, A.L. Levy, J.I. Harris, J. Biol. Chem., 213, (1955), 171– 11 P. Sieber, W. Rittel, B. Riniker, Helv. Chim. Acta, 55, (1972), 1243– 12 W.R. Lyons, Proc. Soc. exp. Biol. N.Y., 35, (1937), 645– 13 H. Papkoff, C.H. Li, Encyclopaedia of Chemical Technology, 11, (1966), 56– 14 Homan, J. D. H. and Ederzeel, L. H., U. S. Patent 2.985.560. 15 M. Saffran, A.V. Schally, Endocrinology, 56, (1955), 523– 16 H.P.J. Bennett, P.J. Lowry, C. McMartin, Biochem. J., (1974), in press Citing Literature Volume45, Issue1-2September 01, 1974Pages 172-174 ReferencesRelatedInformation

Behavior of angiotensin octapeptides and dinitrophenyl-angiotensin during chromatography on polyacrylamide and dextran gels

The behavior of the synthetic angiotensin II octapeptides (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe, molecular weight 1046, and its Asn 1-Val 5 congener, molecular weight 1031) have been studied during gel chromatography on cross-linked polyacrylamide (Bio-Gel, P-2), and dextran (Sephadex G-15). In the case of the asparagine peptide adsorption was observed with both media. On polyacrylamide adsorption was marked at acid pH (0.05 N HCl), but at pH 5.5 in 0.1 M pyridinium acetate the asparagine compound could be separated from and emerged between a larger peptide (bacitracin, molecular weight 1411) and smaller molecules (pyridine—Cu 2+ complex; Na +). On dextran gel asparagine 1-angiotensin was retarded due to adsorption not only at acid pH but also in 0.1 M pyridinium acetate, with adsorption even more marked in dilute alkali (0.01 N NH 4OH). Under none of these conditions was it possible with ordinary dextran gel to separate asparagine 1-angiotensin from amino acids or salts. In sharp contrast, the aspartic acid 1-angiotensin was excluded from G-15 at alkaline pH, and the two angiotensins were thus readily separated from one another under these conditions. Adsorption of the asparagine 1-angiotensin was nearly abolished by 1 M pyridine. The separation of the two angiotensins under these conditions is attributed to the greater negative charge of the aspartic acid 1-argiotensin which results in exclusion from the gel and overcomes the “aromatic” adsorption of the remainder of the molecule. The dinitrophenyl (DNP) derivative of asparagine 1-angiotensin is readily separable from DNP-amino acids by chromatography in absolute methanol through an alkylated dextran gel (Sephadex LH-20).

Selective Chemical Cleavage of Asparagine Peptides

Abstract Asparagine peptide was selectively cleaved by the Hofmann rearrangement followed by an alkaline treatment at the peptide linkage in which an amino group of the asparagine residue participated. Upon reaction of N-benzyloxycarbonyl-l-alanyl-l-asparagine with one equivalent of bromine and three equivalents of aqueous sodium hydroxide solution at 60°C, 1-(N-benzyloxycarbonyl-l-alanyl)-2-oxoimidazolidine-5-carboxylic acid was obtained in quantitative yield. When this was treated with an aqueous methanolic sodium hydroxide solution at room temperature, a cleavage reaction occurred to give N-benzyloxycarbonyl-l-alanine and 2-oxo-imidazolidine-5-carboxylic acid. Under the same condition of the rearrangement, N-benzyl-oxycarbonyl-l-asparaginyl-l-phenylalanine was converted to 1-benzyloxycarbonyl-2-oxoimidazo-lidine-5-carbonylphenylalanine. Since glutamine peptide could not give the corresponding ring compound, this cleavage reaction was found to be specific to asparagine peptide.

Chemical stability and metabolic utilization of asparagine peptides

l-Leucyl- l-asparagine and l-asparaginyl- l-leucine are utilized as well as l-asparaginylglycine and glycyl- l-asparagine by Leuc. mesenteroides. The growth response to these peptides approximates that to l-aspartic acid and is far superior to that to l-asparagine. l-Aspartylglycine and glycyl- l-aspartic acid at high concentrations are superior to l-aspartic acid as a source of the dicarboxylic acid. The glycine peptides serve as better sources of glycine than glycine itself. The growth response to the leucine peptides is equal to that to leucine. Cell-free extracts of Leuc. mesenteroides show strong asparaginase activity. Observations on the enzymatic splitting of the asparagine peptides suggest that the peptides are cleaved into the amide and glycine or leucine and that the free amide is deamidated. It appears that the superior utilization of asparagine peptides when compared with that of asparagine is the result of the inability of the latter to reach the sites of its metabolism by the bacterial cell. Procedures for the syntheses of leucylasparagine, asparaginylleucine, α-aspartylglycine and glycylaspartic acid are described. The instability of glycylasparagine in acid and of asparaginylglycine in alkali is demonstrated and discussed.

The utilization of glutamine and asparagine peptides by microorganisms

Summary The utilization of glutaminylglycine and glycylglutamine by Lactobacillus arabinosus was compared with that of glutamine and glutamic acid. The growth response to these peptides in its dependence upon concentration or upon time as well as the action of these peptides toward glutamic acid antimetabolites was indistinguishable from that of glutamine. It is therefore suggested that the peptides serve as a source of free glutamine liberated by enzymatic action. In contrast to the behavior of the glutamine peptides, asparaginyl-glycine and glycylasparagine are significantly better utilized than asparagine by both Leconostoc mesenteroides and L. arabinosus . Their utilization approximates that of aspartic acid. The significance of this finding is discussed.

The synthesis of glutamine and asparagine peptides and of glutamine

Summary A new synthesis of glutaminylglycine and the synthesis of a new peptide, asparaginylglycine, are reported. The syntheses of glycylglutamine, glycylasparagine, and glutamine have been reinvestigated. A method for the purification of commercial glutamine is proposed.