Formaldehyde as an Active Site Label of α-Chymotrypsin

1972 ◽  
Vol 50 (10) ◽  
pp. 1114-1121 ◽  
Author(s):  
Charles J. Martin ◽  
Narendra B. Oza ◽  
Mario A. Marini
Keyword(s):  
Active Site ◽  
Competitive Inhibition ◽  
Catalytic Efficiency ◽  
Formaldehyde Concentration ◽  
Binding Studies ◽  
Photometric Analysis ◽  
Limit Values ◽  
Catalytic Rate Constant ◽  
Catalytic Rate ◽  
Hydrolysis Of

The effect of formaldehyde concentration on the steady state parameters of the chymotrypsin-catalyzed hydrolysis of specific ester substrates has been investigated. At the limit values which are attained in about 3 M formaldehyde, the catalytic rate constant is decreased eightfold and [Formula: see text] increased ca. 2.5-foid. The reduction in activity does not conform to competitive, noncompetitive, uncompetitive, or partially competitive inhibition. The effect of increasing formaldehyde concentration is, however, in accord with an equimolar equilibrium reaction between chymotrypsin and formaldehyde with Kassoc of 5 M−1. Spectro-photometric analysis of the same reaction (J. Biol. Chem. 242, 5736 (1967)) and binding studies with 14C-elabeled formaldehyde (Biochim. Biophys. Acta, 242, 320 (1971)) have shown that both histidine residues react with formaldehyde.From a study of the imidazole group catalyzed hydrolysis of p-nitrophenyl acetate, the effect of formaldehyde on such processes is qualitatively similar to that observed for reactions catalyzed by chymotrypsin. The Kassoc values, however, are higher: 36 M−1 for imidazole and 25 M−1 for acetylhistidine.On the basis of these and other results, it is concluded that formaldehyde reacts with the active site of chymotrypsin to form a modified enzyme with decreased catalytic efficiency. The causative event is most probably due to the formation of an N-hydroxymethyl derivative of the His-57 residue.

THE TRYPSIN CATALYZED HYDROLYSIS OF p-NITROPHENYL ACETATE

1959 ◽  
Vol 37 (4) ◽  
pp. 751-759 ◽  
Author(s):  
James A. Stewart ◽  
Ludovic Ouellet
Keyword(s):  
Active Site ◽  
Initial Rate ◽  
Competitive Inhibition ◽  
Early Stage ◽  
Stopped Flow ◽  
Hydrogen Ions ◽  
Experimental Conditions ◽  
Influence Of Ph ◽  
Kinetics Of ◽  
Hydrolysis Of

The hydrolysis of p-nitrophenyl acetate (NPA) by trypsin has been investigated in the early stage of the reaction using stopped-flow techniques. The influence of pH on the initial rate suggests competitive inhibition of the active site of the enzyme by hydrogen ions. The dissociation constant of the enzyme obtained from the kinetics of this reaction (pK = 6.9) indicates possible catalysis by an ammo group or an imidazole group of the enzyme. Lysine methyl ester as an analogue of the enzyme catalyzes the hydrolysis of NPA under similar experimental conditions. The results are described in terms of an assumed mechanism and the nature of the catalytic site is discussed.

scholarly journals A new chromophoric substrate for penicillopepsin and other fungal aspartic proteinases

1982 ◽  
Vol 203 (3) ◽  
pp. 603-610 ◽  
Author(s):  
Theo Hofmann ◽  
Robert S. Hodges
Keyword(s):  
Catalytic Efficiency ◽  
Aspartic Proteinase ◽  
Spectrophotometric Assay ◽  
Water Soluble ◽  
Burst Release ◽  
Penicillium Roqueforti ◽  
Aspartic Proteinases ◽  
Catalytic Rate Constant ◽  
Human Renin ◽  
Hydrolysis Of

The hexapeptide N-α-acetylalanylalanyl-lysyl-p- nitrophenylalanylalanylalanylamide has been synthesized and was found to be a good substrate for fungal aspartic proteinases that possess trypsinogen-activating activity, namely penicillopepsin, Rhizopus aspartic proteinase, Endothia aspartic proteinase and the aspartic proteinases from Aspergillus oryzae and Penicillium roqueforti. The peptide is rapidly cleaved between the lysine and p-nitrophenylalanine residues. Calf chymosin and human renin cleave the same bond, but only very slowly. The cleavage is accompanied by an absorbance decrease with a maximum at 296nm (Δε —1800m−1·cm−1). Pig pepsin and the aspartic proteinases from two Rhizomucor species cleave the peptide slowly on the carboxy side of p-nitrophenylalanine. For the five enzymes that hydrolysed the peptide rapidly, Km values range from 0.16 to 0.42mm and kcat. from 6 to 46.6s−1 at pH 4.5 and 25°C. A comparison of the kinetic parameters of the hexapeptide with those of the dipeptide N-α-acetyllysyl-p-nitrophenylalanylamide obtained with penicillopepsin shows that at pH 6.0 the catalytic rate constant kcat. is over 5000-fold greater for the hexapeptide, whereas the Km values are essentially the same, showing that the catalytic efficiency is strongly dependent on secondary binding. The new substrate with a p-nitrophenylalanine residue in the P′1 position has advantages over previously used substrates for aspartic proteinases in that it offers a more sensitive spectrophotometric assay that is independent of pH up to 5.5 and can readily be used up to pH 7.0. The presence of lysine makes it very water-soluble. Stopped-flow spectrophotometric experiments with penicillopepsin gave clear evidence that the hydrolysis of the substrate by penicillopepsin is not accompanied by a ‘burst’ release of p-nitrophenylalanylalanylalanylamide.

Barley arabinoxylan arabinofuranohydrolases: purification, characterization and determination of primary structures from cDNA clones

2001 ◽  
Vol 356 (1) ◽  
pp. 181-189 ◽  
Author(s):  
Robert C. LEE ◽  
Rachel A. BURTON ◽  
Maria HRMOVA ◽  
Geoffrey B. FINCHER
Keyword(s):  
Catalytic Efficiency ◽  
Exchange Chromatography ◽  
Cdna Clones ◽  
Amino Acid Residues ◽  
Hordeum Vulgare L ◽  
Ph Optimum ◽  
Catalytic Rate Constant ◽  
Arabinoxylan Arabinofuranohydrolase ◽  
Mature Enzyme ◽  
Hydrolysis Of

A family 51 arabinoxylan arabinofuranohydrolase, designated AXAH-I, has been purified from extracts of 7-day-old barley (Hordeum vulgare L.) seedlings by fractional precipitation with (NH4)2SO4 and ion-exchange chromatography. The enzyme has an apparent molecular mass of 65kDa and releases l-arabinose from cereal cell wall arabinoxylans with a pH optimum of 4.3, a catalytic rate constant (kcat) of 6.9s−1 and a catalytic efficiency factor (kcat/Km) of 0.76 (ml·s−1·mg−1). Whereas the hydrolysis of α-l-arabinofuranosyl residues linked to C(O)3 of backbone (1 → 4)-β-xylosyl residues proceeds at the fastest rate, α-l-arabinofuranosyl residues on doubly substituted xylosyl residues are also hydrolysed, at lower rates. A near full-length cDNA encoding barley AXAH-I indicates that the mature enzyme consists of 626 amino acid residues and has a calculated pI of 4.8. A second cDNA, which is 81% identical with that encoding AXAH-I, encodes another barley AXAH, which has been designated AXAH-II. The barley AXAHs are likely to have key roles in wall metabolism in cereals and other members of the Poaceae. Thus the enzymes could participate in the modification of the fine structure of arabinoxylan during wall deposition, maturation or expansion, or in wall turnover and the hydrolysis of arabinoxylans in germinated grain.

scholarly journals Past times: The efficiency of enzyme catalysis

2003 ◽  
Vol 25 (4) ◽  
pp. 52-53
Author(s):  
Michael I. Page
Keyword(s):  
Active Site ◽  
Enzyme Catalysis ◽  
Catalytic Efficiency ◽  
Low Concentration ◽  
Rapid Turnover ◽  
Significant Rate ◽  
Diffusion Controlled ◽  
Biological Interest ◽  
Rate Of Reaction ◽  
Hydrolysis Of

Understanding enzyme catalysis on a molecular and energetic basis has fascinated scientists for more than half a century. In addition to their obvious physiological involvement, the incredible efficiency of enzymes continues to intrigue us. In the absence of enzymes, many reactions of biological interest, e.g. the hydrolysis of proteins, carbohydrates and DNA, have half-lives of hundreds to millions of years. After a substrate is bound at an enzyme's active site, its halflife is usually milliseconds. The low concentration of enzymes in cells, which is often at or below the micromolar level, means that a rapid turnover is necessary to produce a significant rate of reaction and many reactions occur at near the diffusion controlled limit. The high catalytic efficiency of enzymes has not been emulated by artificial systems and therefore many have wondered if they could even be understood by ordinary chemistry.

scholarly journals Effects of secondary binding by activator and inhibitor peptides on covalent intermediates of pig pepsin

1976 ◽  
Vol 153 (3) ◽  
pp. 701-712 ◽  
Author(s):  
T T Wang ◽  
T Hofmann
Keyword(s):  
Binding Sites ◽  
Competitive Inhibition ◽  
Catalytic Efficiency ◽  
Acyl Transfer ◽  
High Substrate Concentration ◽  
Substrate Activation ◽  
Substrate Cleavage ◽  
Kinetics Of ◽  
Hydrolysis Of

A number of peptides were found to increase the activity of pig pepsin towards small synthetic substrates. The activators increase transpeptidation of both the acyl-transfer and the amino-transfer types by as much as 45-fold. The effect on hydrolysis varies from inhibition to modest activation, but is always less than the effect on transpeptidation. The kinetics of substrate cleavage are the converse of non-competitive inhibition and show an increase in kcat. and no effect on Km values. Lineweaver-Burk plots of results obtained in the presence of the activators indicate a substrate activation at high substrate concentration. This appears to be a co-operative effect, since it is not observed in the absence of the activators. The activation is greatest at pH 4.7, less at pH 3.4, and at pH 2.0 is observable only with some of the activator peptides. The results show directly the effect of secondary binding on the catalytic efficiency of pepsin. The most effective activators are those that are most hydrophobic. The results suggest that binding in the secondary binding sites causes an increase in hydrophobicity in the catalytic site which results in increased stability of the acyl and amino intermediates, and preferential reaction with acceptors other than water. The implication that the present results strengthen the case for a role of covalent intermediates in the hydrolysis of good substrates (high kcat. values) is discussed.

Structure-Based Design, Synthesis, Biological Evaluation and Molecular Docking Study of 4-Hydroxy-N'-methylenebenzohydrazide Derivatives Acting as Tyrosinase Inhibitors with Potentiate Anti-Melanogenesis Activities

2020 ◽  
Vol 16 (7) ◽  
pp. 892-902 ◽  
Author(s):  
Aida Iraji ◽  
Mahsima Khoshneviszadeh ◽  
Pegah Bakhshizadeh ◽  
Najmeh Edraki ◽  
Mehdi Khoshneviszadeh
Keyword(s):  
Molecular Docking ◽  
Active Site ◽  
Competitive Inhibition ◽  
Docking Study ◽  
Biological Evaluation ◽  
Primary Response ◽  
Ratio Method ◽  
Molecular Docking Study ◽  
Metal Chelating

Background: Melanogenesis is a process of melanin synthesis, which is a primary response for the pigmentation of human skin. Tyrosinase is a key enzyme, which catalyzes a ratelimiting step of the melanin formation. Natural products have shown potent inhibitors, but some of these possess toxicity. Numerous synthetic inhibitors have been developed in recent years may lead to the potent anti– tyrosinase agents. Objective: A number of 4-hydroxy-N'-methylenebenzohydrazide analogues with related structure to chalcone and tyrosine were constructed with various substituents at the benzyl ring of the molecule and evaluate as a tyrosinase inhibitor. In addition, computational analysis and metal chelating potential have been evaluated. Methods: Design and synthesized compounds were evaluated for activity against mushroom tyrosinase. The metal chelating capacity of the potent compound was examined using the mole ratio method. Molecular docking of the synthesized compounds was carried out into the tyrosine active site. Results: Novel 4-hydroxy-N'-methylenebenzohydrazide derivatives were synthesized. The two compounds 4c and 4g showed an IC50 near the positive control, led to a drastic inhibition of tyrosinase. Confirming in vitro results were performed via the molecular docking analysis demonstrating hydrogen bound interactions of potent compounds with histatidine-Cu+2 residues with in the active site. Kinetic study of compound 4g showed competitive inhibition towards tyrosinase. Metal chelating assay indicates the mole fraction of 1:2 stoichiometry of the 4g-Cu2+ complex. Conclusion: The findings in the present study demonstrate that 4-Hydroxy-N'- methylenebenzohydrazide scaffold could be regarded as a bioactive core inhibitor of tyrosinase and can be used as an inspiration for further studies in this area.

scholarly journals Encapsulated NOLA™ Fit 5500 Lactase—An Economically Beneficial Way to Obtain Lactose-Free Milk at Low Temperature

Catalysts ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 527
Author(s):  
Katarzyna Czyzewska ◽  
Anna Trusek
Keyword(s):  
Low Temperature ◽  
Storage Temperature ◽  
Competitive Inhibition ◽  
Caloric Content ◽  
Substrate Diffusion ◽  
Galactose Inhibition ◽  
The Subject ◽  
And Storage ◽  
Food Processes ◽  
Hydrolysis Of

The current requirements of industrial biocatalysis are related to economically beneficial and environmentally friendly processes. Such a strategy engages low-temperature reactions. The presented approach is essential, especially in food processes, where temperature affects the quality and nutritional value foodstuffs. The subject of the study is the hydrolysis of lactose with the commercial lactase NOLA™ Fit 5500 (NOLA). The complete decomposition of lactose into two monosaccharides gives a sweeter product, recommended for lactose intolerant people and those controlling a product’s caloric content. The hydrolysis reaction was performed at 15 °C, which is related to milk transportation and storage temperature. The enzyme showed activity over the entire range of substrate concentrations (up to 55 g/L lactose). For reusability and easy isolation, the enzyme was encapsulated in a sodium alginate network. Its stability allows carrying out six cycles of the complete hydrolysis of lactose to monosaccharides, lasting from two to four hours. During the study, the kinetic description of native and encapsulated NOLA was conducted. As a result, the model of competitive galactose inhibition and glucose mixed influence (competitive inhibition and activation) was proposed. The capsule size does not influence the reaction rate; thus, the substrate diffusion into capsules can be omitted from the process description. The prepared 4 mm capsules are easy to separate between cycles, e.g., using sieves.

scholarly journals Kinetic studies and homology modeling of a dual-substrate linalool/nerolidol synthase from Plectranthus amboinicus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Nur Suhanawati Ashaari ◽  
Mohd Hairul Ab. Rahim ◽  
Suriana Sabri ◽  
Kok Song Lai ◽  
Adelene Ai-Lian Song ◽  
...  
Keyword(s):  
Active Site ◽  
Catalytic Efficiency ◽  
Kinetic Studies ◽  
Homology Model ◽  
Biochemical Properties ◽  
Terpene Synthase ◽  
Monoterpene Synthase ◽  
Terminal Domain ◽  
Catalytic Active Site ◽  
Plectranthus Amboinicus

AbstractLinalool and nerolidol are terpene alcohols that occur naturally in many aromatic plants and are commonly used in food and cosmetic industries as flavors and fragrances. In plants, linalool and nerolidol are biosynthesized as a result of respective linalool synthase and nerolidol synthase, or a single linalool/nerolidol synthase. In our previous work, we have isolated a linalool/nerolidol synthase (designated as PamTps1) from a local herbal plant, Plectranthus amboinicus, and successfully demonstrated the production of linalool and nerolidol in an Escherichia coli system. In this work, the biochemical properties of PamTps1 were analyzed, and its 3D homology model with the docking positions of its substrates, geranyl pyrophosphate (C10) and farnesyl pyrophosphate (C15) in the active site were constructed. PamTps1 exhibited the highest enzymatic activity at an optimal pH and temperature of 6.5 and 30 °C, respectively, and in the presence of 20 mM magnesium as a cofactor. The Michaelis–Menten constant (Km) and catalytic efficiency (kcat/Km) values of 16.72 ± 1.32 µM and 9.57 × 10–3 µM−1 s−1, respectively, showed that PamTps1 had a higher binding affinity and specificity for GPP instead of FPP as expected for a monoterpene synthase. The PamTps1 exhibits feature of a class I terpene synthase fold that made up of α-helices architecture with N-terminal domain and catalytic C-terminal domain. Nine aromatic residues (W268, Y272, Y299, F371, Y378, Y379, F447, Y517 and Y523) outlined the hydrophobic walls of the active site cavity, whilst residues from the RRx8W motif, RxR motif, H-α1 and J-K loops formed the active site lid that shielded the highly reactive carbocationic intermediates from the solvents. The dual substrates use by PamTps1 was hypothesized to be possible due to the architecture and residues lining the catalytic site that can accommodate larger substrate (FPP) as demonstrated by the protein modelling and docking analysis. This model serves as a first glimpse into the structural insights of the PamTps1 catalytic active site as a multi-substrate linalool/nerolidol synthase.

Effect of Modifiers on the Hydrolysis of Basic and Neutral Peptides by Carboxypeptidase B

1975 ◽  
Vol 53 (7) ◽  
pp. 747-757 ◽  
Author(s):  
Graham J. Moore ◽  
N. Leo Benoiton
Keyword(s):  
Active Site ◽  
Active Sites ◽  
Kinetic Behavior ◽  
Carboxypeptidase A ◽  
Phenyllactic Acid ◽  
Carboxypeptidase B ◽  
Substrate Complex ◽  
Enzyme Substrate ◽  
Basic Peptides ◽  
Hydrolysis Of

The initial rates of hydrolysis of Bz-Gly-Lys and Bz-Gly-Phe by carboxypeptidase B (CPB) are increased in the presence of the modifiers β-phenylpropionic acid, cyclohexanol, Bz-Gly, and Bz-Gly-Gly. The hydrolysis of the tripeptide Bz-Gly-Gly-Phe is also activated by Bz-Gly and Bz-Gly-Gly, but none of these modifiers activate the hydrolysis of Bz-Gly-Gly-Lys, Z-Leu-Ala-Phe, or Bz-Gly-phenyllactic acid by CPB. All modifiers except cyclohexanol display inhibitory modes of binding when present in high concentration.Examination of Lineweaver–Burk plots in the presence of fixed concentrations of Bz-Gly has shown that activation of the hydrolysis of neutral and basic peptides by CPB, as reflected in the values of the extrapolated parameters, Km(app) and keat, occurs by different mechanisms. For Bz-Gly-Gly-Phe, activation occurs because the enzyme–modifier complex has a higher affinity than the free enzyme for the substrate, whereas activation of the hydrolysis of Bz-Gly-Lys derives from an increase in the rate of breakdown of the enzyme–substrate complex to give products.Cyclohexanol differs from Bz-Gly and Bz-Gly-Gly in that it displays no inhibitory mode of binding with any of the substrates examined, activates only the hydrolysis of dipeptides by CPB, and has a greater effect on the hydrolysis of the basic dipeptide than on the neutral dipeptide. Moreover, when Bz-Gly-Lys is the substrate, cyclohexanol activates its hydrolysis by CPB by increasing both the enzyme–substrate binding affinity and the rate of the catalytic step, an effect different from that observed when Bz-Gly is the modifier.The anomalous kinetic behavior of CPB is remarkably similar to that of carboxypeptidase A, and is a good indication that both enzymes have very similar structures in and around their respective active sites. A binding site for activator molecules down the cleft of the active site is proposed for CPB to explain the observed kinetic behavior.

The crystal structure of human mitochondrial 3-ketoacyl-CoA thiolase (T1): insight into the reaction mechanism of its thiolase and thioesterase activities

2014 ◽  
Vol 70 (12) ◽  
pp. 3212-3225 ◽  
Author(s):  
Tiila-Riikka Kiema ◽  
Rajesh K. Harijan ◽  
Malgorzata Strozyk ◽  
Toshiyuki Fukao ◽  
Stefan E. H. Alexson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Reaction Mechanism ◽  
Active Site ◽  
Quaternary Structure ◽  
Fatty Acyl ◽  
Physiological Importance ◽  
Loop Domain ◽  
Solution Studies ◽  
Hydrolysis Of ◽  
Insight Into

Crystal structures of human mitochondrial 3-ketoacyl-CoA thiolase (hT1) in the apo form and in complex with CoA have been determined at 2.0 Å resolution. The structures confirm the tetrameric quaternary structure of this degradative thiolase. The active site is surprisingly similar to the active site of theZoogloea ramigerabiosynthetic tetrameric thiolase (PDB entries 1dm3 and 1m1o) and different from the active site of the peroxisomal dimeric degradative thiolase (PDB entries 1afw and 2iik). A cavity analysis suggests a mode of binding for the fatty-acyl tail in a tunnel lined by the Nβ2–Nα2 loop of the adjacent subunit and the Lα1 helix of the loop domain. Soaking of the apo hT1 crystals with octanoyl-CoA resulted in a crystal structure in complex with CoA owing to the intrinsic acyl-CoA thioesterase activity of hT1. Solution studies confirm that hT1 has low acyl-CoA thioesterase activity for fatty acyl-CoA substrates. The fastest rate is observed for the hydrolysis of butyryl-CoA. It is also shown that T1 has significant biosynthetic thiolase activity, which is predicted to be of physiological importance.

Sign in / Sign up

Export Citation Format

Share Document