Determining optimum conditions for lipase-catalyzed synthesis of triethanolamine (TEA)-based esterquat cationic surfactant by a Taguchi robust design method

A Taguchi robust design method with an L? orthogonal array was implemented to optimize experimental conditions for the biosynthesis of triethanolamine (TEA)-based esterquat cationic surfactants using an enzymatic reaction method. The esterification reaction conversion% was considered as the response. Enzyme amount, reaction time, reaction temperature and molar ratio of substrates, [oleic acid: triethanolamine (OA:TEA)] were chosen as main parameters. As a result of the Taguchi analysis in this study, the molar ratio of substrates was found to be the most influential parameter on the esterification reaction conversion%. The amount of enzyme in the reaction had also a significant effect on reaction conversion%.     

Selectivity, directionality, and promiscuity in peptide processing from a Bacillus sp. Al Hakam cyclodehydratase

The thiazole/oxazole-modified microcins (TOMMs) represent a burgeoning class of ribosomal natural products decorated with thiazoles and (methyl)oxazoles originating from cysteines, serines, and threonines. The ribosomal nature of TOMMs allows for the generation of derivative products from mutations in the amino acid sequence of the precursor peptide, which ultimately manifest in differing structures and, sometimes, biological functions. Employing a TOMM system for the purpose of creating new structures and functions via combinatorial biosynthesis requires processing machinery that can tolerate highly variable substrates. In this study, TOMM enzymatic promiscuity was assessed using a currently uncharacterized cluster in Bacillus sp. Al Hakam. As determined by Fourier transform tandem mass spectrometry (FT-MS/MS), azole rings were formed in both a regio- and chemoselective fashion. Cognate and noncognate precursor peptides were modified in an overall C- to N-terminal directionality, which to date is unique among characterized ribosomal natural products. Studies focused on the inherent promiscuity of the biosynthetic machinery elucidated a modest bias for glycine at the preceding (-1) position and a remarkable flexibility in the following (+1) position, even allowing for the incorporation of charged amino acids and bisheterocyclization. Two unnatural substrates were utilized as the conclusive test of substrate flexibility, of which both were processed in a predictable fashion. A greater understanding of substrate processing and enzymatic tolerance toward unnatural substrates will prove beneficial when designing combinatorial libraries to screen for artificial TOMMs that exhibit desired activities.     

Synthesis of uridine 5'-diphosphoiduronic acid: a potential substrate for the chemoenzymatic synthesis of heparin

An improved understanding of the biological activities of heparin requires structurally defined heparin oligosaccharides. The chemoenzymatic synthesis of heparin oligosaccharides relies on glycosyltransferases that use UDP-sugar nucleotides as donors. Uridine 5'-diphosphoiduronic acid (UDP-IdoA) and uridine 5'-diphosphohexenuronic acid (UDP-HexUA) have been synthesized as potential analogues of uridine 5'-diphosphoglucuronic acid (UDP-GlcA) for enzymatic incorporation into heparin oligosaccharides. Non-natural UDP-IdoA and UDP-HexUA were tested as substrates for various glucuronosyltransferases to better understand enzyme specificity.     

Selection of new chromogenic substrates of serine proteinases using combinatorial chemistry methods

Chemical synthesis, physicochemical characterization and kinetic investigations of a tetrapeptide library of chromogenic substrates containing the amide of 5-amino-2-nitrobenzoic acid (Anb(5,2)-NH(2)) at their C-termini are reported. Anb(5,2)-NH(2) served as a chromophore released upon enzymatic action. The library consisting of 9567 peptides was synthesized using the portioning-mixing method and was screened against bovine a-chymotrypsin and human leukocyte elastase in solution applying an iterative approach. The selected chromogenic substrates were resynthesized and further modified at their N- and C-termini. Finally, two sequences, Z-Phe-Ala-Thr-Tyr-Anb(5,2)-NH(2) and Z-Phe-Phe-Pro-Val-Anb(5,2)-NH(2), were obtained as highly specific substrates for bovine alpha-chymotrypsin and human leukocyte elastase, respectively. The method of synthesis and selection of chromogenic substrates of serine proteinases described herein is straightforward and can be applied to design substrates for other proteases.     

生物合成咖啡酸苯乙酯体系的液相色谱-串联质谱快速分析

建立液相色谱-串联质谱(LC-MS/MS)检测生物合成咖啡酸苯乙酯体系中咖啡酸(Caffeic acid,CA)和咖啡酸苯乙酯(Caffeic acid phenethylester,CAPE)的方法。采用LC-MS/MS电喷雾电离(ESI),负离子选择反应监测(SRM)模式检测。以V(乙腈)∶V(水)∶V(冰醋酸)=55∶45∶0.5为流动相,流速1.0mL/min,Hypersil C18色谱柱分离并检测生物合成咖啡酸苯乙酯体系中的咖啡酸以及咖啡酸苯乙酯的含量,并对生物合成咖啡酸苯乙酯的收率进行了动力学分析。本方法在进样量为0.2～20μg时具有良好的线性关系,咖啡酸和咖啡酸苯乙酯样品的加标回收率分别为93.4%～98.2%和90.3%～97.8%,相对标准偏差分别为1.79%～2.56%和1.82%～3.67%,咖啡酸苯乙酯收率在3d内可以达到15.54%,表明本方法简便、快速、可靠。     

Stereospecificity of an enzymatic monoene 1,4-dehydrogenation reaction: conversion of (Z)-11-tetradecenoic acid into (E,E)-10,12-tetradecadienoic acid

In this article, we report the first stereochemical study of an enzymatic 1,4-dehydrogenation reaction, namely, the transformation of (Z)-11-tetradecenoic acid into (E,E)-10,12-tetradecadienoic acid, involved in the sex pheromone biosynthesis of the moth Spodoptera littoralis. The investigation was carried out using the labeled substrates (R)-[10-(2)H]- and (S)-[10-(2)H]-tridecanoic acids ((R)-2 and (S)-2, respectively) and (R)-[2,2,3,3,13-(2)H(5)]- and (S)-[2,2,3,3,13-(2)H(5)]-tetradecanoic acids ((R)-1 and (S)-1, respectively). Probes (R)-2 and (S)-2 were prepared as described in a previous article.(1) The synthesis of the pentadeuterated chiral substrates (R)-1 and (S)-1 was accomplished by kinetic resolution of the racemic 12-tridecyn-2-ol (6) with immobilized porcine pancreatic lipase. The enantiomerically pure alcohols (R)-6 and (S)-6 were transformed into the final acids (S)-1 and (R)-1, respectively, by a sequence of well-established reactions. The analyses of methanolyzed lipidic extracts from glands incubated separatedly with each individual probe showed that in the transformation of (Z)-11-tetradecenoic acid into (E,E)-10,12-tetradecadienoic acid, both pro-(R) hydrogen atoms at C-10 and C-13 are removed from the substrate. This is the first example reported of a desaturase with pro-(R)/pro-(R) stereospecificities that gives rise to (E)-double bonds. A mechanistic explanation for the stereochemical outcome of this reaction is advanced.     

Discovery and characterization of a group of fungal polycyclic polyketide prenyltransferases

The prenyltransferase (PTase) gene vrtC was proposed to be involved in viridicatumtoxin (1) biosynthesis in Penicillium aethiopicum. Targeted gene deletion and reconstitution of recombinant VrtC activity in vitro established that VrtC is a geranyl transferase that catalyzes a regiospecific Friedel-Crafts alkylation of the naphthacenedione carboxamide intermediate 2 at carbon 6 with geranyl diphosphate. VrtC can function in the absence of divalent ions and can utilize similar naphthacenedione substrates, such as the acetyl-primed TAN-1612 (4). Genome mining using the VrtC protein sequence leads to the identification of a homologous group of PTase genes in the genomes of human and animal-associated fungi. Three enzymes encoded by this new subgroup of PTase genes from Neosartorya fischeri, Microsporum canis, and Trichophyton tonsurans were shown to be able to catalyze transfer of dimethylallyl to several tetracyclic naphthacenedione substrates in vitro. In total, seven C(5)- or C(10)-prenylated naphthacenedione compounds were generated. The regioselectivity of these new polycyclic PTases (pcPTases) was confirmed by characterization of product 9 obtained from biotransformation of 4 in Escherichia coli expressing the N. fischeri pcPTase gene. The discovery of this new subgroup of PTases extends our enzymatic tools for modifying polycyclic compounds and enables genome mining of new prenylated polyketides.     

Concurrent Prebiotic Formation of Nucleoside-Amidophosphates and Nucleoside-Triphosphates Potentiates Transition from Abiotic to Biotic Polymerization

Polymerization of nucleic acids in biology utilizes 5′-nucleoside triphosphates (NTPs) as substrates. The prebiotic availability of NTPs has been unresolved and other derivatives of nucleoside-monophosphates (NMPs) have been studied. However, this latter approach necessitates a change in chemistries when transitioning to biology. Herein we show that diamidophosphate (DAP), in a one-pot amidophosphorylation-hydrolysis setting converts NMPs into the corresponding NTPs via 5′-nucleoside amidophosphates (NaPs). The resulting crude mixture of NTPs are accepted by proteinaceous- and ribozyme-polymerases as substrates for nucleic acid polymerization. This phosphorylation also operates at the level of oligonucleotides enabling ribozyme-mediated ligation. This one-pot protocol for simultaneous generation of NaPs and NTPs suggests that the transition from prebiotic-phosphorylation and oligomerization to an enzymatic processive-polymerization can be more continuous than previously anticipated.     

Characterization of the azinomycin B biosynthetic gene cluster revealing a different iterative type I polyketide synthase for naphthoate biosynthesis

Azinomycin B is a complex natural product containing densely assembled functionalities with potent antitumor activity. Cloning and sequence analysis of the azi gene cluster revealed an iterative type I polyketide synthase (PKS) gene, five nonribosomal peptide synthetases (NRPSs) genes and numerous genes encoding the biosynthesis of unusual building blocks and tailoring steps for azinomycin B production. Characterization of AziB as a 5-methyl-naphthoic acid (NPA) synthase showed a distinct selective reduction pattern in aromatic polyketide biosynthesis governed by bacterial iterative type I PKSs. Heterologous expression established the PKS-post modification route from 5-methyl-NPA to reach the first building block 3-methoxy-5-methyl-NPA. This proposed azinomycin B biosynthetic pathway sets the stage to investigate the enzymatic mechanisms for building structurally unique and pharmaceutically important groups, including the unprecedented azabicyclic ring system and highly active epoxide moiety.     

Trypsin-catalyzed synthesis of dipeptide containing alpha-aminoisobutyric acid using p- and m-(amidinomethyl)phenyl esters as acyl donor

Two series of inverse substrates, p- and m-(amidinomethyl)phenyl esters derived from N-(tert-butyloxycarbonyl)amino acid, were prepared as acyl donor components for enzymatic peptide synthesis. They were found to be readily coupled with an acyl acceptor such as L-alanine p-nitroanilide to produce dipeptide. An alpha-aminoisobutyric acid containing dipeptide was especially obtained in satisfactory yield. Streptomyces griseus trypsin was a more efficient catalyst than the bovine trypsin. The optimum condition for the coupling reaction was studied by changing the organic solvent, pH, and acyl acceptor concentration. It was found that the enzymatic hydrolysis of the resulting product was negligible.     

Structure-Function Analysis of the S-Glycosylation Reaction in the Biosynthesis of Lincosamide Antibiotics

The S-glycosyltransferase LmbT, involved in the biosynthesis of lincomycin A, is the only known enzyme that catalyzes the enzymatic incorporation of rare amino acid L-ergothioneine (EGT) into secondary metabolites. Here, we show the structure and function analyses of LmbT. Our in vitro analysis of LmbT revealed that the enzyme shows promiscuous substrate specificity toward nitrogenous base moieties in the generation of unnatural nucleotide diphosphate (NDP)-D-α-D-lincosamides. Furthermore, the X-ray crystal structures of LmbT in its apo form and in complex with substrates indicated that the large conformational changes of the active site occur upon binding of the substrates, and that EGT is strictly recognized by salt-bridge and cation-π interactions with Arg260 and Trp101, respectively. The structure of LmbT in complex with its substrates, the docking model with the EGT-S-conjugated lincosamide, and the structure-based site-directed mutagenesis analysis revealed the structural details of the LmbT-catalyzed S_N2-like S-glycosylation reaction with EGT.     

Enzymatic Cascade Reactions in Biosynthesis

Enzyme‐mediated cascade reactions are widespread in biosynthesis. To facilitate comparison with the mechanistic categorizations of cascade reactions by synthetic chemists and delineate the common underlying chemistry, we discuss four types of enzymatic cascade reactions: those involving nucleophilic, electrophilic, pericyclic, and radical reactions. Two subtypes of enzymes that generate radical cascades exist at opposite ends of the oxygen abundance spectrum. Iron‐based enzymes use O₂ to generate high valent iron‐oxo species to homolyze unactivated C?H bonds in substrates to initiate skeletal rearrangements. At anaerobic end, enzymes reversibly cleave S‐adenosylmethionine (SAM) to generate the 5′‐deoxyadenosyl radical as a powerful oxidant to initiate C?H bond homolysis in bound substrates. The latter enzymes are termed radical SAM enzymes. We categorize the former as “thwarted oxygenases”.     

Deciphering the mode of action of the processive polysaccharide modifying enzyme dermatan sulfate epimerase 1 by hydrogen–deuterium exchange mass spectrometry

Distinct from template-directed biosynthesis of nucleic acids and proteins, the enzymatic synthesis of heterogeneous polysaccharides is a complex process that is difficult to study using common analytical tools. Therefore, the mode of action and processivity of those enzymes are largely unknown. Dermatan sulfate epimerase 1 (DS-epi1) is the predominant enzyme during the formation of iduronic acid residues in the glycosaminoglycan dermatan sulfate. Using recombinant DS-epi1 as a model enzyme, we describe a tandem mass spectrometry-based method to study the mode of action of polysaccharide processing enzymes. The enzyme action on the substrate was monitored by hydrogen–deuterium exchange mass spectrometry and the sequence information was then fed into mathematical models with two different assumptions of the mode of action for the enzyme: processive reducing end to non-reducing end, and processive non-reducing end to reducing end. Model data was scored by correlation to experimental data and it was found that DS-epi1 attacks its substrate on a random position, followed by a processive mode of modification towards the non-reducing end and that the substrate affinity of the enzyme is negatively affected by each additional epimerization event. It could also be shown that the smallest active substrate was the reducing end uronic acid in a tetrasaccharide and that octasaccharides and longer oligosaccharides were optimal substrates. The method of using tandem mass spectrometry to generate sequence information of the complex enzymatic products in combination with in silico modeling can be potentially applied to study the mode of action of other enzymes involved in polysaccharide biosynthesis.     

Development of off-line and on-line capillary electrophoresis methods for the screening and characterization of adenosine kinase inhibitors and substrates

Fast and convenient CE assays were developed for the screening of adenosine kinase (AK) inhibitors and substrates. In the first method, the enzymatic reaction was performed in a test tube and the samples were subsequently injected into the capillary by pressure and detected by their UV absorbance at 260 nm. An MEKC method using borate buffer (pH 9.5) containing 100 mM SDS (method A) was suitable for separating alternative substrates (nucleosides). For the CE determination of AMP formed as a product of the AK reaction, a phosphate buffer (pH 7.5 or 8.5) was used and a constant current (95 microA) was applied (method B). The methods employing a fused-silica capillary and normal polarity mode provided good resolution of substrates and products of the enzymatic reaction and a short analysis time of less than 10 min. To further optimize and miniaturize the AK assays, the enzymatic reaction was performed directly in the capillary, prior to separation and quantitation of the product employing electrophoretically mediated microanalysis (EMMA, method C). After hydrodynamic injection of a plug of reaction buffer (20 mM Tris-HCl, 0.2 mM MgCl2, pH 7.4), followed by a plug containing the enzyme, and subsequent injection of a plug of reaction buffer containing 1 mM ATP, 100 microM adenosine, and 20 microM UMP as an internal standard (I.S.), as well as various concentrations of an inhibitor, the reaction was initiated by the application of 5 kV separation voltage (negative polarity) for 0.20 min to let the plugs interpenetrate. The voltage was turned off for 5 min (zero-potential amplification) and again turned on at a constant current of -60 microA to elute the products within 7 min. The method employing a polyacrylamide-coated capillary of 20 cm effective length and reverse polarity mode provided good resolution of substrates and products. Dose-response curves and calculated K(i) values for standard antagonists obtained by CE were in excellent agreement with data obtained by the standard radioactive assay.     

Bifunctional coumarin derivatives in solution and solid phase synthesis of fluorogenic enzyme substrates

The use of the fluorescent bifunctional compounds 7‐amino‐4‐coumarinyl‐acetic acid 1 , 7‐hydroxy‐4‐coumarinyl‐acetic acid 2 and ethyl 7‐amino‐4‐coumarinyl‐acetate 3 in solution and solid phase synthesis of fluorogenic enzyme substrates was examined. The intramolecularly quenched fluorogenic substrate N‐(7‐amino‐4‐coumarinyl‐acetyl)‐L‐phenylalanyl‐p‐nitroanilide 5 , and the fluorogenic one ethyl 7‐(glutaryl‐L‐phenylalanilamido)‐4‐coumarinyl‐acetate 8 , both suitable for chymotrypsin and/or chymotrypsin like enzymes determination, were prepared in solution. The substrates 7‐oleyloxy‐4‐coumarinyl‐acetic acid 13 and 7‐palmitoyloxy‐4‐coumarinyl‐acetic acid 14 , suitable for the enzymatic study of lipases, were prepared by solid phase technique using 2‐chloro‐chlorotrityl‐resin. The study of the fluorescence properties of the fluorophores 1, 2, 3 , and substrates 5, 8,13,14 showed that the examined bifunctional coumarin derivatives are suitable markers for solution and solid phase synthesis of fluorogenic enzyme substrates.     

An Engineered Aryl Acid Adenylation Domain with an Enlarged Substrate Binding Pocket

Adenylation (A) domains act as the gatekeepers of non‐ribosomal peptide synthetases (NRPSs), ensuring the activation and thioesterification of the correct amino acid/aryl acid building blocks. Aryl acid building blocks are most commonly observed in iron‐chelating siderophores, but are not limited to them. Very little is known about the reprogramming of aryl acid A‐domains. We show that a single asparagine‐to‐glycine mutation in an aryl acid A‐domain leads to an enzyme that tolerates a wide range of non‐native aryl acids. The engineered catalyst is capable of activating non‐native aryl acids functionalized with nitro, cyano, bromo, and iodo groups, even though no enzymatic activity of wild‐type enzyme was observed toward these substrates. Co‐crystal structures with non‐hydrolysable aryl‐AMP analogues revealed the origins of this expansion of substrate promiscuity, highlighting an enlargement of the substrate binding pocket of the enzyme. Our findings may be exploited to produce diversified aryl acid containing natural products and serve as a template for further directed evolution in combinatorial biosynthesis.     

Effect of Pretreatment Severity on Accumulation of Major Degradation Products from Dilute Acid Pretreated Corn Stover and Subsequent Inhibition of Enzymatic Hydrolysis of Cellulose

The concept of reaction severity, which combines residence time and temperature, is often used in the pulp and paper and biorefining industries. The influence of corn stover pretreatment severity on yield of sugar and major degradation products and subsequent effects on enzymatic cellulose hydrolysis was investigated. The pretreatment residence time and temperature, combined into the severity factor (Log R _o), were varied with constant acid concentration. With increasing severity, increasing concentrations of furfural and 5-hydroxymethylfurfural (5-HMF) coincided with decreasing yields of oligosaccharides. With further increase in severity factor, the concentrations of furans decreased, while the formation of formic acid and lactic acid increased. For example, from severity 3.87 to 4.32, xylose decreased from 6.39 to 5.26?mg/mL, while furfural increased from 1.04 to 1.33?mg/mL; as the severity was further increased to 4.42, furfural diminished to 1.23?mg/mL as formate rose from 0.62 to 1.83?mg/mL. The effects of dilute acid hydrolyzate, acetic acid, and lignin, in particular, on enzymatic hydrolysis were investigated with a rapid microassay method. The microplate method gave considerable time and cost savings compared to the traditional assay protocol, and it is applicable to a broad range of lignocellulosic substrates.     

Enzymatic desaturation of fatty acids: delta11 desaturase activity on cyclopropane acid probes

The formation of methylenecyclopropanes by enzymatic desaturation of 11-cyclopropylundecanoic acid (1) and its disubstituted derivatives cis- and trans-3-5 has been investigated using the Delta(11) desaturase of Spodoptera littoralis as model enzyme. Gas chromatography coupled to mass spectrometry analyses of methanolyzed lipidic extracts from tissues incubated with each probe revealed that all the cyclopropyl fatty acids were transformed into the corresponding 11-cyclopropylidene acids, except for compound trans-5 (5b), which was not desaturated at C11. The formation of methylenecyclopropane 9 as the only reaction product from 1 indicates that a potential radical intermediate is too short-lived to allow rearrangement reactions. Information on the Delta(11) desaturase substrate binding domain is provided considering the cyclopropyl probes 3-5 as conformationally restricted analogues of the straight-chain substrates.     

Norcholanic acids as substrates for recombinant 3β-hydroxysteroid dehydrogenase and progesterone 5β-reductase, enzymes of the 5β-cardenolide biosynthesis

The conversion of 23-nor-5,20(22)E-choladienic acid-3β-ol and other intermediates of the putative norcholanic acid pathway of cardenolide biosynthesis by recombinant 3β-hydroxysteroid dehydrogenase from Digitalis lanata in dehydrogenation and reduction reactions was investigated. 23-nor-4,20(22)E-choladienic acid-3-one was found to be a substrate of recombinant progesterone 5β-reductases from D. lanata and Arabidopsis thaliana. The role of various substrates in cardenolide biosynthesis is discussed.     

Deficiency of Cellulase Activity Measurements for Enzyme Evaluation

Switchgrass was used as a model feedstock to determine the influence of pretreatment conditions and biomass quality on enzymatic hydrolysis using different enzyme products. Dilute sulfuric acid and soaking in aqueous ammonia pretreatments were used to produce biomass with varied levels of hemicellulose and lignin sheathing. Pretreated switchgrass solids were tested with simple enzymatic hydrolysis and simultaneous saccharification and fermentation (SSF) with three commercial enzyme products: Accellerase 1000 (Genencor), Spezyme CP (Genencor)/Novozyme 188 (Novozymes), and Celluclast/Novozyme 188 (Novozymes). Enzymes were loaded on a common activity basis (FPU/g cellulose and CBU/g cellulose). Despite identical enzyme loadings, glucose yields were significantly different for both acid and alkaline pretreatments but differences diminished as hydrolysis progressed for acid-pretreated biomass. Cellobiose concentrations in Accellerase treatments indicated an initial β-glucosidase limitation that became less significant over time. SSF experiments showed that differences in glucose and ethanol yields could not be attributed to enzyme product inhibition. Yield discrepancies of glucose or ethanol in acid pretreatment, alkaline pretreatment, and acid pretreatment/SSF were as much as 15%, 19%, and 5%. These results indicate that standardized protocols for measuring enzyme activity may not be adequate for assessing activity using pretreated biomass substrates.