Flexizymes: their evolutionary history and the origin of catalytic function

Transfer RNA (tRNA) is an essential component of the cell's translation apparatus. These RNA strands contain the anticodon for a given amino acid, and when "charged" with that amino acid are termed aminoacyl-tRNA. Aminoacylation, which occurs exclusively at one of the 3'-terminal hydroxyl groups of tRNA, is catalyzed by a family of enzymes called aminoacyl-tRNA synthetases (ARSs). In a primitive translation system, before the advent of sophisticated protein-based enzymes, this chemical event could conceivably have been catalyzed solely by RNA enzymes. Given the evolutionary implications, our group attempted in vitro selection of artificial ARS-like ribozymes, successfully uncovering a functional ribozyme (r24) from an RNA pool of random sequences attached to the 5'-leader region of tRNA. This ribozyme preferentially charges aromatic amino acids (such as phenylalanine) activated with cyanomethyl ester (CME) onto specific kinds of tRNA. During the course of our studies, we became interested in developing a versatile, rather than a specific, aminoacylation catalyst. Such a ribozyme could facilitate the preparation of intentionally misacylated tRNAs and thus serve a convenient tool for manipulating the genetic code. On the basis of biochemical studies of r24, we constructed a truncated version of r24 (r24mini) that was 57 nucleotides long. This r24mini was then further shortened to 45 nucleotides. This ribozyme could charge various tRNAs through very simple three-base-pair interactions between the ribozyme's 3'-end and the tRNA's 3'-end. We termed this ribozyme a "flexizyme" (Fx3 for this particular construct) owing to its flexibility in addressing tRNAs. To devise an even more flexible tool for tRNA acylation, we attempted to eliminate the amino acid specificity from Fx3. This attempt yielded an Fx3 variant, termed dFx, which accepts amino acid substrates having 3,5-dinitrobenzyl ester instead of CME as a leaving group. Similar selection attempts with the original phenylalanine-CME and a substrate activated by (2-aminoethyl)amidocarboxybenzyl thioester yielded the variants eFx and aFx (e and a denote enhanced and amino, respectively). In this Account, we describe the history and development of these flexizymes and their appropriate substrates, which provide a versatile and easy-to-use tRNA acylation system. Their use permits the synthesis of a wide array of acyl-tRNAs charged with artificial amino and hydroxy acids. In parallel to these efforts, we initiated a crystallization study of Fx3 covalently conjugated to a microhelix RNA, which is an analogue of tRNA. The X-ray crystal structure, solved as a co-complex with phenylalanine ethyl ester and U1A-binding protein, revealed the structural basis of this enzyme. Most importantly, many biochemical observations were consistent with the crystal structure. Along with the predicted three regular-helix regions, however, the flexizyme has a unique irregular helix that was unexpected. This irregular helix constitutes a recognition pocket for the aromatic ring of the amino acid side chain and precisely brings the carbonyl group to the 3'-hydroxyl group of the tRNA 3'-end. This study has clearly defined the molecular interactions between Fx3, tRNA, and the amino acid substrate, revealing the fundamental basis of this unique catalytic system.     

Acyl specificity in glyceride synthesis by lactating rat mammary gland

We have investigated the possibility that the nonrandom association of fatty acids in rat milk triglycerides results from specificity of the acyl transferases in the glycerolphosphate pathway. Subcellular fractionation of lactating rat mammary gland revealed that the microsomal fraction was the most active in acylation of 3-sn-[U-¹⁴C] glycerolphosphate with various acyl-CoA's. The major products were diacylglycerolphosphate and diglyceride; no monoacylglycerolphosphate was detected. Maximum rate of acylation occurred at or below the critical micelle concentration for each acyl-CoA, indicating that only the monomeric substrate molecules were acceptable by the enzyme system. The observed acyl specificity, 16∶0>18∶0≏14∶0>12∶0>10∶0>8∶0 is consistent with the concept that, in general, milk triglycerides are synthesized by insertion of a short or medium chain fatty acid into a long chain diglyceride.     

Additive manufacturing of architected catalytic ceramic substrates based on triply periodic minimal surfaces

The exhibited geometry of catalytic substrates can have a significant influence on the chemical activity and efficiency. Controlling their geometry can be challenging using the traditional techniques. In this work, we propose new and novel catalytic substrates with architected and controllable topologies based on the minimal surfaces framework. A novel design approach and an additive manufacturing (AM) technique were proposed to manufacture the catalytic substrates using ceramic materials. After 3D printing, their mechanical and flow properties were investigated experimentally. An elastic-plastic-damage coupled model was employed to investigate the underlying deformation mechanism of the investigated substrates. Results showed that the CLP substrate exhibited the highest mechanical properties as well as the least pressure drop among the tested substrates. Also, numerical simulations showed that the strut-based substrates exhibit stress localization which leads to faster failure, while stress is distributed more homogeneously in the sheet-based substrates. While the model showed to have a good agreement in the experimental and simulation stress-strain responses, the damage mechanism was not fully captured by the numerical simulations. This was attributed mainly to the process-induced defects in the form of microcracks and microvoids that can alter the nature of deformation and damage.     

Alteration of substrate specificity of rat neurolysin from matrix metalloproteinase-2/9-type to -3-type specificity by comprehensive mutation

The substrate specificity of rat brain neurolysin was rapidly modified by semirational mutagenesis coupled with a yeast molecular display system. Neurolysin mainly recognizes substrates with sequential six residues close to the scissile bond in polypeptides, cleaving a peptide bond in the center position of the six residues. To alter the recognition of the P2' amino acid of substrates by neurolysin, six residues of neurolysin, Asp467, Arg470, Glu510, Tyr606, Tyr610 and Tyr611, which might be involved in the formation of the neurolysin S2' subsite, were individually and comprehensively substituted. The protein libraries of mutant neurolysins comprising 120 species were displayed on the yeast cell surface and screening was carried out using two fluorescence-quenching peptides, the matrix metalloproteinase-2/9- (MMPs-2/9-) and MMP-3-specific substrates, which consisted of similar amino acids, except for alanine (for MMPs-2/9) or glutamic acid (for MMP-3) at the P2' amino acid position. Among mutant neurolysins, the Y610L mutant neurolysin exhibited a marked change in substrate specificity. Steady-state kinetic analysis of the purified Y610L mutant neurolysin revealed that the binding efficiency toward the MMP-3-specific substrate was about 3-fold higher than that toward the MMP-2/9-specific substrate. These results indicate that Tyr610 of neurolysin is the important residue to recognize the P2' amino acid of substrates.     

Engineered Bacterial Flavin-Dependent Monooxygenases for the Regiospecific Hydroxylation of Polycyclic Phenols

4-Hydroxyphenylacetate 3-hydroxylase (4HPA3H), a flavin-dependent monooxygenase from E. coli that catalyzes the hydroxylation of monophenols to catechols, was modified by rational redesign to convert also more bulky substrates, especially phenolic natural products like phenylpropanoids, flavones or coumarins. Selected amino acid positions in the binding pocket of 4HPA3H were exchanged with residues from the homologous protein from Pseudomonas aeruginosa, yielding variants with improved conversion of spacious substrates such as the flavonoid naringenin or the alkaloid mimetic 2-hydroxycarbazole. Reactions were followed by an adapted Fe(III)-catechol chromogenic assay selective for the products. Especially substitution of the residue Y301 facilitated modulation of substrate specificity: introduction of nonaromatic but hydrophobic (iso)leucine resulted in the preference of the substrate ferulic acid (having a guaiacyl (guajacyl) moiety, part of the vanilloid motif) over unsubstituted monophenols. The in vivo (whole-cell biocatalysts) and in vitro (three-enzyme cascade) transformations of substrates by 4HPA3H and its optimized variants was strictly regiospecific and proceeded without generation of byproducts.     

2种脂肪酸甲酯烯烃交叉复分解制备长链终端烯烃化学品的对比研究

为实现烯烃交叉复分解直接应用于植物油甲酯中获取长链终端烯烃化合物,本研究分别以油酸甲酯(MO)和亚油酸甲酯(ML)为原料,通过烯烃交叉复分解反应制备长链终端烯烃化合物1-癸烯(CM1)、1-庚烯(CM2)和9-癸烯酸甲酯(CM3)。对4种典型的Grubbs催化剂,10种短链液体烯烃底物以及不同的反应条件(反应温度、时间、催化剂用量和脂肪酸甲酯与烯烃底物物质的量之比)的影响规律进行对比分析,结果表明:4种催化剂中第二代Hoveyda-Grubbs催化剂(C3)适合于MO,第二代Grubbs催化剂(C2)适合ML,10种短链液体烯烃底物中丁香酚较有利于目标产物的生成。在反应温度0℃、反应时间20~60 min、催化剂用量0.5%~1%以及n(脂肪酸甲酯)∶n(丁香酚)为1∶10~1∶20范围内,两种原料均可获得较佳的结果,MO与ML的转化率最高均可达99%,CM1、CM2和CM3产率最高分别为80%、92%和73%。     

The role of Glu87 and Trp89 in the lid of Humicola lanuginosa lipase

The importance of Glu87 and Trp89 in the lid of Humicola lanuginosalipase for the hydrolytic activity at the water/lipid interfacewas investigated by site-directed mutagenesis. It was foundthat the effect on the hydrolytic activity upon the replacementof Trp89 with Phe, Leu, Gly or Glu was substrate dependent TheTrp89 mutants displayed an altered chain length specificitytowards triglycerides, with a higher relative activity towardstriacetin and trioctanoin compared with tributyrin. Trp89 wasshown to be lessimportant in the hydrolysis of vinyl esterscompared with ethylesters and triglycerides. An exclusive effecton the acylation reaction rate by the mutation of Trp89 wasconsistent with the data. It is suggested that Trp89 is importantin the process of binding the acyl chain of thesubstrate intothe activesite for optimal acylation reaction rate. The Trp89Phemutation resulted in an increased hydrolytic activity towards2-alkylalkanoic acid esters. This is suggested to be due toreduction of unfavourable van der Waals contacts between Trp89and the 2-substituent of the substrate. Thus, in contrast tonatural substrates, Trp89 has a negative impact on the catalyticefficiencywhen substrates with bulky acyl chains are used. Incontrast to the Trp89 mutations, the effect on the hydrolyticactivity of the Glu87Ala mutation was almost substrate independent,35–70% activity of wild-type lipase. Areduction of boththe acylation and deacylation reaction was consistent with thedata.     

HPLC measurement of testicular long chain acyl-CoA synthetases with different substrate specificities

Acyl-CoA synthetase activity with various long chain fatty acid substrates was measured in microsomes from rat testes, isolated spermatids and testes of hypophysectomized adult rats, using reversed-phase high performance liquid chromatography (HPLC). The spectrophotometric HPLC method produced results comparable to those of parallel radiometric assays and was highly specific for acyl-CoA products. At optimal pH and cofactor concentrations, specific activity from whole testis was similar for 18∶1, 20∶4 and 22∶5 but somewhat lower for 16∶0 over the substrate range 0.01–3.2 mM. Activity from spermatids or from testes of hypophysectomized rats was much lower with 22∶5 than with 18∶1 or 20∶4, whereas activities with 18∶1 and 20∶4 were similar at all substrate concentrations. All substrates exhibited Michaelis-Menten type saturation kinetics and linear Lineweaver-Burke plots at lower substrate concentrations but inhibited activity at higher concentrations. Apparent values of K_M for 16∶0, 18∶1 and 20∶4 were more than twice that of 22∶5, whereas both observed and calculated maximum velocities were similar for the four fatty acids. Differences in pseudokinetic parameters and differential expression of the testicular acyl-CoA synthetase activities with different fatty acids suggest the presence of multiple enzymes, at least one of which may be hormonally regulated.     

The Proto-Ribosome: An Ancient Nano-machine for Peptide Bond Formation

The ribosome is a ribozyme whose active site, the peptidyl transferase center (PTC), is situated within a highly conserved universal symmetrical region that connects all ribosomal functional centers involved in amino acid polymerization. The linkage between this elaborate architecture and A-site tRNA position revealed that the A- to P-site passage of the tRNA 3′ terminus during protein synthesis is performed by a rotary motion, synchronized with the overall tRNA/mRNA sideways movement, and guided by the PTC. This rotary motion leads to suitable stereochemistry for peptide bond formation as well as for substrate-mediated catalysis. Analysis of the substrate binding modes to ribosomes led to the hypothesis that the ancient ribosome produced single peptide bonds and non-coded chains, potentially in a similar manner to the modern PTC. Later in evolution, a mechanism, enabling some type of decoding genetic control triggered the emergence of the small ribosomal subunit or part of it. This seems to be the result of the appearance of reaction products that could have evolved after polypeptides capable of enzymatic function were generated sporadically, while an ancient stable RNA fold was converted into an old version of a tRNA molecule. Since in the contemporary ribosome, the symmetry relates only to the backbone fold and nucleotide orientations but not nucleotide sequences, it emphasizes the superiority of functional requirement over sequence conservation, and indicates that the PTC may have evolved by gene fusion or gene duplication.     

稠环缩氨基脲衍生物的合成与杀虫活性研究

以4-氯苯乙酸为原料,经环化、氧化、缩合、加氢、酰化反应合成了6个新的具有茚结构的稠环缩氨基脲衍生物,总收率7%～9%。其结构经核磁共振氢谱和高分辨质谱确认正确。初步生物活性测试表明:大多数化合物对多种害虫具有很好的杀虫活性。7-氯-2,3,4a,5-四氢-2-[N-甲氧羰基-N-(4-三氟甲基苯基)氨基甲酰基]茚戊[1,2-e][1,3,4]口恶二嗪-4a-甲酸甲酯(Ⅻb)的活性略高于已商品化杀虫剂茚虫威。     

改性二氧化硅负载离子液体催化合成2-(4-乙基苯甲酰基)苯甲酸

对负载离子液体催化乙苯与邻苯二甲酸酐酰化反应合成2-(4-乙基苯甲酰基)苯甲酸(BE酸)进行了研究。以AlCl₃溶液和混合酸为改性剂，对二氧化硅载体进行改性，采用浸渍法制备系列负载离子液体，采用FT-IR、BET、SEM和XRD对催化剂进行表征，考察载体改性剂、负载温度和负载量对催化剂性能的影响，并对反应条件进行了优化。结果表明，负载型离子液体在催化合成BE酸的反应中有较高的活性，但目标产物BE酸的选择性较低。经过混合酸对载体改性后，邻苯二甲酸酐的转化率和BE酸的选择性达到100％和91.1％，催化剂综合性能明显提高。催化剂再生后，BE酸的选择性为88.92%。     

Effect of substrate polarity on the activity of soybean lipoxygenase isoenzymes

In order to characterize the several isoenzymes of soybeans, they were examined with respect to the effect of the polar nature of the substrate. In general, lipoxygenase-1 was most active when presented with charged substrates such as the anionic form of linoleic acid or of potassium linoleyl sulfate, whereas lipoxygenase-2 and-3 preferred nonpolar substrates such as unionized linoleic acid, methyl linoleate, linoleyl methane sulfonate, 10,13-nonadecadieneamine, or linoleyl acetate. Linoleyl sulfate, which has been advanced as an excellent readily soluble substrate for lipoxygenase, was indeed the best substrate found for lipoxygenase-1. Lipoxygenase-2 and-3 were, by contrast, totally inactive against this substrate. The favorable response of linnoleic acid to lipoxygenase-2 and-3 at pH 6.8 was ascribed to the anomalously high pK_a value of linoleic acid compared to that of short chain carboxylic acids. The pH-activity profile obtained with lipoxygenase acting on linoleyl sulfate (which was charged at all pH values examined) was shifted to lower pH values compared to the linoleic acid activity profile. The effect of changing from the charged to the uncharged substrate, when tested against lipoxygenase-1, was to increase the K_m by an order of magnitude.     

Comparative Studies of Chlorine Dioxide Reactions with Muconic Acid Derivatives and Lignin Model Compounds

Abstract

The reaction of chlorine dioxide with different types of lignin model compounds was investigated in order to compare the kinetics and to evaluate the amount of oxidant consumed by the different substrates. Complete reaction of lignin model compounds was observed at ClO₂‐to‐substrate molar ratios of 0.9–1.2, which corresponds to an electron transfer varying between 5–6 equivalents per mole of substrate. Muconic acid derivatives also fully reacted, at a ClO₂‐to‐substrate molar ratio of 1.2, with the oxidant consumption being about 4 equivalents per mole of substrate. The reaction of mixtures of phenolic, non‐phenolic, and muconic acid type substrates showed that the reaction rates of non‐phenolic and muconic acid type substrates were rather similar. This study suggests that further reaction between ClO₂ and the primary lignin oxidation products, such as muconic acid type structures could be the cause of overconsumption of oxidant in a D stage.     

One for Many: A Universal Reagent for Acylation Processes

This work describes acylation reactions facilitated by a type of heterocycle‐based acyl transfer agent, 2‐acyloxypyridazinone. Reactions of 2‐acyloxypyridazinone with carboxylic acids yield mixed carbonic anhydride intermediates, which are reactive and could be coupled with a wide range of substrates including acids, amines, alcohols, and thiols. The wide substrate scope, ease of operation (no additive or catalyst), storage and handling stability, and atom‐efficiency from recycling the heterocycle carrier make the reported acylating agent attractive for acylation‐based coupling reactions.

     

污泥厌氧发酵产酸机理及应用研究进展

为了实现污水中污泥减量化和资源化,对其进行厌氧消化是目前国际上应用最广泛的处理方法。酸化阶段的重要产物——挥发性脂肪酸（VFAs）不仅可以作为污水脱氮除磷的碳源,还是合成生物质塑料聚羟基脂肪酸酯（PHAs）的理想底物。简单介绍了污泥厌氧发酵产酸的代谢机理和微生物机理,对近年来污泥厌氧发酵产酸的研究成果进行了梳理,重点论述了底物种类、预处理技术、pH值、发酵温度等因素对污泥厌氧发酵产酸的影响及研究进展,总结并对比了不同底物类型、发酵温度、酸性和碱性条件下都可影响发酵产酸的产量及酸种类分布,而污泥预处理技术则倾向于提高酸的产量,对酸种类分布影响不大。介绍了污泥厌氧发酵产酸在合成PHAs、生物能源和污水的脱氮除磷等方面的应用情况。最后,针对污泥厌氧发酵产酸会因底物有机成分不同,导致酸化效率有所差异,同时控制底物种类、pH值和温度等因素不仅影响产酸量,还会影响产酸类型和产物种类。提出了今后的研究方向主要是深入分析不同底物的酸化效率差异原因、污泥定向发酵产酸,实现总VFAs中各种酸比例调控。     

N-(3-甲酰吡啶)-脯氨酸甲酯的合成及其卷烟加香应用研究

以3-吡啶甲酸为起始原料,经酰氯化反应制成3-吡啶甲酰氯。另以脯氨酸为原料,经酰氯化后再与甲醇反应生成相应的氨基酸甲酯盐酸盐。在室温下,以三乙胺为缚酸剂,3-吡啶甲酰氯与氨基酸甲酯经过酰化反应生成目标产物N-(3-甲酰吡啶)-脯氨酸甲酯化合物。并将其应用于卷烟加香中,以改善卷烟制品品质。化合物结构通过1HNMR、13CNMR、IR和HRMS技术进行了表征。并对产物进行热重分析以及热裂解行为研究,分析鉴定出了40多种裂解产物,其多数为致香物质。对目标物进行卷烟加香评吸,结果表明,该物质能改善卷烟吸味,减轻卷烟吸食刺激性,增强香气。     

Triacylglycerol assembly from binary mixtures of fatty acids byApiotrichum curvatum

To observe how the stereospecific distribution of acyl groups in triglycerides is affected by the composition of fatty acids available for esterification, the oleaginous yeastApiotrichum curvatum was grown on various binary mixture of palmitic, stearic, oleic and linoleic acids as carbon sources, and the yeast triglycerides were analyzed. When oleic acid-linoleic acid mixtures in various ratios were used as substrates, the yeast grew well, and the composition of the intracellular triglycerides reflected the substrate composition, but more linoleate than oleate was deposited in the triglycerides. Oleate was favored over linoleate at thesn-2 position of the glycerol. With substrates containing palmitic and stearic acids, the yeast accumulated less oil, and incorporation of stearic acid into the triglycerides also was very limited. When mixtures of palmitic acid-oleic acid and palmitic acid-linoleic acid were used as substrates, the yeast triglyceride composition did not reflect that of the substrate, and the accumulation in the yeast of the unsaturated acid in the substrate was favored. Possibly, the yeast had more limited access to solid than to liquid substrates. For oleic acid-linoleic acid substrates, when the percentages of oleate and linoleate at the three glycerol positions were plottedvs. the percentage of these acyl groups in the total triglyceride, apparent linear relations were observed for most of the range, and the sums of the intercepts and slopes of the three lines for each acyl group were 0 and 3, respectively. Two mathematical models of triglyceride assembly are proposed, both of which fit the experimental data. One model assumes that for a certain proportion of the glycerol molecules, the acyl composition of the threesn positions is rigidly controlled independently of the substrate concentration. The other assumes that the various acyl groups are distributed on the threesn positions of glycerol with different affinities.     

Lewis acid induced additions to unsaturated fatty compounds IV: Synthesis of cyclopentenones from Friedel- Crafts acylation products of unsaturated fatty compounds with α,β-unsaturated acyl chlorides

The ethylaluminium dichloride induced Friedel- Crafts acylation of unsaturated fatty compounds such as oleic acid ( 1a ), methyl oleate ( 1b ) and 10-undecenoic acid ( 9b ) and furthermore of 1-octene ( 9a ) with α,β-unsaturated acyl chlorides e.g. crotonic acid chloride ( 2a ) and acrylic acid chloride ( 2b ) gave the corresponding allyl vinyl ketones. Nazarov cyclizations of the acylation products 3a/4a, 3b/4b, 10a and 10b afforded the alkyl substituted 2-cyclopentenones 5a/6a, 5b/6b, 11a/12a and 11b/12b . Catalytic hydrogenation of 5b/6b and 11b/12b gave the respective saturated cyclic products 7b/8b and 13b/14b as diastereomeric mixtures.