Enantioselectivity of epoxide hydrolase catalysed oxirane ring opening: a 3D QSAR study

A 3D QSAR analysis (quantitative structure activity relationships) of a set of 2,2-disubstituted epoxides, substrates for epoxide hydrolases originating from four different organisms, was conducted by CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis), with respect to the enantioselective ring opening to the corresponding vicinal diol. Structural variations of the substrates include alkyl chains of different lengths, unsaturated moieties ((E)- and (Z)-alkenyl, alkinyl, aryl) and electronegative groups (ether oxygens, halogen atoms) at different locations within the 2-substituent group. Generally, all four organisms, namely Rhodococcus ruber NCIMB 11216, Rhodococcus ruber DSM 43338, Rhodococcus ruber DSM 44540 and Rhodococcus ruber DSM 44539, preferentially react with the (S)-enantiomer of the epoxide. Enantioselectivities (enantiomeric ratio, lnE values) show a rather large variation, ranging from almost no (lnE<1) to nearly complete selectivity (lnE>5.3). In addition, the response of the epoxide hydrolases stemming from the four organisms towards structural modifications of the substrate is different. Models for the enantioselectivity (enantiomeric ratio, ln E values) obtained by CoMFA and CoMSIA are of different but reasonable predictive power, e.g., q² _CV=0.701 and r²=0.937 for the CoMFA model of Rhodococcus ruber DSM 43338. Enantiomeric ratios for the test molecules can be well predicted. Plots of steric and electrostatic CoMFA (CoMSIA) fields allow conclusions to be drawn for the choice of the most suitable organism for a specific type of substrate.     

Syntheses,Characterization and Equilibrium between Mono—and Aqua—bridged Dicobalt（Ⅱ）Complexes.A Structural Model for Methionine Aminopeptidase

A monomeric complex [Co(Im)₂(O₂CMe)2] (1) and a novel aquabridged dimeric complex [Co₂(μ‐H₂O)(μ‐CMe)₂(Im)₄‐(O₂CMe)₂] (2) (Im = imidazole) have been synthesized and characterized. Complexes 1 and 2 coexisted in solution. Pure forms of either complex can be obtained from the same solution by controlling the crystallization conditions. All two complexes possess a carboxylate‐Im‐cobalt(II) triad system analogous to the carboxylate‐histidine‐metal triad systems that have been found in many zinc enzymes and cobalt(II)‐substituted enzymes. In 2, two Co²⁺ ions are connected by a water molecule in a bridging fashion with Co°Co [0.3687(1) nm], Co—OH₂ [0.2159(3) nm], and Co‐OH₂‐Co [117.2(3)°], in which the water molecule is further stabilized by two intramolecular hydrogen bonds with the oxygens of the terminal monodentate acetate groups with the distance of O…0 [0.2609(7) nm]. The terminal monodentate acetate groups display quite abnormal geometry due to the strong “pulling effect” on the carboxylates by intermolecular and intramolecular hydrogen bonds. Complex 2 showed weak antiferromagnetic coupling at low temperature with g = 2.22 and J = ?1.60 cm^?1.     

Chemo-enzymatic enantio-convergent asymmetric synthesis of (R)-(+)-Marmin

Asymmetric biohydrolysis of trisubstituted terpenoid oxiranes (rac-1a-rac-3a) was accomplished by employing the epoxide hydrolase activity Rhodococcus and Streptomyces spp. Depending on the biocatalyst, the biohydrolysis proceeded in an enantio-convergent fashion and gave the corresponding vic-diols in up to 97% ee at conversions beyond the 50%-threshold. In order to avoid a depletion of the ee of product by further oxidative metabolism, bioconversions had to be conducted in an inert atmosphere with exclusion of molecular oxygen. The synthetic applicability of this method was demonstrated by the asymmetric total synthesis of the monoterpenoid coumarin (R)-(+)-Marmin in 95% ee.     

Furcatin 水解酶的三维结构模建和与furcatin 的对接研究

利用同源模建和动力学模拟方法，模建了furcatin水解酶（FH）的三维结构．并在这基础上，分析了活性位点的组成和结构．研究了furcatin与FH的对接．结果表明，Ser84，Arg146，Thr189，Thr234和Gly372在复合物的形成过程中起重要的作用．其中，Ser84，Argl46和Thr189是在FH的活性口袋的二糖部分的亚单位一1中重要的氨基酸，Thr234和Gly372是亚单位-2中重要的氨基酸．     

诺卡氏菌催化环氧琥珀酸水解反应的影响因素

诺卡氏菌经超声波破碎后，环氧琥珀酸水解酶活性比完整细胞提高40倍以上，表明细胞通透性对酶的表现活性影响很大。用顺式环氧琥珀酸二钠溶液处理诺卡氏菌细胞，可使细胞的通透性提高，表观环氧琥珀酸水解酶活增大，转化反应时间缩短。底物不存在时，诺卡氏菌细胞的环氧琥珀酸水解酶在37℃不稳定，游离细胞的表观酶活半衰期为19min，破碎细胞酶活仅10．4min，表明内源蛋白酶是造成破碎细胞环氧琥珀酸水解酶不稳定的重要原因。完整诺卡氏菌细胞于37℃放置后再将细胞破碎，环氧琥珀酸水解酶的半衰期为144min，表明37℃放置后细胞通透性受到较大影响。存在底物时完整诺卡氏菌细胞于37℃放置后表现酶活基本不变。     

环糊精水解酶底物运输通道的动态结构分析

【目的】环糊精水解酶是作用于特殊底物的水解酶,可以水解圆锥形结构的底物。分析这个酶的底物通道为水解特殊结构底物提供研究基础。【方法】利用分子动力学模拟环糊精水解酶存在的底物通道,比较环糊精水解酶BsCMD_1J0H和TspCMD_1SMA在底物运输通道上的差异。【结果】BsCMD_1J0H和TspCMD_1SMA都为糖基水解酶家族13的蛋白质,它们的碳骨架基本吻合,而在α?螺旋分布上,TspCMD_1SMA相比于BsCMD_1J0H来说,螺旋结构更趋向于在蛋白质中心聚集。BsCMD_1J0H有6条底物通道连通蛋白质表面和活性中心,TspCMD_1SMA有8条底物通道连通。BsCMD_1J0H的底物通道平均半径为1,TspCMD_1SMA的底物通道平均半径为1.2。【结论】本研究提供了BsCMD_1J0H和TspCMD_1SMA两个蛋白质在和底物接触中的相关底物通道信息。     

Structural modeling of glucanase–substrate complexes suggests a conserved tyrosine is involved in carbohydrate recognition in plant 1,3-1,4-β-<Emphasis Type="SmallCaps">d</Emphasis>-glucanases

Glycosyl hydrolase family 16 (GHF16) truncated Fibrobacter succinogenes (TFs) and GHF17 barley 1,3-1,4-β-d-glucanases (β-glucanases) possess different structural folds, β-jellyroll and (β/α)₈, although they both catalyze the specific hydrolysis of β-1,4 glycosidic bonds adjacent to β-1,3 linkages in mixed β-1,3 and β-1,4 β-d-glucans or lichenan. Differences in the active site region residues of TFs β-glucanase and barley β-glucanase create binding site topographies that require different substrate conformations. In contrast to barley β-glucanase, TFs β-glucanase possesses a unique and compact active site. The structural analysis results suggest that the tyrosine residue, which is conserved in all known 1,3-1,4-β-d-glucanases, is involved in the recognition of mixed β-1,3 and β-1,4 linked polysaccharide.     

Β-d-Xylosidase from Selenomonas ruminantium: Catalyzed Reactions with Natural and Artificial Substrates

Catalytically efficient β-d-xylosidase from Selenomonas ruminantium (SXA) exhibits pK _as 5 and 7 (assigned to catalytic base, D14, and catalytic acid, E186) for k _cat/K _m with substrates 1,4-β-d-xylobiose (X2) and 1,4-β-d-xylotriose (X3). Catalytically inactive, dianionic SXA (D14⁻E186⁻) has threefold lower affinity than catalytically active, monoanionic SXA (D14⁻E186^H) for X2 and X3, whereas D14⁻E186⁻ has twofold higher affinity than D14⁻E186^H for 4-nitrophenyl-β-d-xylopyranoside (4NPX), and D14⁻E186⁻ has no affinity for 4-nitrophenyl-α-l-arabinofuranoside. Anomeric isomers, α-d-xylose and β-d-xylose, have similar affinity for SXA. 4-Nitrophenol competitively inhibits SXA-catalyzed hydrolysis of 4NPX. SXA steady-state kinetic parameters account for complete progress curves of SXA-catalyzed hydrolysis reactions. The mention of firm names or trade products does not imply that they are endorsed or recommended by the U.S. Department of Agriculture over other firms or similar products not mentioned.     

Unraveling Synergism between Various GH Family Xylanases and Debranching Enzymes during Hetero-Xylan Degradation

Enzymes classified with the same Enzyme Commission (EC) that are allotted in different glycoside hydrolase (GH) families can display different mechanisms of action and substrate specificities. Therefore, the combination of different enzyme classes may not yield synergism during biomass hydrolysis, as the GH family allocation of the enzymes influences their behavior. As a result, it is important to understand which GH family combinations are compatible to gain knowledge on how to efficiently depolymerize biomass into fermentable sugars. We evaluated GH10 (Xyn10D and XT6) and GH11 (XynA and Xyn2A) β-xylanase performance alone and in combination with various GH family α-l-arabinofuranosidases (GH43 AXH-d and GH51 Abf51A) and α-d-glucuronidases (GH4 Agu4B and GH67 AguA) during xylan depolymerization. No synergistic enhancement in reducing sugar, xylose and glucuronic acid released from beechwood xylan was observed when xylanases were supplemented with either one of the glucuronidases, except between Xyn2A and AguA (1.1-fold reducing sugar increase). However, overall sugar release was significantly improved (≥1.1-fold reducing sugar increase) when xylanases were supplemented with either one of the arabinofuranosidases during wheat arabinoxylan degradation. Synergism appeared to result from the xylanases liberating xylo-oligomers, which are the preferred substrates of the terminal arabinofuranosyl-substituent debranching enzyme, Abf51A, allowing the exolytic β-xylosidase, SXA, to have access to the generated unbranched xylo-oligomers. Here, it was shown that arabinofuranosidases are key enzymes in the efficient saccharification of hetero-xylan into xylose. This study demonstrated that consideration of GH family affiliations of the carbohydrate-active enzymes (CAZymes) used to formulate synergistic enzyme cocktails is crucial for achieving efficient biomass saccharification.