Creating Space for Large Acceptors: Rational Biocatalyst Design for Resveratrol Glycosylation in an Aqueous System

Polyphenols display a number of interesting properties but their low solubility limits practical applications. In that respect, glycosylation offers a solution for which sucrose phosphorylase has been proposed as a cost‐effective biocatalyst. However, its activity on alternative acceptor substrates is too low for synthetic purposes and typically requires the addition of organic (co‐)solvents. Here, we describe the engineering of the enzyme from Thermoanaerobacterium thermosaccharolyticum to enable glycosylation of resveratrol as test case. Based on docking and modeling studies, an active‐site loop was predicted to hinder binding. Indeed, the unbolted loop variant R134A showed useful affinity for resveratrol (K_m=185 mM ) and could be used for the quantitative production of resveratrol 3‐α‐glucoside in an aqueous system. Improved activity was also shown for other acceptors, introducing variant R134A as promising new biocatalyst for glycosylation reactions on bulky phenolic acceptors.     

Design of new secreted phospholipase A<Subscript>2</Subscript> inhibitors based on docking calculations by modifying the pharmacophore segments of the FPL67047XX inhibitor

Docking calculations that allow the estimation of the binding energy of small ligands in the GIIA sPLA₂ active site were used in a structure-based design protocol. Four GIIA sPLA₂ inhibitors co-crystallised with the enzyme, were used for examining the enzyme active site and for testing the FlexX in SYBYL 6.8 molecular docking program to reproduce the crystallographic experimental data. The FPL67047XX inhibitor was chosen as a prototype structure for applying free energy perturbation (FEP) studies. Structural modifications of the initial structure of the FPL67047XX inhibitor (IC₅₀ 0.013 μM) were performed in an effort to optimise the interactions in the GIIA sPLA₂ active site. The structural modifications were based on: (1) the exploration of absolute configuration (i.e. comparison of the binding score of (R)- and (S)-enantiomers); (2) bioisosterism (i.e. replacement of the carboxylate group with the bioisosteric sulphonate and phosphonate groups); (3) insertion of substituents that fit better in the active site. The generated new structures exhibited higher binding energy. Such structures may spark off the interest of medicinal chemists for synthesizing potentially more active GIIA sPLA₂ inhibitors.     

Structures of the crystalline supramolecular associates of imidazole with 1,1′-binaphthyl-8,8′-dicarboxylic acid and 2,2′-dihydroxy-1,1′-binaphthyl. Spatial similarity of the acid associate crystal packing to the active site of a serine protease

Abstract

Crystal structure analysis of the imidazole associates with 1,1′-binaphthyl-8,8′-dicarboxylic acid (1), [1a, triclinic, P1, a = 7.569(4), b = 8.393(2), c = 8.634(1) Å, α = 93.21(2), β = 106.88(3), γ = 105.17(3)°, D_c = 1.36 g/cm³, Z = 1, R = 0.045 for 1031 data] and with 2,2′-dihydroxy-1,1′-binaphthyl (2), [2a, tetragonal P4₁2₁2, a = 8.519(1), c = 29.821(2), D_c = 1.30 g/cm³, Z = 4, R = 0.051 for 1236 reflections] revealed 1:1 and 1:2 stoichiometry, respectively. Spontaneous resolution occur during crystallization in both compound crystals. 1a is a salt-like associate with hydrogen bonds between the carboxylate and imidazolium ion pairs while the neutral 2a has also well defined hydrogen bonds between host and guest molecules. In a modeling experiment corresponding Brookhaven Protein Data Bank atomic coordinates from the active site of the bacterial serine protease enzyme Subtilisin BPN were fitted to the crystal packing of the small molecule associate 1a crystal. The relative displacement of the ion pair components and a symmetry related carboxyl function in 1a has fair steric resemblance to similar moieties in the active site of Subtilisin (Δ_ave = 0.24 Å for 9 fitted atoms). The agreement in the results of two fully independent and totally different (i.e. a native protein active site and an artificial small molecule associate) crystal structure determinations underlines the assumed conceptual similarity of crystals (“giant supramolecules”) to protein sequences optimized through evolution.     

铜离子配位甲烷氧化菌素功能化纳米金模拟过氧化物酶的研究

合成了纳米金-甲烷氧化菌素(Mb)-铜配合物,该配合物可以作为模拟过氧化物酶用于催化过氧化氢氧化对苯二酚的反应.通过紫外光谱、荧光光谱、红外光谱对纳米金-甲烷氧化菌素(Mb)-铜进行了表征.利用紫外-可见分光光度法研究了配合物催化过氧化氢氧化对苯二酚的动力学.考察了体系p H、体系温度及过氧化氢/催化剂摩尔比对催化反应速率的影响.结果表明纳米金-甲烷氧化菌素(Mb)-铜配合物符合生物催化剂条件影响的一般规律,但比生物酶具有更高的热稳定性.     

Chemical physics: The standing of a mature discipline

Background

The use of immobilized enzymes for catalyzing various biotransformations is now a widely used approach. In recent years, cross-linked enzyme aggregates (CLEAs) have emerged as a novel and versatile biocatalyst design. The present work deals with the preparation of a CLEA from a commercial preparation, Pectinex? Ultra SP-L, which contains pectinase, xylanase and cellulase activities. The CLEA obtained could be used for any of the enzyme activities. The CLEA was characterized in terms of kinetic parameters, thermal stability and reusability in the context of all the three enzyme activities.

Results

Complete precipitation of the three enzyme activities was obtained with n-propanol. When resulting precipitates were subjected to cross-linking with 5 mM glutaraldehyde, the three activities initially present (pectinase, xylanase and cellulase) were completely retained after cross-linking. The V_max/K_m values were increased from 11, 75 and 16 to 14, 80 and 19 in case of pectinase, xylanase and cellulase activities respectively. The thermal stability was studied at 50°C, 60°C and 70°C for pectinase, xylanase and cellulase respectively. Half-lives were improved from 17, 22 and 32 minutes to 180, 82 and 91 minutes for pectinase, xylanase and cellulase respectively. All three of the enzymes in CLEA could be reused three times without any loss of activity.

Conclusion

A single multipurpose biocatalyst has been designed which can be used for carrying out three different and independent reactions; 1) hydrolysis of pectin, 2) hydrolysis of xylan and 3) hydrolysis of cellulose. The preparation is more stable at higher temperatures as compared to the free enzymes.     

Characterization of a putative sensory [FeFe]-hydrogenase provides new insight into the role of the active site architecture

[FeFe]-hydrogenases are known for their high rates of hydrogen turnover, and are intensively studied in the context of biotechnological applications. Evolution has generated a plethora of different subclasses with widely different characteristics. The M2e subclass is phylogenetically distinct from previously characterized members of this enzyme family and its biological role is unknown. It features significant differences in domain- and active site architecture, and is most closely related to the putative sensory [FeFe]-hydrogenases. Here we report the first comprehensive biochemical and spectroscopical characterization of an M2e enzyme, derived from Thermoanaerobacter mathranii. As compared to other [FeFe]-hydrogenases characterized to-date, this enzyme displays an increased H₂ affinity, higher activation enthalpies for H⁺/H₂ interconversion, and unusual reactivity towards known hydrogenase inhibitors. These properties are related to differences in active site architecture between the M2e [FeFe]-hydrogenase and “prototypical” [FeFe]-hydrogenases. Thus, this study provides new insight into the role of this subclass in hydrogen metabolism and the influence of the active site pocket on the chemistry of the H-cluster.

Characterization of a group D putative sensory [FeFe]-hydrogenase reveals how the active site can be tuned to decrease CO inhibition and increase stability of a reduced H-cluster while retaining the ability to catalyze H⁺/H₂ interconversion.     

Selective Activation of C−H Bonds in a Cascade Process Combining Photochemistry and Biocatalysis

Selective oxyfunctionalizations of inert C−H bonds can be achieved under mild conditions by using peroxygenases. This approach, however, suffers from the poor robustness of these enzymes in the presence of hydrogen peroxide as the stoichiometric oxidant. Herein, we demonstrate that inorganic photocatalysts such as gold–titanium dioxide efficiently provide H₂O₂ through the methanol‐driven reductive activation of ambient oxygen in amounts that ensure that the enzyme remains highly active and stable. Using this approach, the stereoselective hydroxylation of ethylbenzene to (R )‐1‐phenylethanol was achieved with high enantioselectivity (>98 % ee ) and excellent turnover numbers for the biocatalyst (>71 000).     

Protoglobin-Catalyzed Formation of cis-Trifluoromethyl-Substituted Cyclopropanes by Carbene Transfer

Trifluoromethyl-substituted cyclopropanes (CF₃-CPAs) constitute an important class of compounds for drug discovery. While several methods have been developed for synthesis of trans-CF₃-CPAs, stereoselective production of corresponding cis-diastereomers remains a formidable challenge. We report a biocatalyst for diastereo- and enantio-selective synthesis of cis-CF₃-CPAs with activity on a variety of alkenes. We found that an engineered protoglobin from Aeropyrnum pernix (ApePgb) can catalyze this unusual reaction at preparative scale with low-to-excellent yield (6–55 %) and enantioselectivity (17–99 % ee), depending on the substrate. Computational studies revealed that the steric environment in the active site of the protoglobin forced iron-carbenoid and substrates to adopt a pro-cis near-attack conformation. This work demonstrates the capability of enzyme catalysts to tackle challenging chemistry problems and provides a powerful means to expand the structural diversity of CF₃-CPAs for drug discovery.     

溶胶凝胶法合成Li3V6O16及其电化学性能研究

本文以双氧水为配位剂,以CH3COOLi·2H2O和V2O5为原料,采用溶胶凝胶法合成了一种新型的晶体Li3V6O16。随后分别采用X射线衍射(XRD)、扫描电子显微镜(SEM)、透射电子显微镜(TEM)和电子衍射(SAED)、X光电子能谱(XPS)和充放电测试等手段对材料进行了表征。SEM观察表明,产物主要是表面比较光滑的纳米片状晶体,TEM和SAED研究都证实了XRD和SEM的研究结果。充放电测试结果表明,该物质具有较高的比容量、良好的可逆性和循环稳定性。     

CmlI is an N-oxygenase in the biosynthesis of chloramphenicol

The N-oxygenation of an amine group is one of the steps in the biosynthesis of the antibiotic chloramphenicol. The non-heme di-iron enzyme CmlI was identified as the enzyme catalyzing this reaction through bioinformatics studies and reconstitution of enzymatic activity. In vitro reconstitution was achieved using phenazine methosulfate and NADH as electron mediators, while in vivo activity was demonstrated in Escherichia coli using two substrates. Kinetic analysis showed a biphasic behavior of the enzyme. Oxidized hydroxylamine and nitroso compounds in the reaction were detected both in vitro and in vivo based on LC–MS. The active site metal was confirmed to be iron based on a ferrozine assay. These findings provide new insights into the biosynthesis of chloramphenicol and could lead to further development of CmlI as a useful biocatalyst.     

A 2-Tyr-1-carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase

N,N-dimethyl formamide (DMF) is an extensively used organic solvent but is also a potent pollutant. Certain bacterial species from genera such as Paracoccus, Pseudomonas, and Alcaligenes have evolved to use DMF as a sole carbon and nitrogen source for growth via degradation by a dimethylformamidase (DMFase). We show that DMFase from Paracoccus sp. strain DMF is a halophilic and thermostable enzyme comprising a multimeric complex of the α₂β₂ or (α₂β₂)₂ type. One of the three domains of the large subunit and the small subunit are hitherto undescribed protein folds of unknown evolutionary origin. The active site consists of a mononuclear iron coordinated by two Tyr side-chain phenolates and one carboxylate from Glu. The Fe³⁺ ion in the active site catalyzes the hydrolytic cleavage of the amide bond in DMF. Kinetic characterization reveals that the enzyme shows cooperativity between subunits, and mutagenesis and structural data provide clues to the catalytic mechanism.     

Application to Photocatalytic H2 Production of a Whole‐Cell Reaction by Recombinant Escherichia coli Cells Expressing [FeFe]‐Hydrogenase and Maturases Genes

A photocatalytic H₂ production system using an inorganic–bio hybrid photocatalyst could contribute to the efficient utilization of solar energy, but would require the development of a new approach for preparing a H₂‐forming biocatalyst. In the present study, we constructed a recombinant strain of Escherichia coli expressing the genes encoding the [FeFe]‐hydrogenase and relevant maturases from Clostridium acetobutylicum NBRC 13948 for use as a biocatalyst. We investigated the direct application of a whole‐cell of the recombinant E. coli. The combination of TiO₂, methylviologen, and the recombinant E. coli formed H₂ under light irradiation, demonstrating that whole cells of the recombinant E. coli could be employed for photocatalytic H₂ production without any time‐consuming and costly manipulations (for example, enzyme purification). This is the first report of the direct application of a whole‐cell reaction of recombinant E. coli to photocatalytic H₂ production.     

Influence of inorganic fullerene‐like WS2 nanoparticles on the thermal behavior of isotactic polypropylene

A new family of thermoplastic nanocomposites based on isotactic polypropylene (iPP) and inorganic fullerene‐like tungsten disulfide (IF‐WS₂) has been successfully prepared. A very efficient dispersion of IF‐WS₂ material was obtained by mixing in the melted polymer without using modifiers or surfactants. The addition of IF‐WS₂ nanoparticles induces a remarkable enhancement of the thermal stability of iPP, as well as an increase in the crystallization rate of the matrix when compared with pure iPP. The nucleating efficiency of IF‐WS₂ solid lubricant nanoparticles on the α‐phase of iPP reaches very high values (60–70%), the highest values observed hitherto for polypropylene nanocomposites. The incorporation of IF‐WS₂ has also been observed to increase the size and stability of the crystals formed. The melting behavior of the nanocomposites indicates the formation of more perfect crystals as determined by differential scanning calorimetry and time‐resolved synchrotron X‐ray scattering experiments. The new nanocomposites show an increase in the storage modulus with respect to pure iPP measured by dynamic mechanical analysis. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2309–2321, 2007     

Enantioselective Aminohydroxylation of Styrenyl Olefins Catalyzed by an Engineered Hemoprotein

Chiral 1,2‐amino alcohols are widely represented in biologically active compounds from neurotransmitters to antivirals. While many synthetic methods have been developed for accessing amino alcohols, the direct aminohydroxylation of alkenes to unprotected, enantioenriched amino alcohols remains a challenge. Using directed evolution, we have engineered a hemoprotein biocatalyst based on a thermostable cytochrome c that directly transforms alkenes to amino alcohols with high enantioselectivity (up to 2500 TTN and 90 % ee) under anaerobic conditions with O‐pivaloylhydroxylamine as an aminating reagent. The reaction is proposed to proceed via a reactive iron‐nitrogen species generated in the enzyme active site, enabling tuning of the catalyst's activity and selectivity by protein engineering.     

A 2‐Tyr‐1‐carboxylate Mononuclear Iron Center Forms the Active Site of a Paracoccus Dimethylformamidase

N,N‐dimethyl formamide (DMF) is an extensively used organic solvent but is also a potent pollutant. Certain bacterial species from genera such as Paracoccus, Pseudomonas, and Alcaligenes have evolved to use DMF as a sole carbon and nitrogen source for growth via degradation by a dimethylformamidase (DMFase). We show that DMFase from Paracoccus sp. strain DMF is a halophilic and thermostable enzyme comprising a multimeric complex of the α₂β₂ or (α₂β₂)₂ type. One of the three domains of the large subunit and the small subunit are hitherto undescribed protein folds of unknown evolutionary origin. The active site consists of a mononuclear iron coordinated by two Tyr side‐chain phenolates and one carboxylate from Glu. The Fe³⁺ ion in the active site catalyzes the hydrolytic cleavage of the amide bond in DMF. Kinetic characterization reveals that the enzyme shows cooperativity between subunits, and mutagenesis and structural data provide clues to the catalytic mechanism.     

Oxygen diffusion pathways in a cofactor-independent dioxygenase

Molecular oxygen plays an important role in a wide variety of enzymatic reactions. Through recent research efforts combining computational and experimental methods a new view of O₂ diffusion is emerging, where specific channels guide O₂ to the active site. The focus of this work is DpgC, a cofactor-independent oxygenase. Molecular dynamics simulations, together with mutagenesis experiments and xenon-binding data, reveal that O₂ reaches the active site of this enzyme using three main pathways and four different access points. These pathways connect a series of dynamic hydrophobic pockets, concentrating O₂ at a specific face of the enzyme substrate. Extensive molecular dynamics simulations provide information about which pathways are more frequently used. This data is consistent with the results of kinetic measurements on mutants and is difficult to obtain using computational cavity-location methods. Taken together, our results reveal that although DpgC is rare in its ability of activating O₂ in the absence of cofactors or metals, the way O₂ reaches the active site is similar to that reported for other O₂-using proteins: multiple access channels are available, and the architecture of the pathway network can provide regio- and stereoselectivity. Our results point to the existence of common themes in O₂ access that are conserved among very different types of proteins.     

Biomimetic versus enzymatic high-potential electrocatalytic reduction of hydrogen peroxide on a functionalized carbon nanotube electrode

We report the non-covalent functionalization of a multi-walled carbon nanotube (MWCNT) electrode with a biomimetic model of the horseradish peroxidase (HRP) active site. By modifying the MWCNT electrode surface with imidazole-modified polypyrrole, a new biomimetic complex of HRP was synthesized on the MWCNT sidewalls via the coordination of imidazole (Im) to the metal centre of iron protoporphyrin IX, affording (Im)(PP)Fe^III. Compared to the pi-stacking of non-coordinated (PP)Fe^III on a MWCNT electrode, the (Im)(PP)Fe^III-modified MWCNT electrode exhibits higher electrocatalytic activity with an I _max = 0.52 mA cm^–2 for the reduction of H₂O₂, accompanied by a high onset potential of 0.43 V vs. Ag/AgCl. The performances of these novel surface-confined HRP mimics were compared to those of a MWCNT electrode modified by HRP. Although the enzyme electrode displays a higher electrocatalytic activity towards H₂O₂ reduction, the (Im)(PP)Fe^III-modified MWCNT electrode exhibits a markedly higher operational stability, retaining 63% of its initial activity after one month.     

Selective Oxidations Using a Cytochrome P450 Enzyme Variant Driven with Surrogate Oxygen Donors and Light

Cytochrome P450 monooxygenase enzymes are versatile catalysts, which have been adapted for multiple applications in chemical synthesis. Mutation of a highly conserved active site threonine to a glutamate can convert these enzymes into peroxygenases that utilise hydrogen peroxide (H₂O₂). Here, we use the T252E-CYP199A4 variant to study peroxide-driven oxidation activity by using H₂O₂ and urea-hydrogen peroxide (UHP). We demonstrate that the T252E variant has a higher stability to H₂O₂ in the presence of substrate that can undergo carbon-hydrogen abstraction. This peroxygenase variant could efficiently catalyse O-demethylation and an enantioselective epoxidation reaction (94 % ee). Neither the monooxygenase nor peroxygenase pathways of the P450 demonstrated a significant kinetic isotope effect (KIE) for the oxidation of deuterated substrates. These new peroxygenase variants offer the possibility of simpler cytochrome P450 systems for selective oxidations. To demonstrate this, a light driven H₂O₂ generating system was used to support efficient product formation with this peroxygenase enzyme.     

A Miniature glucose/O2 biofuel cell with single-walled carbon nanotubes-modified carbon fiber microelectrodes as the substrate

This study demonstrates a new kind of miniature glucose/O₂ biofuel cells (BFCs) based on carbon fiber microelectrodes (CFMEs) modified with single-walled carbon nanotubes (SWNTs). SWNTs are used as a support both for stably confining the electrocatalyst (i.e., methylene green, MG) for the oxidation of NADH and the anodic biocatalyst (i.e., NAD⁺-dependent glucose dehydrogenase, GDH) for the oxidation of glucose and for efficiently facilitating direct electrochemistry of the cathodic biocatalyst (i.e., laccase) for the O₂ reduction. The prepared micro-sized GDH-based bioanode and laccase-based biocathode exhibit good bioelectrocatalytic activity toward the oxidation of glucose and the reduction of oxygen, respectively. In 0.10 M phosphate buffer containing 10 mM NAD⁺ and 45 mM glucose under ambient air, the power density of the assembled miniature compartment-less glucose/O₂ BFC reaches 58 μW cm⁻² at 0.40 V. The stability of the miniature glucose/O₂ BFC is also evaluated.