Bipyridyl- and biphenyl-DNA: a recognition motif based on interstrand aromatic stacking

The synthesis and incorporation into oligonucleotides of C-nucleosides containing the two aromatic, non-hydrogen-bonding nucleobase substitutes biphenyl (I) and bipyridyl (Y) are described. Their homo- and hetero-recognition properties in different sequential arrangements were then investigated via UV-melting curve analysis, gel mobility assays, CD- and NMR spectroscopy. An NMR analysis of a dodecamer duplex containing one biphenyl pair in the center, as well as CD data on duplexes with multiple insertions provide further evidence for the zipper-like interstrand stacking motif that we proposed earlier based on molecular modeling. UV-thermal melting experiments with duplexes containing one to up to seven I- or Y base pairs revealed a constant increase in T(m) in the case of I and a constant decrease for Y. Mixed I/Y base pairs lead to stabilities in between the homoseries. Insertion of alternating I/abasic site- or Y/abasic site pairs strongly decreases the thermal stability of duplexes. Asymmetric distribution of I- or Y residues on either strand of the duplex were also investigated in this context. Duplexes with three natural base pairs at both ends and 50 % of I pairs in the center are still readily formed, while duplexes with blunt ended I pairs tend to aggregate unspecifically. Duplexes with one natural overhang at the end of a I-I base pair tract can both aggregate or form ordered duplexes, depending on the nature of the natural bases in the overhang.     

Stereopositional Outcome in the Packing of Dissimilar Aromatics in Designed β‐Hairpins

A popular strategy in the de novo design of stable β‐sheet structures for various biomedical applications is the incorporation of aromatic pairs at the non‐hydrogen‐bonding (NHB) position. However, it is important to explicitly understand how aryl pair packing at the NHB region is coordinated with backbone structural rearrangements, and to delineate the benefits and drawbacks associated with stereopositional choice of dissimilar aromatic pairs. Here, we probe the consequences of flipped Trp/Tyr pairs by using engineered permutants at the NHB position of dodecapeptide β‐hairpins, proximal and distal to the turn. Extensive conformational analysis of these peptides using NMR and CD spectroscopy reveal that a classic Edge‐to‐Face and Face‐to‐Edge geometry at the proximal and distal aromatic pairs, respectively, in YW‐WY, is the most stabilizing. Such a preferred packing geometry in YW‐WY results in a highly twisted β‐sheet backbone, with Trp always providing a ‘Face’ orientation to its dissimilar aromatic partner Tyr. Flipping the proximal and/or distal aromatic pair distorts the ideal T‐shaped geometry, and results in alternate aryl arrangements that can adversely affect strand twist and β‐sheet stability. Our study reveals the existence of a strong stereopositional influence on the packing of dissimilar aromatic pairs. Our findings highlight the importance of modeling physical interaction forces while designing protein and peptide structures for functional applications.     

Array of aromatic amino acid side chains located near the chromophore of photoactive yellow protein

The role of the array of aromatic amino acid side chains located close to the chromophore binding loop of photoactive yellow protein (PYP) was studied using the alanine-substitution mutagenesis. Phe92, Tyr94, Phe96 and Tyr98 were replaced with alanine (F92A, Y94A, F96A and Y98A, respectively), then these mutants were characterized by UV-visible absorption spectra, circular dichroism (CD) spectra, thermal stability and photocycle kinetics. Absorption maxima of F92A, Y94A, F96A and Y98A were 444, 442, 439 and 447 nm, respectively, different to wild type (WT) at 446 nm. Far-UV CD spectra of mutants other than F92A were different from WT, indicating that Tyr94, Phe96 and Tyr98 maintain the native secondary structure of PYP. Mid-point temperatures of thermal denaturation of F92A, Y94A and F96A, estimated by the CD signal at 222 nm, were 5-10 degrees C lower than WT. Time constants of the photocycle estimated by flash-induced absorbance change were 0.36 s for WT and 1.4 s for Y98A, however, 100, 30 and 3000 times slower than WT for F92A, Y94A and F96A, respectively. Tyr98 is located in the loop region, whereas Phe92, Tyr94 and Phe96 are incorporated in the beta4 strand, showing that aromatic amino acid residues in the beta-sheet regulate the absorption spectrum, thermal stability and photocycle of PYP. Aromatic rings of Phe92, Tyr94 and Phe96 lie nearly perpendicular to the aromatic ring of Phe75 or chromophore. Possible weak hydrogen bonds between the aromatic ring hydrogen and pi-electrons of these residues are discussed.     

Catalytically enhanced endocellulase cel5a from Acidothermus cellulolyticus

When Tyr245 in endocellulase Cel5A from Acidothermus cellulolyticus was changed to Gly (Y245G) by designed mutation, the value of K _i for inhibition of the enzyme by the product cellobiose was increased more than 1480%. This reduction in product inhibition enabled the mutant enzyme (used in conjunction with Trichoderma reesei cellobiohydrolase-I) to release soluble sugars from biomass cellulose at a rate as much as 40% greater than that achieved by the wild-type (WT) enzyme. The mutant was designed on the basis of the previously published crystal structure of the WT enzyme/substrate complex (at a resolution of 2.4 Å), which provided insights into the enzyme mechanism at the atomic level and identified Tyr245 as a key residue interacting with a leaving group. To determine the origin of the change in activity, the crystal structure of Y245G was solved at 2.4-Å resolution to an R-factor of 0.19 (R-free=0.25). To obtain additional information on the enzyme-product interactions, density functional calculations were performed on representative fragments of the WT Cel5A and Y245G. The combined results indicate that the loss of the platform (Y245G) and of a hydrogen bond (from a conformational change in Gln247) reduces the binding energy between product and enzyme by several kilo calories per mole. Both kinetic and structural analyses thus relate the increased enzymatic activity to reduced product inhibition.     

Impact of a Water-Soluble Gallic Acid-Based Dendrimer on the Color-Stabilizing Mechanisms of Anthocyanins

The interaction of two anthocyanins with a water-soluble polyanionic dendrimer was studied through UV/Vis, stopped-flow, and NMR spectroscopy. Cyanidin-3-glucoside (cy3glc) revealed a stronger interaction than malvidin-3-glucoside (mv3glc) at pH 1 according to their apparent association constants. A higher color increased was also obtained for cy3glc at pH 3.5 as a result of this stronger interaction. A high-frequency chemical shift of the cy3glc aromatic protons suggest the formation of ionic pairs. The interaction parameters (K≈700 m ⁻¹, n≈295) indicated the binding of approximately two anthocyanin molecules by each sulfate group. The equilibrium and rate constants of cy3glc in the presence of dendrimer showed an increased stability of the flavylium cation and a higher protection of this species from hydration (pK′_a and pK_h increased almost one pH unit). The tuning and color stabilization of anthocyanins by using this dendrimer allow novel applications as colorimetric sensors for food packaging.     

Arylidene Polymers. XVII. Cyclization of Aromatic Poly[dibenzylidenecyclopentanone-Hydrazide] as a Route to Polyheterocyclic 1,3,4-Oxadiazole and 1,2,4-Triazole

A new interesting class of thermal stable arylidene polymers containing 1,3,4-oxadiazole and 1,2,4-triazole moieties in the main chain have been synthesized from aromatic polyhydrazide I. Cyclization of I at 250°C in the absence of solvent was found to be the best pathway for the inclusion of the 1,3,4-oxadiazole moiety in the main chain. Heating of I with aniline, cyclohexyl amine, or 3-amino pyridine at 180°C for 30 h gave the corresponding 1,2,4-triazole polymers III. The introducing effect of different aromatic, cycloalkyl, and heterocyclic amines in III_a-c and IV_a-c on thermal stability behavior was studied by TGA analysis. Moreover, all the polymers were characterized by elemental and spectral analyses, solubility, and viscometry measurements. X-ray diffractograms of the synthesized polymers showed they had less crystallinity than the polyhydrazide precursors.     

Improvement of Thermostability and Activity of Firefly Luciferase Through [TMG][Ac] Ionic Liquid Mediator

Firefly luciferase catalyzes production of light from luciferin in the presence of Mg²⁺?CATP and oxygen. This enzyme has wide range of applications in biotechnology and development of biosensors. The low thermal stability of wild-type firefly luciferase is a limiting factor in most applications. Improvements in activity and stability of few enzymes in the presence of ionic liquids were shown in many reports. In this study, kinetic and thermal stability of firefly luciferase from Photinus pyralis in the presence of three tetramethylguanidine-based ionic liquids was investigated. The enzyme has shown improved activity in the presence of [1, 1, 3, 3-tetramethylguanidine][acetate], but in the presence of [TMG][trichloroacetate] and [TMG][triflouroacetate] activity, it decreased or unchanged significantly. Among these ionic liquids, only [TMG][Ac] has increased the thermal stability of luciferase. Incubation of [TMG][Ac] with firefly luciferase brought about with decrease of K _m for ATP.     

Tyr72 and Tyr80 are Involved in the Formation of an Active Site of a Luciferase of Copepod Metridia longa

Luciferase of copepod Metridia longa (MLuc) is a naturally secreted enzyme catalyzing the oxidative decarboxylation of coelenterazine with the emission of light. To date, three nonallelic isoforms of different lengths (17–24 kDa) for M. longa luciferase have been cloned. All the isoforms are single‐chain proteins consisting of a 17‐residue signal peptide for secretion, variable N‐terminal part and conservative C‐terminus responsible for luciferase activity. In contrast to other bioluminescent proteins containing a lot of aromatic residues which are frequently involved in light emission reaction, the C‐terminal part of MLuc contains only four Phe, two Tyr, one Trp and two His residues. To figure out whether Tyr residues influence bioluminescence, we constructed the mutants with substitution of Tyr to Phe (Y72F and Y80F). Tyrosine substitutions do not eliminate the ability of luciferase to bioluminescence albeit significantly reduce relative specific activity and change bioluminescence kinetics. In addition, the Tyr replacements have no effect on bioluminescence spectrum, thereby indicating that tyrosines are not involved in the emitter formation. However, as it was found that the intrinsic fluorescence caused by Tyr residues is quenched by a reaction substrate, coelenterazine, in concentration‐dependent manner, we infer that both tyrosine residues are located in the luciferase substrate‐binding cavity.     

Improving the electrochemical performances of active carbon-based supercapacitors through the combination of introducing functional groups and using redox additive electrolyte

High-performance and low-cost electrochemical capacitors (ECs) are essential for large-scale applications in energy storage. In this work, the specific capacitance of active carbon (AC) electrode was significantly improved through the combination of introducing functional groups on the surface of AC and adding redox-active molecules (K₃Fe(CN)₆) into 2?M KOH aqueous electrolytes. The surface-oxygen functionalized AC (FAC) was synthesized using HNO₃ echoed as the electrode and 2?M KOH with 0.1?M K₃Fe(CN)₆ as the electrolyte. The surface functional groups of the AC not only contribute to the pseudocapacitance but also increase the active sites of the electrode/electrolyte interface, which enhances the electrochemical activity of the Fe(CN)₆^3?/Fe(CN)₆^4? redox pair, thus leading to high capacitance. In the redox electrolyte, the specific capacitance was much higher in 229.17?F?g^?1 (1?A?g^?1) achieved for those FAC than in raw AC (only 147.06?F?g^?1). Similarly, the FAC electrode suggested high energy density and extended cycling stability in the KOH?+?K₃Fe(CN)₆ electrolyte.     

Immobilization of a Recombinant Esterase from <Emphasis Type="Italic">Lactobacillus plantarum</Emphasis> on Polypropylene Accurel MP1000

A recombinant esterase from Lactobacillus plantarum was immobilized on hydrophobic support polypropylene Accurel MP1000 by adsorption. Adsorption efficiency was 83%, and the immobilized protein was 12.4 mg/g of support. Esterase activity was determined using p-nitrophenyl butyrate as substrate, and highest activities were observed at 50 °C for immobilized enzyme and 30 °C for free enzyme extract. Concerning thermal stability, after enzyme incubation at 80 °C for 30 min, immobilized and free enzyme retained 91% and 56% of initial activity, respectively. Immobilized enzyme presented lower V _max and higher K _m than free enzyme. Protein was not released from the support, and esterase activity increased after 3 cycles of reuse.     

Aggregation and solvation of 9-propylfluorenyllithium and of α,ω-BIS(9-fluorenyllithium)polymethylenes in toluene

Bolaform salts of the type Li⁺,Fl^?(CH₂)_n Fl^?,Li⁺ (Fl^? = 9-fluorenyl, n = 2,4 or 6), when dissolved in toluene, were shown to be present as intramolecular aggregates (λ_m 370 nm) which can be broken up on addition of tetrahydrofuran (THF) or tetrahydropyran (THP) to form solvated tight ion pairs (λ_m 361 nm) and loose ion pairs (λ_m 386 nm). For n = 6 the ratio K₁/K₂ of the loose ion pair formation constants for the two terminal ion pairs is close to the statistical factor 4, but for n = 2 the ratio is only 0.3. This is attributed to a higher stability of the intramolecular aggregate for this compound. The data for the bolaform salts were compared with those obtained for the one ended salt 9-(n-propyl)-fluorenyllithium. For the latter compound, an equilibrium between the monomeric ion pair (λ_m 353 nm) and the dimeric ion pair aggregate (λ_m 370 nm) was found, the dissociation constant K_d being 2.9 X 10^?6M. Addition of THP produces the THP solvated tight ion pair (λ_m 361 nm) and the loose ion pair (λ_m 386 nm).     

Y443F mutation in the substrate-binding domain of extracellular PHB depolymerase enhances its PHB adsorption and disruption abilities

Extracellular poly[(R)-3-hydroxybutyrate] (PHB) depolymerase (PhaZ_RpiT1) from Ralstonia pickettii T1 adsorbs to the PHB surface via its substrate-binding domain (SBD) and cleaves the PHB chain using its catalytic domain. Our previous study (Biomacromolecules 2010; 11: 113-119) has suggested that the hydrophobic interaction between the amino acid residues at positions 441, 443, and 445 in the SBD and the PHB surface plays a crucial role in facilitating the association phase of the enzyme adsorption process. In the present study, in order to improve PhaZ_RpiT1 for effective PHB degradation, we targeted Tyr at position 443 for substitution with a more highly hydrophobic amino acid residue because its hydrophobicity shows medium to high degree compared to those of general naturally occurring amino acid residues. We designed a mutant enzyme with an amino acid substitution at this position, taking the following factors into consideration: (1) to achieve higher hydrophobicity than the original residue, (2) to retain the β-sheet structure, and (3) to change as little as possible the volume of the amino acid residue after the substitution. As a result, the substitution of Tyr443 with Phe (Y443F) was considered to be appropriate. The purified Y443F enzyme showed identical CD spectrum and hydrolysis activity for a water-soluble substrate with the wild type, indicating that the mutation had no influence on the structure and the ester bond cleavage activity. In contrast, the Y443F enzyme had higher PHB degradation activity than the wild type. Kinetic analysis of PHB degradation suggests that this amino acid substitution promoted not only the adsorption of the mutant enzyme to PHB, but also the disruption of the PHB surface to enhance the hydrolysis of the PHB polymer chain.     

A Practical System for High-Throughput Screening of Mutants of <Emphasis Type="Italic">Bacillus fastidiosus</Emphasis> Uricase

For high-throughput screening (HTS) of Bacillus fastidiosus uricase mutants, a practical system was proposed. By error-prone PCR with final 1.5 mM MnCl₂, two focused libraries of mutants for A1-V158 and V150-D212 were generated separately. After induced expression of individual clones in 48-well microplates, Escherichia coli cells (BL21) were lyzed by 1.0 M Tris-HCl at pH 9.0 in 96-well microplates at 25 °C for 7.5 ~ 10.5 h; uricase reaction was continuously monitored with 0.15 mM uric acid in 96-well plates by absorbance at 298 nm to estimate V _m/K _m by kinetic analysis of reaction curve for comparison. V _m/K _m was resistant to initial uric acid levels with an upper limit 3-fold over that of initial rates. By receiver-operator-characteristic analysis of the recognition of the one of higher activity in uricase pair whose specific activity ratio was 1.8 or 3.3, the area-under-the-curve was comparable to that with cell lysates prepared by sonication treatment. A cutoff for the maximum Youden index was thus developed to recognize positive mutants of 1-fold higher activity. Indeed, mutant L171I/Y182F/Y187F/A193S of higher activity but lower thermostability at pH 7.4 and mutant V144A of higher activity and consistent thermostability were discovered. Therefore, the proposed system was practical for HTS of uricase mutants.     

大尺寸SiO2大孔材料固定化漆酶

以表面固定Cu2+的改性大尺寸SiO2大孔材料作为载体,考察了时间、pH和给酶量对漆酶固定化效果的影响,并对固定化漆酶的活性和稳定性进行了研究。结果表明:5 h时吸附达到平衡,pH为4.5、漆酶与载体比例为5 mg·g-1时固定化效果最好,酶活回收率可达到100.4%;固定化漆酶的最适pH和最适温度较游离漆酶的均有升高且范围变宽,固定化后,漆酶的pH稳定性和热稳定性都得到显著提高;固定化漆酶的K m值略高于游离漆酶的;固定化漆酶具有良好的操作稳定性,与底物反应反复操作10批次后剩余酶活为72.7%。     

Using of silica particles as porogen for preparation of macroporous chitosan macrospheres suitable for enzyme immobilization

Porous chitosan macrospheres were prepared at the first time by using silica particles as porogen, and the optimal weight ratio of silica to chitosan during preparation was determined. Scanning electron microscopy micrographs showed that the support with silica as porogen (support I) had a much more porous surface structure than the support without porogen (support II). Both supports were applied to immobilize β-galactosidase from Aspergillus oryzae. Much higher specific activity and yield of galactose hydrolysis products were observed for the support I. Properties of both immobilized enzyme were determined and compared with the free enzyme, satisfactory results were obtained in thermostability, pH arid operational stability, Michaelis constants K _m and in maximum velocity of hydrolysis (V _m). Suggested method allow to prepare chitosan macrospheres as immobilized enzyme carrier with moreporous surface structure and more active reaction groups.     

Immobilization of bromelain onto porous copoly(γ-methyl-l-glutamate/l-leucine) beads

Water-insoluble bromelain was prepared by immobilizing bromelain onto the surface of porous copoly(γ-methyl-l-glutamate/l-leucine) (ML) beads with and without spacer. The mode of the immobilization between bromelain and porous copolypeptide ML beads was covalent fixation. The relative activity and the stability of the immobilized bromelain was investigated. The retained activity of the bromelain covalently immobilized by the azide method was found to be excellent toward a small ester substrate, N-benzyl-l-arginine ethyl ester, but rather low toward casein, a high molecular weight substrate. The values of the Michaelis constant K_m and the maximum reaction velocity V_m for free and immobilized bromelain on the porous copolypeptide ML beads were estimated. Apparent K_m was larger for immobilized bromelain than for the free one, while V_m was smaller for the immobilized bromelain. The thermal stability of the covalently immobilized bromelain was higher than that of the free bromelain. The initial enzymatic activity of the immobilized bromelain remained approximately unchanged with storage time, when the batch enzyme reaction was performed repeatedly, indicating the excellent durability.     

A new method to prepare macroporous copolymer of glycidyl methacrilate and ethylene dimethacrilate as enzyme carrier

Macroporous copolymer of glycidyl methacrylate and ethylene dimethacrylate containing surface epoxy groups was firstly synthesized with dodecyl alcohol and cyclohexanol as liquid pore-forming agents and nanosize calcium carbonate as solid porogenic agent. The scanning electron microscopy was used to characterize their surface structure. Under the optimum conditions, β-galactosidase from Aspergillus oryzae was immobilized on the support obtained above, and the basic property and the kinetic data of the reaction on immobilized enzyme were determined. These data were compared with those obtained for the enzyme immobilized on the support prepared only with the liquid solution as pore-forming agent. Satisfactory results were obtained in enzyme activity, immobilization yield, pH stability, thermal stability, operational stability, and Michaelis constants K _M. The results indicated that the copolymer of glycidyl methacrilate and ethylene dimethacrylate newly prepared was more suitable to immobilize enzyme than the carrier synthesized with traditional method.     

Time-resolved fluorescence analysis of the mobile flavin cofactor in p -hydroxybenzoate hydroxylase

Conformational heterogeneity of the FAD cofactor in p-hydroxybenzoate hydroxylase (PHBH) was investigated with time-resolved polarized flavin fluorescence. For binary enzyme/substrate (analogue) complexes of wild-type PHBH and Tyr222 mutants, crystallographic studies have revealed two distinct flavin conformations; the ‘in’ conformation with the isoalloxazine ring located in the active site, and the ‘out’ conformation with the isoalloxazine ring disposed towards the protein surface. Fluorescence-lifetime analysis of these complexes revealed similar lifetime distributions for the ‘in’ and ‘out’ conformations. The reason for this is twofold. First, the active site of PHBH contains various potential fluorescence-quenching sites close to the flavin. Fluorescence analysis of uncomplexed PHBH Y222V and Y222A showed that Tyr222 is responsible for picosecond fluorescence quenching free enzyme. In addition, other potential quenching sites, including a tryptophan and two tyrosines involved in substrate binding, are located nearby. Since the shortest distance between these quenching sites and the isoalloxazine ring differs only little on average, these aromatic residues are likely to contribute to fluorescence quenching. Second, the effect of flavin conformation on the fluorescence lifetime distribution is blurred by binding of the aromatic substrates: saturation with aromatic substrates induces highly efficient fluorescence quenching. The flavin conformation is therefore only reflected in the small relative contributions of the longer lifetimes.     

Properties of pectinesterase and endo-d-polygalacturonase coimmobilized in a porous glass support

Derivatives of pectinesterase and polygalacturonase, both individually immobilized and coimmobilized, were obtained and characterized. Homologous soluble systems were also studied to establish differences between the effect of the immobilization process and the presence of the other enzyme. Immobilization or coimmobilization did not change the optima pH or temperature for the enzymes. However, optimum ionic strength was displaced toward higher values for immobilized pectinesterase, while for polygalacturonase immobilization resulted in a wider range for activity.K _m value remained nearly unchanged for pectinesterase, and decreased for polygalacturonase. TheV _m value decreased with the immobilization process for the two enzymes, except for polygalacturonase immobilization in presence of pectinesterase. Soluble pectinesterase activity showed a competitive inhibition by polygalacturonic acid (K_i = 0.44 mg/mL). Either immobilization or presence of polygalacturonase rendered the enzyme insensitive to the inhibitory effect. Thermal stability of pectinesterase was not improved after immobilization. On the contrary, the thermal stability of endo-D-polygalacturonase was improved slightly by presence of pectinesterase, and in a greater extent by immobilization. Individually immobilized and coimmobilized pectinesterase activities kept 90 and 60%, respectively, of their initial values after more than one year stored at 3-5 °C. The two endo-D-polygalacturonase derivatives showed the same activity decay pattern along 10 mo storage at 3-5 °C. The two immobilized pectinesterase derivatives showed similar operational stabilities during continuous operation. The presence of pectinesterase remarkably increased the operational stability of the immobilized endo-D-poly galacturonase.     

Single-Point Mutant Inverts the Stereoselectivity of a Carbonyl Reductase toward β-Ketoesters with Enhanced Activity

Enzyme stereoselectivity control is still a major challenge. To gain insight into the molecular basis of enzyme stereo-recognition and expand the source of antiPrelog carbonyl reductase toward β-ketoesters, rational enzyme design aiming at stereoselectivity inversion was performed. The designed variant Q139G switched the enzyme stereoselectivity toward β-ketoesters from Prelog to antiPrelog, providing corresponding alcohols in high enantiomeric purity (89.1–99.1 % ee). More importantly, the well-known trade-off between stereoselectivity and activity was not found. Q139G exhibited higher catalytic activity than the wildtype enzyme, the enhancement of the catalytic efficiency (k_cat/K_m) varied from 1.1- to 27.1-fold. Interestingly, the mutant Q139G did not lead to reversed stereoselectivity toward aromatic ketones. Analysis of enzyme–substrate complexes showed that the structural flexibility of β-ketoesters and a newly formed cave together facilitated the formation of the antiPrelog-preferred conformation. In contrast, the relatively large and rigid structure of the aromatic ketones prevents them from forming the antiPrelog-preferred conformation.