Taking Fingerprints of DNA Polymerases: Multiplex Enzyme Profiling on DNA Arrays

A novel screening approach based on an oligonucleotide‐addressing enzyme assay enables multiplexed simultaneous profiling of DNA polymerases in nanoliter volumes in terms of their different properties. This approach was used to identify enzymes with altered properties out of a library of protein mutants.

     

基于柔性衬底的ZnO葡萄糖酶电极制备及特性

通过水热法在长有ZnO籽晶层的柔性聚酰亚胺(PI)衬底上生长了整齐的ZnO纳米棒,ZnO纳米棒的晶体结构和表面形貌通过X射线衍射(XRD)、扫描电子显微镜(SEM)等进行表征.通过静电吸附方式,将葡萄糖氧化酶(GOx)固定在其表面.分别对GOx及修饰前后的ZnO纳米棒进行了紫外-可见光谱表征,发现修饰后存在ZnO的吸收峰和GOx的特征吸收峰,表明GOx固定在ZnO表面.通过对修饰样品进行傅里叶变换红外(FTIR)光谱测试发现了与GOx相关的吸收峰,这进一步表明GOx仍保持生物活性.最后在循环伏安曲线的测试中,这种在柔性衬底上制备的生物酶电极表现出非常灵敏的电流响应,为制备柔性葡萄糖生物传感器奠定了实验基础.     

Directional Regulation of Enzyme Pathways through the Control of Substrate Channeling on a DNA Origami Scaffold

Artificial multi‐enzyme systems with precise and dynamic control over the enzyme pathway activity are of great significance in bionanotechnology and synthetic biology. Herein, we exploit a spatially addressable DNA nanoplatform for the directional regulation of two enzyme pathways (G6pDH–MDH and G6pDH–LDH) through the control of NAD⁺ substrate channeling by specifically shifting NAD⁺ between the two enzyme pairs. We believe that this concept will be useful for the design of regulatory biological circuits for synthetic biology and biomedicine.     

基于多孔金结构的三相界面酶电极的制备及高效电化学酶传感性能

界面微环境是影响酶催化反应及酶传感性能的关键因素. 本研究基于三维微纳米结构多孔金基底, 通过调控电极表面的亲水和疏水浸润性, 制备了具有固-液-气三相界面微环境的氧化酶电极, 并研究了界面微环境对酶催化反应动力学的影响规律. 基于所制备的三相界面多孔金结构酶电极, 反应物氧气能够从气相直接快速地传输到酶催化反应界面, 极大地提升了界面氧气浓度及其稳定性, 从而大幅度提高了氧化酶活性及酶电极响应的稳定性. 以葡萄糖为模型待测物, 基于该三相界面酶电极的电化学酶生物传感器拥有宽的线性范围、 高的灵敏度、 低的检出限以及良好的稳定性. 这类独特的三相反应界面设计为高效酶生物传感器的建构以及生物分子的精准检测提供了新思路.     

Controlling the Substrate Specificity of an Enzyme through Structural Flexibility by Varying the Salt-Bridge Density

Many enzymes, particularly in one single family, with highly conserved structures and folds exhibit rather distinct substrate specificities. The underlying mechanism remains elusive, the resolution of which is of great importance for biochemistry, biophysics, and bioengineering. Here, we performed a neutron scattering experiment and molecular dynamics (MD) simulations on two structurally similar CYP450 proteins; CYP101 primarily catalyzes one type of ligands, then CYP2C9 can catalyze a large range of substrates. We demonstrated that it is the high density of salt bridges in CYP101 that reduces its structural flexibility, which controls the ligand access channel and the fluctuation of the catalytic pocket, thus restricting its selection on substrates. Moreover, we performed MD simulations on 146 different kinds of CYP450 proteins, spanning distinct biological categories including Fungi, Archaea, Bacteria, Protista, Animalia, and Plantae, and found the above mechanism generally valid. We demonstrated that, by fine changes of chemistry (salt-bridge density), the CYP450 superfamily can vary the structural flexibility of its member proteins among different biological categories, and thus differentiate their substrate specificities to meet the specific biological needs. As this mechanism is well-controllable and easy to be implemented, we expect it to be generally applicable in future enzymatic engineering to develop proteins of desired substrate specificities.     

Physical Insight for Grafting Polymer Chains onto the Substrate via Computer Simulations: Kinetics and Property

Molecules adsorbed or attached on a surface is a quite basic phenomenon in numerous chemical or biological systems. Grafting-onto is considered as a feasible way to achieve it. The grafting reaction is essentially controlled by the diffusion of the molecules, thus it is more likely a physical issue, instead of a chemical issue. Because of the experimental difficulty in measuring the properties of surface-attached molecules(e.g.,the polymeric molecules), the surface-bound molecules are often assu...     

Targeting the Substrate Binding Site of E. coli Nitrile Reductase QueF by Modeling,Substrate and Enzyme Engineering

Nitrile reductase QueF catalyzes the reduction of 2‐amino‐5‐cyanopyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₀) to 2‐amino‐5‐aminomethylpyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₁) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non‐natural substrates. Various structural analogues of the natural substrate preQ₀ were synthesized and screened with wild‐type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non‐natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild‐type and mutant nitrile reductase.     

Modification of a Capillary for Electrophoresis by Electrostatic Self‐Assembly of an Enzyme for Selective Determination of the Enzyme Substrate

The integration of a separation capillary for capillary electrophoresis (CE) with an on‐column enzyme reaction for selective determination of the enzyme substrate is described. Enzyme immobilization is achieved by electrostatic assembly of poly(diallydimethylammonium chloride) (PDDA) followed by adsorption of a mixture of the negatively charged enzyme glucose oxidase (GOx) and anionic poly(styrenesulfonate) (PSS). The reaction of glucose with the GOx produces hydrogen peroxide which migrates the length of the capillary and is detected amperometrically at the capillary outlet. The enzyme reaction occurs during a capillary separation, allowing selective determination of the substrate in complex samples without the need for pre‐ or post‐separation chemical modification of the analyte. The enzyme reactor is found to have an optimal response to glucose when a 5 : 1 mixture of PSS:GOx is used. Under these conditions the limit of detection for glucose is found to be between 5.0×10^?4 and 1.3×10^?3 M, dependent upon the inner‐diameter of the capillary. The apparent Michaelis‐Menten constant for the enzyme reaction was determined to be 0.047 (±0.001) M and 0.0037 (±0.0007) M for a 50 and 10 μm inner‐diameter capillaries, respectively. These results indicate that the enzyme reaction is efficient, having enzyme kinetics similar to that of a reaction occurring in solution. This enzyme immobilization method was also applied to another enzyme, glutamate oxidase, yielding similar results.     

The Thioesterase of the Erythromycin-Producing Polyketide Synthase: Influence of Acyl Chain Structure on the Mode of Release of Substrate Analogues from the Acyl Enzyme Intermediates

The production of genetically engineered polyketides depends critically on thioesterase activity for product release. In vitro studies with the thioesterase from the erythromycin polyketide synthase (PKS) have demonstrated that the ability of this enzyme to act as a universal decoupler is limited, but stereochemical variation is readily tolerated. Synthetic analogues with all four stereochemical configurations of the natural substrate's 2-methyl-3-hydroxy substitution pattern ( 1 – 4 ; X=p-nitrophenoxy) were substrates for the enzyme.     

Evaluating Experiment with Computation in Physical Chemistry: The Particle-In-A-Box Model with Cyanine Dyes

The results from a classic experiment in the undergraduate physical chemistry laboratory, the particle-in-a-box model for spectroscopic transitions of conjugated dyes, is compared to computational results obtained using a molecular mechanics structural approach and the extended Hückel molecular orbital picture. The goal of this exercise is to help students to think critically about their experimental data and to use comparisons of mathematical and computational models to try to understand departures of an experiment from expectations.     

Imaging of Enzyme Activity by Electron Paramagnetic Resonance: Concept and Experiment Using a Paramagnetic Substrate of Alkaline Phosphatase

Enzyme activities are well established biomarkers of many pathologies. Imaging enzyme activity directly in vivo may help to gain insight into the pathogenesis of various diseases but remains extremely challenging. In this communication, we report the use of EPR imaging (EPRI) in combination with a specially designed paramagnetic enzymatic substrate to map alkaline phosphatase activity with a high selectivity, thereby demonstrating the potential of EPRI to map enzyme activity.     

Effect of Physical Properties and Emulsification Conditions on the Microsphere Size Prepared Using a Solvent Extraction Process

Microspheres were prepared using a hydrocarbon-perfluorocarbon solvent extraction process. The effect of the physical properties and the emulsification conditions on the mean microsphere size was investigated. The viscosity of the dispersed and the continuous phase greatly affected the microsphere size. Smaller microspheres were produced at the same mixing intensity when the viscosity of the dispersed phase decreased. Increased continuous phase viscosity reduced the coalescenceof the droplets and hence smaller microspheres were produced. The mean microsphere size first decreased as the volume ratio of the dispersed phase to the continuous phase increased but upon further increase the mean microsphere size increased. The effect of the volume ratio on the microsphere size was linked to the surfactant concentration. The stability of the studied hydrocarbon-in-fluorocarbon emulsion is poor. One reason for the poor stability is the high density difference between the phases. The emulsion droplets were solidified by siphoning part of the emulsion in the fresh continuous phase, which extracted the solvent from the dispersed phase. The effect of emulsion transfer time between the emulsification and solidification steps on the particle size was studied but no significant effect was observedduring the controlled time interval.     

Empirical Evaluation of Inhibitory Product, Substrate, and Enzyme Effects During the Enzymatic Saccharification of Lignocellulosic Biomass

The cellulose hydrolysis kinetics during batch enzymatic saccharification are typified by a rapid initial rate that subsequently decays, resulting in incomplete conversion. Previous studies suggest that changes associated with the solution, substrate, or enzymes may be responsible. In this work, kinetic experiments were conducted to determine the relative magnitude of these effects. Pretreated corn stover (PCS) was used as a lignocellulosic substrate likely to be found in a commercial saccharification process, while Avicel and Kraft lignin were used to create model substrates. Glucose inhibition was observed by spiking the reaction slurry with glucose during initial-rate experiments. Increasing the glucose concentration from 7 to 48 g/L reduced the cellulose conversion rate by 94%. When product sugars were removed using ultrafiltration with a 10 kDa membrane, the glucose-based conversion increased by 9.5%. Reductions in substrate reactivity with conversion were compared directly by saccharifying PCS and Avicel substrates that had been pre-reacted to different conversions. Reaction of substrate with a pre-conversion of 40% resulted in about 40% reduction in the initial rate of saccharification, relative to fresh substrate with identical cellulose concentration. Overall, glucose inhibition and reduced substrate reactivity appear to be dominant factors, whereas minimal reductions of enzyme activity were observed.     

基于固体酶催化反应电化学测定酶含量

提出了以固体辣根过氧化物酶(HRP)对过氧化氢氧化邻苯二胺的催化作用为基础的测定HRP及其标记物的电化学方法.测定中以Au-Pt/PAN/GCE为工作电极,并详细叙述其制备过程.将一定浓度的HRP按规定方法固定在上述修饰电极上制得HRP/Au-Pt/PAN/GCE修饰电极,将此电极浸入含5.0×10-3mol·L-1邻苯二胺及2.5×10-3mol·L-1过氧化氢的磷酸盐缓冲溶液(pH 5.0)中,反应10 min后将电极取出,记录溶液中酶催化反应产物的方波伏安峰及峰电流.结果表明:酶催化反应前,底物在工作电极上于-0.488 V(vs.SCE)处有明显的还原峰,在酶催化反应后,在-0.584 V处出现一个更大的还原峰,电位负移160 mV,且峰电流明显增大.峰电流值(Ip)与修饰在Au-Pt/PAN/GCE电极上的HRP的含量在1.0×10-2～2.0×102μg·L-1之间呈线性关系,方法的检出限(3S/N)为3.0 ng·L-1.     

Silica-graft-polyamidoamine Hybrid Materials: Effect of Constraints on the Polymer Mobility

Organic-inorganic hybrid materials with excellent heavy metal ions chelating properties are synthesized by covalent bonding of multifunctional polymers of polyamidoamine (PAA) type onto silica. Two series of polyamidoamine-silica hybrid materials differing in the PAA chemical structure are prepared and their thermal properties are investigated. Differential Scanning Calorimetry (DSC) is used to study the effects of chain immobilization and ion chelation on the glass-transition temperature (T_g) of the polymers. The T_g of PAA-hybrid materials is elevated with respect to ungrafted PAAs, but when the linear and the corresponding hybrid PAAs are in the complex form with metal ions such as Cu²⁺ and Co²⁺, the materials arrive to the decomposition temperature and no T_g is detected. To highlight the effect of metal ion on the molecular mobility of these systems, an oligomeric plasticizer is added. The behaviour in the T_g region is analyzed and discussed in term of Tool-Narayanaswamy-Moynihan (TNM) model. In particular the apparent activation energy (Δh*) is used to discuss overall segmental co-operativity in order to better understand the effect of complex formation on structural mobility.     

Synthesis of Phenylthioacetomorpholide: Effect of Substrate on the Willgerodt-Kindler Reaction

The effect of substrates on the Willgerodt-Kindler reaction was studied. The existence of acidic protons on these substrates accerelates the formation of thiomorpholide was found.     

以邻苯二胺为底物固体电极方波伏安法检测辣根过氧化物酶及其标记物

以玻碳电极为工作电极,研究了邻苯二胺(OPD)为底物伏安法检测辣根过氧化物酶(HRP)及其标记物的方法。HRP能够催化H_2O_2氧化OPD,其反应产物在玻碳电极上于-0.42V(vs.Ag/Agcl)左右产生一个灵敏的还原峰,峰电流随着HRP浓度的增大而增大,借助此还原电流可以测定HRP,并进而可用于以HRP为标记物的电化学酶免疫分析。用方波伏安法对酶催化反应条件和酶催化反应产物的测定条件进行了详细的研究,在最佳条件下测定游离HRP的线性范围是1.0×10~(-10)～4.0×10~(-9)g/mL,检出限为8.5×10~(-11)g/mL;对游离的酶标记物(IgG-HRP)的测定最大稀释比为1:2000000。