Stereoselective incorporation of an unsaturated isoleucine analogue into a protein expressed in E. coli

The unsaturated amino acid 2-amino-3-methyl-4-pentenoic acid (E-Ile) was prepared in the form of its (2S,3S),(2R,3R) and (2S,3R),(2R,3S) stereoisomeric pairs. The translational activities of SS-E-Ile and SR-E-Ile were assessed in an E. coli strain rendered auxotrophic for isoleucine. SS-E-Ile was incorporated into the test protein mouse dihydrofolate reductase (mDHFR) in place of isoleucine at a rate of up to 72 %; SR-E-Ile yielded no conclusive evidence for incorporation. ATP/PPi exchange assays indicated that SS-E-Ile was activated by the isoleucyl-tRNA synthetase at a rate comparable to that characteristic of isoleucine; SR-E-Ile was activated approximately 100-times more slowly than SS-E-Ile.     

Protein-structure-based prediction of animal model suitability for pharmacodynamic studies of subtype-selective estrogens

Subtype-selective estrogens are of increasing importance as tools used to unravel physiological roles of the estrogen receptors, ERalpha and ERbeta, in various species. Although human ERalpha and ERbeta differ by only two amino acids within the binding pockets, we and others recently succeeded in generating subtype-selective agonists. We have proposed that the selectivity of the steroidal compounds 16alpha-lactone-estradiol (16alpha-LE(2), hERalpha selective) and 8beta-vinyl-estradiol (8beta-VE(2), hERbeta selective) is based on the interaction of certain substituents of these compounds with essentially one amino acid in the respective ER binding pockets. For in vitro and ex vivo pharmacological experiments with these compounds we intended to use bovine tissues available from slaughterhouses in larger quantities. Using homology modeling techniques we determined that the amino acid conferring high hERbeta-selectivity to 8beta-VE(2) is not exchanged between human and bovine ERalpha and bovine ERbeta. Thus, we predicted our steroidal hERbeta-selective compound to exhibit only weak agonistic activity at bERbeta and that bovine tissue is therefore not suited for investigation of ERbeta functions. The situation is presumably identical for pig, sheep, and the common marmoset, whereas rats, mice, and rhesus macaques are appropriate animal models to study pharmacological effects of 8beta-VE(2) in vivo. This prediction was confirmed in transactivation studies assessing estradiol (E(2)) and the two subtype-selective ligands on bovine ERbeta and on a series of hERalpha and hERbeta with mutations in their respective ligand-binding pockets. We have shown that the detailed understanding of the interactions of a compound with its target protein enables the identification of relevant species for pharmacological studies.     

Preliminary characterization of light harvesting in E. coli DNA photolyase

E. coli DNA photolyase is a monomeric light-harvesting enzyme that utilizes a methenyltetrahydrofolate (MTHF) antenna cofactor to harvest light energy for the repair of thymine dimers in DNA. For this purpose, the enzyme evolved to bind the cofactor and red-shift its absorption maximum by 25 nm. Using the crystal structure as a guide, we mutated each protein residue that contacts the cofactor in an effort to identify the interactions responsible for this selective stabilization of the cofactor's excited state. Hydrogen bonding, packing, and electrostatic interactions were examined. Remarkably, a single residue, Glu109, appears to play an important, if not exclusive, role in inducing the observed red-shift. Thus, this protein, the simplest light-harvesting system known, appears to have evolved a remarkably simple mechanism to tune the photophysical properties of the antenna cofactor appropriately for biological function.     

PP1, PP2A and PP2B Interplay in the Regulation of Sperm Motility: Lessons from Protein Phosphatase Inhibitors

Male fertility relies on the ability of spermatozoa to fertilize the egg in the female reproductive tract (FRT). Spermatozoa acquire activated motility during epididymal maturation; however, to be capable of fertilization, they must achieve hyperactivated motility in the FRT. Extensive research found that three protein phosphatases (PPs) are crucial to sperm motility regulation, the sperm-specific protein phosphatase type 1 (PP1) isoform gamma 2 (PP1γ2), protein phosphatase type 2A (PP2A) and protein phosphatase type 2B (PP2B). Studies have reported that PP activity decreases during epididymal maturation, whereas protein kinase activity increases, which appears to be a requirement for motility acquisition. An interplay between these PPs has been extensively investigated; however, many specific interactions and some inconsistencies remain to be elucidated. The study of PPs significantly advanced following the identification of naturally occurring toxins, including calyculin A, okadaic acid, cyclosporin, endothall and deltamethrin, which are powerful and specific PP inhibitors. This review aims to overview the protein phosphorylation-dependent biochemical pathways underlying sperm motility acquisition and hyperactivation, followed by a discussion of the PP inhibitors that allowed advances in the current knowledge of these pathways. Since male infertility cases still attain alarming numbers, additional research on the topic is required, particularly using other PP inhibitors.     

重组人白细胞介素-10在大肠杆菌中的表达及生物学活性分析

目的在大肠杆菌中表达重组人白细胞介素-10(Interleukin-10,IL-10),并检测其生物学活性。方法将IL-10基因重组到质粒pET11c中,转化BL21(DE),提取质粒,经酶切鉴定和测序分析;在25℃用低浓度的IPTG诱导表达,对包涵体IL-10稀释复性;经ELISA检测其含量,MC/9细胞增殖法检测其生物学活性。结果工程菌IL-10/pET11c/BL21诱导表达的目的蛋白以可溶性和包涵体两种形式存在,Westernblot鉴定证实为IL-10蛋白,两种形式的IL-10均具有一定的生物学活性。结论已成功地在大肠杆菌中表达了IL-10,为进一步纯化和制备IL-10的基因工程药物打下了基础。     

人内皮抑素基因的定点突变及其在大肠杆菌中的表达

目的对人内皮抑素(hES)基因进行定点突变,提高其在大肠杆菌中的可溶性表达量。方法根据Internet网站提供的关于hES的结构信息及其结构与功能方面的研究文献,设计突变位点;利用生物信息学的相关网站,对hES突变体进行结构预测,验证突变位点设计的合理性;采用重叠延伸PCR方法进行hES基因的定点突变,并将突变基因和未突变基因分别亚克隆至表达载体pGEX-4T-3,在大肠杆菌中进行融合表达,比较突变前后目的蛋白的可溶性表达量。结果三级结构预测结果表明突变位点设计合理,序列分析结果表明实现了hES基因的定点突变。突变基因的表达产物中,可溶性部分约占总表达量的40%,而未突变基因的表达产物几乎全部为包涵体。结论已成功对hES基因进行了定点突变,突变后的hES可溶性表达量得到了提高。     

Redesigning the Active Site of Transaldolase TalB from Escherichia coli: New Variants with Improved Affinity towards Nonphosphorylated Substrates

Recently, we reported on a transaldolase B variant (TalB F178Y) that is able to use dihydroxyacetone (DHA) as donor in aldol reactions. In a second round of protein engineering, we aimed at improving the affinity of this variant towards nonphosphorylated acceptor aldehydes, that is, glyceraldehyde (GA). The anion binding site was identified in the X‐ray structure of TalB F178Y where a sulfate ion from the buffer was bound in the active site. Therefore, we performed site‐directed saturation mutagenesis at three residues forming the putative phosphate binding site, Arg181, Ser226 and Arg228. The focused libraries were screened for the formation of D ‐fructose from DHA and d,l ‐GA by using an adjusted colour assay. The best results with respect to the synthesis of D ‐fructose were achieved with the TalB F178Y/R181E variant, which exhibited an at least fivefold increase in affinity towards d,l ‐GA (K_M=24 mM ). We demonstrated that this double mutant can use D ‐GA, glycolaldehyde and the L ‐isomer, L ‐GA, as acceptor substrates. This resulted in preparative synthesis of D ‐fructose, D ‐xylulose and L ‐sorbose when DHA was used as donor. Hence, we engineered a DHA‐dependent aldolase that can synthesise the formation of polyhydroxylated compounds from simple and cheap substrates at preparative scale.     

Structured cell simulator coupled with a fluidized bed bioreactor model to predict the adaptive mercury uptake by E. coli cells

A bi-level model is proposed by coupling a three-phase fluidized bioreactor (TPFB), used for mercury uptake from wastewaters by immobilized Escherichia coli cells, with a cellular simulator of the genetic regulatory circuit (GRC) controlling the mercuric ion reduction in the cytosol. While keeping a reasonable agreement with the experimental data from literature (free cell cultures with/without cell membrane permeabilization), the structured model advantages are coming from the prediction detailing degree [simulated 26 + 3 (cell + bulk) vs. 3 (bulk) variable dynamics] covering a wide range of input Hg²⁺ loads (0–100 mg L⁻¹), and cloned E. coli cells with various amounts of mer-plasmids (3–140 nM). The model offers the possibility to predict the inner cell mercury reduction rate (different from the apparent rate observed in the bioreactor), the bacteria metabolism adaptation to environmental changes over several cell cycles, and the effect of cloning cells to modify their behaviour under stationary or perturbed conditions.     

Preliminary study on preparation of E.coli cell-free system for protein expression

In the new era of “Omics”, the traditional techniques of protein expression in vivo can not come up with the exponential increase of genetic information. The cellfree protein synthesis system provides a new strategy of protein expression with advantages of rapid, convenient and high-throughput expression. The preparation of cell extracts, the optimization of substrate concentrations and the energy regeneration system are the key factors for the successful construction of cell-free protein expression system. In this work, the cell extract was prepared from RNase I- defective strain E. coli A19. The cell growth phase, the pressure for cell disruption and the storage condition of cell extracts were optimized. Meanwhile, the optimal substrate concentrations and the energy regeneration system were selected. Under the optimized conditions, the green fluorescent protein (GFP) reporter gene was expressed in the E. coli cell-free system with high expression level (Ca. 154 μg/mL) which was 29 times higher than the expression level before optimization. __________ Translated from Journal of Zhejiang University (Engineering Science), 2007, 41(5): 843–847 [译自: 浙江大学学报(工学版)]     

大肠杆菌色氨酸操纵子基因的克隆与表达

目的克隆并表达大肠杆菌色氨酸操纵子基因,提高其酶活性。方法利用PCR方法,从大肠杆菌31884基因组中直接克隆出色氨酸操纵子,并将其连接到原核表达载体pET-22b(+)中,构建重组质粒pET-22b(+)-Trpoperon,转化大肠杆菌BL21,IPTG诱导重组蛋白表达,表达产物经SDS-PAGE分析,并测定酶活性。结果凝胶电泳可见PCR扩增产物大小约为7000bp,SDS-PAGE鉴定目的蛋白分别得到了表达,邻氨基苯甲酸合成酶和色氨酸合成酶的活性分别比对照提高了2.7和3.2倍。结论已成功构建了重组表达质粒pET-22b(+)-Trpoperon,邻氨基苯甲酸合成酶和色氨酸合成酶的活性在大肠杆菌中得到了提高,为高产色氨酸基因工程菌的构建奠定了基础。     

大肠杆菌体系外源蛋白表达速度的调控策略

介绍和评价了目前针对大肠杆菌体系外源蛋白表达的转录、翻译和折叠阶段的各种表达速度调控策略. 根据现有各类调控策略的作用阶段、特点及优缺点,提出对蛋白表达各步骤分别调节,从而获得合适的整体表达速度以优化表达效果,提高大肠杆菌体系外源蛋白生产效率和产品质量,进一步提高其适用性和经济性.     

The structure of E.coli soluble inorganic pyrophosphatase at 2.7 A resolution

Hie structure of E.coli soluble inorganic pyrophosphatase hasbeen refined at 2.7 resolution to an R-factor of 20.9. Theoverall fold of the molecule is essentially the same as yeastpyrophosphatase, except that yeast pyrophosphatase is longerat both the N- and C-termini. Escherichia coli pyrophosphataseis a mixed +ß protein with a complicated topology.The active site cavity, which is also very similar to the yeastenzyme, is formed by seven ß-strands and an -helixand has a rather asymmetric distribution of charged residues.Our structure-based alignment extends and improves upon earliersequence alignment studies; it shows that probably no more than14, not 15–17 charged and polar residues are part of theconserved enzyme mechanism of pyrophosphatases. Six of theseconserved residues, at the bottom of the active site cavity,form a tight group centred on Asp70 and probably bind the twoessential Mg⁺ ions. The others, more spreadout and more positivelycharged, presumably bind substrate. Escherichia coli pyrophosphatasehas an extra aspartate residue in the active site cavity, whichmay explain why the two enzymes bind divalent cation differently.Based on the structure, we have identified a sequence motifthat seems to occur only in soluble inorganic pyrophosphatases.     

The Solvation of the E. coli CheY Phosphorylation Site Mapped by XFMS

The Escherichia coli CheY protein belongs to a large bacterial response regulator superfamily. X-ray hydroxy radical foot-printing with mass spectroscopy (XFMS) has shown that allosteric activation of CheY by its motor target triggers a concerted internalization of aromatic sidechains. We reanalyzed the XFMS data to compare polar versus non-polar CheY residue positions. The polar residues around and including the 57D phosphorylated site had an elevated hydroxy radical reactivity. Bioinformatic measures revealed that a water-mediated hydrogen bond network connected this ring of residues with the central 57D. These residues solvated 57D to energetically stabilize the apo-CheY fold. The abundance of these reactive residues was reduced upon activation. This result was supported by the bioinformatics and consistent with the previously reported activation-induced increase in core hydrophobicity. It further illustrated XFMS detection of structural waters. Direct contacts between the ring residues and the phosphorylation site would stabilize the aspartyl phosphate. In addition, we report that the ring residue, 18R, is a constant central node in the 57D solvation network and that 18R non-polar substitutions determine CheY diversity as assessed by its evolutionary trace in bacteria with well-studied chemotaxis. These results showcase the importance of structured water dynamics for phosphorylation-mediated signal transduction.     

Biosynthesis of winter flounder antifreeze proprotein in E.coli

A semisynthetic winter flounder antifreeze proprotein (proAFP)coding region was constructed and inserted into a lacZ expressionvector. ProAFP was produced from the vector in Escherichia colias a C-terminal fusion to the first 289 amino acids of ß-galactosidase(ß-gal). The proAFP and ß-gal domains ofthe ß-gal–proAFP fusion protein were separatedby the recognition signal for the blood coagulation protease,factor X_a. Upon induction with isopropylthio-ß-D-galactosidethe fusion protein accumulated to levels of 15% of the totalprotein. The ß-gal–proAFP fusion protein waspartially purified by differential centrifugation, but requiredsolubilization prior to factor X_a digestion. The solubilizedfusion protein was efficiently and correctly cleaved by factorX_a, after which the proAFP was purified by gel permeation. BacterialproAFP was indistinguishable from natural proAFP by the criteriaof antifreeze activity, amino-terminal sequence (15 cycles),reverse-phase HPLC and SDS–polyacrylamide gel electrophoresis.Circular dichroism measurements showed that proAFP is a compositeof random coil and -helical secondary structure, with an -helicalcontent of 44% at 0°C. It seems probable that the C-terminalregion of proAFP, which corresponds to the mature AFP protein,is mainly -helical, and that the N-terminal pro-segment is randomcoiled.     

Rational Mutagenesis in the Lid Domain of Ribokinase from E. coli Results in an Order of Magnitude Increase in Activity towards D-arabinose

Development of efficient approaches for the production of medically important nucleosides is a highly relevant challenge for biotechnology. In particular, cascade synthesis of arabinosides would allow relatively easy production of various cytostatic and antiviral drugs. However, the biocatalyst necessary for this approach, ribokinase from Escherichia coli (EcoRK), has a very low activity towards D-arabinose, making the synthesis using the state-of-art native enzyme technologically unfeasible. Here, we report the results of our enzyme design project, dedicated to engineering a mutant form of EcoRK with elevated activity towards arabinose. Analysis of the active site structure has allowed us to hypothesize the reasons behind the low EcoRK activity towards arabinose and select feasible mutations. Enzyme assay and kinetic studies have shown that the A98G mutation has caused a large 15-fold increase in k_cat and 1.5-fold decrease in K_M for arabinose phosphorylation. As a proof of concept, we have performed the cascade synthesis of 2-chloroadenine arabinoside utilizing the A98G mutant with 10-fold lower amount of enzyme compared to the wild type without any loss of synthesis efficiency. Our results are valuable both for the development of new technologies of synthesis of modified nucleosides and providing insight into the structural reasons behind EcoRK substrate specificity.     

大肠杆菌GBP的定点突变与制备方法研究

在mglB基因上进行了E149C、 A213S、 L238S三个定点突变,并利用大肠杆菌BL21(DE3)/pET28c系统,构建了表达突变型GBP的基因工程菌BL21(DE3)/pLE3.工程菌经诱导培养后收获细胞,利用渗透休克法提取周质空间蛋白,经Ni-NTA柱纯化,从1 L培养液中可得到约3.5 mg SDS-PAGE纯度的GBP.     

Structural Basis for the Regiospecificity of a Lipase from Streptomyces sp. W007

The efficiency and accuracy of the synthesis of structural lipids are closely related to the regiospecificity of lipases. Understanding the structural mechanism of their regiospecificity contributes to the regiospecific redesign of lipases for meeting the technological innovation needs. Here, we used a thermostable lipase from Streptomyces sp. W007 (MAS1), which has been recently reported to show great potential in industry, to gain an insight into the structural basis of its regiospecificity by molecular modelling and mutagenesis experiments. The results indicated that increasing the steric hindrance of the site for binding a non-reactive carbonyl group of TAGs could transform the non-specific MAS1 to a α-specific lipase, such as the mutants G40E, G40F, G40Q, G40R, G40W, G40Y, N45Y, H108W and T237Y (PSI > 80). In addition, altering the local polarity of the site as well as the conformational stability of its composing residues could also impact the regiospecificity. Our present study could not only aid the rational design of the regiospecificity of lipases, but open avenues of exploration for further industrial applications of lipases.