Molecular recognition in (+)-alpha-pinene oxidation by cytochrome P450cam

Oxygenated derivatives of the monoterpene (+)-alpha-pinene are found in plant essential oils and used as fragrances and flavorings. (+)-alpha-Pinene is structurally related to (+)-camphor, the natural substrate of the heme monooxygenase cytochrome P450(cam) from Pseudomonas putida. The aim of the present work was to apply the current understanding of P450 substrate binding and catalysis to engineer P450(cam) for the selective oxidation of (+)-alpha-pinene. Consideration of the structures of (+)-camphor and (+)-alpha-pinene lead to active-site mutants containing combinations of the Y96F, F87A, F87L, F87W, and V247L mutations. All mutants showed greatly enhanced binding and rate of oxidation of (+)-alpha-pinene. Some mutants had tighter (+)-alpha-pinene binding than camphor binding by the wild-type. The most active was the Y96F/V247L mutant, with a (+)-alpha-pinene oxidation rate of 270 nmol (nmol of P450(cam))(-)(1) min(-)(1), which was 70% of the rate of camphor oxidation by wild-type P450(cam). Camphor is oxidized by wild-type P450(cam) exclusively to 5-exo-hydroxycamphor. If the gem dimethyl groups of (+)-alpha-pinene occupied similar positions to those found for camphor in the wild-type structure, (+)-cis-verbenol would be the dominant product. All P450(cam) enzymes studied gave (+)-cis-verbenol as the major product but with much reduced selectivity compared to camphor oxidation by the wild-type. (+)-Verbenone, (+)-myrtenol, and the (+)-alpha-pinene epoxides were among the minor products. The crystal structure of the Y96F/F87W/V247L mutant, the most selective of the P450(cam) mutants initially examined, was determined to provide further insight into P450(cam) substrate binding and catalysis. (+)-alpha-Pinene was bound in two orientations which were related by rotation of the molecule. One orientation was similar to that of camphor in the wild-type enzyme while the other was significantly different. Analysis of the enzyme/substrate contacts suggested rationalizations of the product distribution. In particular competition rather than cooperativity between the F87W and V247L mutations and substrate movement during catalysis were proposed to be major factors. The crystal structure lead to the introduction of the L244A mutation to increase the selectivity of pinene oxidation by further biasing the binding orientation toward that of camphor in the wild-type structure. The F87W/Y96F/L244A mutant gave 86% (+)-cis-verbenol and 5% (+)-verbenone. The Y96F/L244A/V247L mutant gave 55% (+)-cis-verbenol but interestingly also 32% (+)-verbenone, suggesting that it may be possible to engineer a P450(cam) mutant that could oxidize (+)-alpha-pinene directly to (+)-verbenone. Verbenol, verbenone, and myrtenol are naturally occurring plant fragrance and flavorings. The preparation of these compounds by selective enzymatic oxidation of (+)-alpha-pinene, which is readily available in large quantities, could have applications in synthesis. The results also show that the protein engineering of P450(cam) for high selectivity of substrate oxidation is more difficult than achieving high substrate turnover rates because of the subtle and dynamic nature of enzyme-substrate interactions.     

Relationship between redox function and protein stability of cytochromes c

Electrochemical, 1H NMR, and optical studies on mesophile Pseudomonas aeruginosa cytochrome c551, its single (F34Y) and quintuple (F7A/V13M/F34Y/E43Y/V78I) mutants, and thermophile Hydrogenobacter thermophilus cytochrome c552 at wide temperature range demonstrated that the stable protein exhibits the low redox potential predominantly due to the enthalpic contribution to the redox reaction. The overall stability of the oxidized form was shown to determine the stability of the Fe-methionine coordination bond, which then directly regulates the redox function.     

Butane and propane oxidation by engineered cytochrome P450cam

The haem monooxygenase cytochrome P450cam has been engineered to oxidise the gaseous alkanes butane and propane to butan-2-ol and propan-2-ol, respectively, by the use of bulky amino acid substitutions to reduce the volume of the substrate pocket and thus improve the enzyme-substrate fit: the F87W/Y96F/T101L/V247L mutant oxidizes butane with a turnover rate of 750 min-1 and 95% yield based on NADH consumed while the wild-type enzyme has an activity of 0.4 min-1 with 4% yield.     

Influence of amino acid side chain packing on Fe-methionine coordination in thermostable cytochrome C

Paramagnetic NMR and optical studies of the oxidized forms of mesophile Pseudomonas aeruginosa cytochrome c(551) and its quintuple mutant (F7A/V13M/F34Y/E43Y/V78I), and thermophile Hydrogenobacter thermophilus cytochrome c(552) demonstrated that the amino acid side chain packings in the protein interior influence the coordination bond between the heme iron and the axial methionine in the proteins. The strength of heme axial coordinations was found to correlate with the overall protein thermostability.     

Functional organization of the outer membrane of escherichia coli: phage and colicin receptors as components of iron uptake systems.

The functional interaction of outer membrane proteins of E. coli can be studied using phage and colicin receptors which are essential components of penetration systems. The uptake of ferric iron in the form of the ferrichrome complex requires the ton A and ton B functions in the outer membrane of E. coli. The ton A gene product is the receptor protein for phage T5 and is required together with the ton B function by the phages T1 and ?80 to infect cells and by colicin M and the antibiotic albomycin, a structural analogue of ferrichrome, to kill cells. The ton B function is necessary for the uptake of ferric iron complexed by citrate. Iron complexed by enterochelin is only transported in the presence of the ton B and feu functions. Cells which have lost the feu function are resistant to the colicins B, I or V while ton B mutants are resistant to all 3 colicins. The interaction of the ton A, ton B, and feu functions apparently permits quite different "substrates" to overcome the permeability barrier of the outer membrane. It was shown for ferrichrome dependent iron uptake that the complexing agent was not altered and could be used repeatedly. Only very low amounts of 3H-labeled ferrichrome were found in the cell. It is possible that the iron is mobilized in the membrane and that desferri-ferrichrome is released into the medium without having entered the cytoplasm. Growth on ferrichrome as the sole iron source was used to select revertants of T5 resistant ton A mutants. All revertants exhibited wild-type properties with the exception of partial revertants. In these 4 strains, as in the ton A mutants, the ton A protein was not detectable by SDS polyacrylamide gel electrophoreses of outer membranes. Albomycin resistant mutants were selected and shown to fall into 5 categories: 1) ton A; 2) ton B mutants; 3) mutants with no iron transport defects and normal ton A/ton B functions, which might be target site mutants; 4) mutants which were deficient in ferrichrome-mediated iron uptake but had normal ton A/ton B functions. We tentatively consider that the defect might be located in the active transport system of the cytoplasmic membrane; 5) a variety of mutants with the following general properties: most of them were resistant to colicin M, transported iron poorly, and, like ton B mutants, contained additional proteins in the outer membrane. The outer membrane protein patterns of wild-type and ton B mutant strains were compared by slab gel electrophoresis in an attempt to identify a ton B protein. It was observed that under most growth conditions, ton B mutants overproduced 3 proteins of molecular weights 74,000-83,000. In extracted, iron-deficient medium, both the wild-type and ton B mutant strains had similar large amounts of these proteins in their outer membranes. The appearance of these proteins was suppressed by excess iron in both wild-type and mutant. From this evidence it is apparent that the proteins appear as a response to low intracellular iron rather than being controlled by the ton B gene...     

Capture efficiency of Escherichia coli in fimbriae-mediated immunoimmobilization

Capturing pathogens on a sensor surface is one of the most important steps in the design of a biosensor. The efficiency of a biosensor at capturing pathogens has direct bearing on its sensitivity. In this work we investigated the capturing of Escherichia coli on substrates modified with antibodies targeting different types of fimbriae: K88ab (F4), K88ac (F4), K99 (F5), 987P (F6), F41, and CFA/I. The results suggest that all these fimbriae can be used for the efficient immobilization of living E. coli cells. The immobilization efficiency was affected by the purity and clone type of the antibody and the fimbriae expression level of the bacteria. For a specific fimbriae type, a higher immobilization efficiency was often observed with the monoclonal antibodies. Immunoimmobilization was utilized in an antibody microarray immersed in a mixed culture of pathogens to demonstrate the rapid and simultaneous label-free detection of multiple pathogens within less than 1 h using a single test. The capture rate of living pathogens exceeds a single bacterium per 100 × 100 μm(2) area per 0.5 h of incubation for a bulk concentration of 10(5) cfu/mL.     

Designer gene therapy using an Escherichia coli purine nucleoside phosphorylase/prodrug system

Activation of prodrugs by Escherichia coli purine nucleoside phosphorylase (PNP) provides a method for selectively killing tumor cells expressing a transfected PNP gene. This gene therapy approach requires matching a prodrug and a known enzymatic activity present only in tumor cells. The specificity of the method relies on avoiding prodrug cleavage by enzymes already present in the host cells or the intestinal flora. Using crystallographic and computer modeling methods as guides, we have redesigned E. coli PNP to cleave new prodrug substrates more efficiently than does the wild-type enzyme. In particular, the M64V PNP mutant cleaves 9-(6-deoxy-alpha-L-talofuranosyl)-6-methylpurine with a kcat/Km over 100 times greater than for native E. coli PNP. In a xenograft tumor experiment, this compound caused regression of tumors expressing the M64V PNP gene.     

Antimicrobial activity and phytochemical analysis of crude extracts and essential oils from medicinal plants

We aimed to establish a phytochemical analysis of the crude extracts and performed GC-MS of the essential oils (EOs) of Eugenia uniflora L. (Myrtaceae) and Asteraceae species Baccharis dracunculifolia DC, Matricaria chamomilla L. and Vernonia polyanthes Less, as well as determining their antimicrobial activity. Establishment of the minimal inhibitory concentrations of the crude extracts and EOs against 16 Staphylococcus aureus and 16 Escherichia coli strains from human specimens was carried out using the dilution method in Mueller-Hinton agar. Some phenolic compounds with antimicrobial properties were established, and all EOs had a higher antimicrobial activity than the extracts. Matricaria chamomilla extract and E. uniflora EO were efficient against S. aureus strains, while E. uniflora and V. polyanthes extracts and V. polyanthes EO showed the best antimicrobial activity against E. coli strains. Staphylococcus aureus strains were more susceptible to the tested plant products than E. coli, but all natural products promoted antimicrobial growth inhibition.     

Influences of the Hydrophobicity of the Heme－binding Pocket on the Properties and Functions of Cytochrome b5 Mutants

The mutation sites of the four mutants F35Y, P40V, V45E and V45Y of cytochrome b5 are located at the edge of the heme-binding pocket. The solvent accessible areas of the “pocket inte-rior“ of the four mutants and the wild-type cytochrome b5 have been calculated based on their crystal structures at high resolu-tion. The change in the hydrophobicity of the heme-binding pocket resulting from the mutation can be quantitatively de-scribed using the difference of the solvent accessible area of the “pocket interior“ of each mutant from that of the wild-type cy-tochrome b5. The influences of the hydrophobicity of the heme-binding pocket on the protein stability and redox potential are discussed.     

基于气相色谱-质谱联用技术的高通量细胞表型分析方法

研究开发了一种基于96孔板培养和气相色谱-质谱联用(GC-MS)技术的高通量细胞表型分析方法。该方法分别以48种物质作为唯一能源对大肠杆菌进行培养,利用GC-MS研究野生型和yfcC基因改造大肠杆菌对各物质的分解代谢情况,实现高通量的细胞表型分析。结果显示,野生型和yfcC基因过表达大肠杆菌对14种物质的代谢能力有显著差异,yfcC基因过表达大肠杆菌对甘氨酸和柠檬酸的代谢能力明显强于野生型大肠杆菌,而对其他物质的代谢能力较弱,我们推测可能是由于yfcC基因促进乙醛酸代谢,导致yfcC过表达菌株对甘氨酸的代谢能力较强;野生型和yfcC基因敲除大肠杆菌间分解有显著差异的共16种物质,其中yfcC基因敲除大肠杆菌对丙氨酸、乳糖、肌醇和柠檬酸的代谢能力较强。该方法简单、高效,可以为未知基因功能研究提供更多代谢功能相关的参考数据。     

β-发夹多肽的全新设计和构象研究

引入跨股氨基酸队的方法进行β-发夹结构的设计,序列[R1G2T3F4W5V6d-p7S8V9N10Y11F12,β2]中包含二个氨基酸对V6V9和F4Y11,并以d-p7S8作转角来稳定结构.多肽合成采用Fmoc/Bu4固相合成方法.圆二色谱研究显示,β2在202 nm呈现正峰,在217.5 nm处呈负峰,为β转角和β折叠共同贡献的叠加,是典型的β-发夹结构圆二色谱特征.红外光谱研究进一步验证了圆二色谱的结果,表明β2在溶液中主要以β-发夹结构存在.     

Structural features responsible for GFPuv and S147P-GFP’s improved fluorescence

Green fluorescent protein (GFP) is used as a biological marker. It is a protein in the jellyfish, Aequorea victorea, which is found in the cold Pacific Northwest. Mature GFP, i.e. fully fluorescent GFP, is most efficiently formed at temperatures well below 37 °C. The GFPuv (F99S/M153T/V163A) and S147P-GFP mutants mature more efficiently at room temperature than wild-type GFP, and therefore result in increased fluorescence at room temperature. Computational methods have been used to examine whether the low-energy precyclized forms of these improved GFP-mutants are preorganized so that they can more efficiently form the chromophore than the wild-type and S65T-GFP. All mutations examined (S147P, F99S, M153T, V163A and F99S/M153T/V163A) more efficiently preorganize the immature precyclized forms of GFP for chromophore formation than immature wild-type GFP. It has been proposed that Arg96 is involved in chromophore formation. Our calculations suggest that the M153T and V163A mutations in GFPuv maybe partially responsible for the increased maturation efficiency observed in GFPuv because they improve the Arg96–Tyr66 interaction. The same is true for the S147P mutation in S147P-GFP.     

Enhanced Activity and Substrate Specificity by Site-Directed Mutagenesis for the P450 119 Peroxygenase Catalyzed Sulfoxidation of Thioanisole

P450 119 peroxygenase was found to catalyze the sulfoxidation of thioanisole and the sulfonation of sulfoxide in the presence of tert-butyl hydroperoxide (TBHP) for the first time with turnover rates of 1549 min⁻¹ and 196 min⁻¹ respectively. Several mutants were designed to improve the peroxygenation activity and thioanisole specificity by site-directed mutagenesis. The F153G/T213G mutant gave an increase of sulfoxide yield and a decrease of sulfone yield. Moreover the S148P/I161T/K199E/T214V mutant and the K199E mutant with acidic Glu residue contributed to improving the product ratio of sulfoxide to sulfone. Addition of short-alkyl-chain organic acids to the P450 119 peroxygenase-catalyzed sulfur oxidation of thioanisole was investigated. Octanoic acid was found to induce a preferred sulfoxidation of thioanisole catalyzed by the F153G/T213G mutant to give approximately 2.4-fold increase in turnover rate with a k_cat value of 3687 min⁻¹ relative to that of the wild-type, and by the F153G mutant to give the R-sulfoxide up to 30 % ee. The experimental control and the proposed mechanism for the P450 119 peroxygenase-catalyzed sulfoxidation of thioanisole in the presence of octanoic acid suggested that octanoic acid could partially occupy the substrate pocket; meanwhile the F153G mutation could enhance the substrate specificity, which could lead to efficiently regulate the spatial orientation of thioanisole and facilitate the formation of Compound I. This is the most effective catalytic system for the P450 119 peroxygenase-catalyzed sulfoxidation of thioanisole.     

Ligation independent cloning (LIC) as a rapid route to families of recombinant biocatalysts from sequenced prokaryotic genomes

A technique is presented for the high throughput generation of families of recombinant biocatalysts sourced from prokaryotic genomes, providing rapid access to the naturally evolved diversity of enzyme specificity for biocatalyst discovery. The method exploits a novel ligation independent cloning strategy, based on the locally engineered vector pET-YSBLIC and has been used for the rapid generation of a suite of expression plasmids containing genes encoding a family of six Baeyer-Villiger monooxygenases (BVMOs) from Mycobacterium tuberculosis H37Rv (MTb). The six resultant recombinant strains of E. coli B834 (DE3) expressing the genes were assayed for oxygenating activity in respect of the target reaction; the resolution of bicyclo[3.2.0]hept-2-en-6-one. The analysis of biotransformations catalysed by growing cells of E. coli was complicated by the production of indole in the reaction mixtures, possibly resulting from the in vivo activity of E. coli tryptophanase. Four of the recombinant strains expressing different BVMOs catalysed the oxidation of one or more of four screening substrates, well above controls that had been transformed with the re-ligated parent vector. One of the recombinant strains, E. coli B834 (DE3) pDB5, expressing the Rv3049c gene from MTb, was found to effectively resolve the target substrate, yielding a 19% yield of (1R, 5S)-(+)-bicyclo[3.2.0]hept-2-en-6-one with >95% enantiomeric excess in a 4 L fermentation reaction.     

Effect of mutations to amino acid A301 and F361 in thermostability and catalytic activity of the β-galactosidase from <Emphasis Type="Italic">Bacillus subtilis</Emphasis> VTCC-DVN-12-01

Background

Beta-galactosidase (EC 3.2.1.23), a commercially important enzyme, catalyses the hydrolysis of β-1,3- and β-1,4-galactosyl bonds of polymer or oligosaccharidesas well as transglycosylation of β-galactopyranosides. Due to catalytic properties; β-galactosidase might be useful in the milk industry to hydrolyze lactose and produce prebiotic GOS. The purpose of this study is to characterize β-galactosidase mutants from B. subtilis.

Results

Using error prone rolling circle amplification (epRCA) to characterize some random mutants of the β-galactosidase (LacA) from B. subtilisVTCC-DVN-12-01, amino acid A301 and F361 has been demonstrated significantly effect on hydrolysis activity of LacA. Mutants A301V and F361Y had markedly reduced hydrolysis activity to 23.69 and 43.22 %, respectively. Mutants the site-saturation of A301 reduced catalysis efficiency of LacA to 20–50 %, while the substitution of F361 by difference amino acids (except tyrosine) lost all of enzymatic activity, indicating that A301 and F361 are important for the catalytic function. Interestingly, the mutant F361Y exhibited enhanced significantly thermostability of enzyme at 45–50 °C. At 45 °C, LacA-361Y retained over 93 % of its original activity for 48 h of incubation, whereas LacA-WT and LacA-301Vwere lost completely after 12 and 24 h of incubation, respectively. The half-life times of LacA-361Y and LacA-301 V were about 26.8 and 2.4 times higher, respectively, in comparison to the half-life time of LacA-WT. At temperature optimum 50 °C, LacA-361Y shows more stable than LacA-WT and LacA-301 V, retaining 79.88 % of its original activities after 2 h of incubation, while the LacA-WT and LacA-301 V lost all essential activities. The half-life time of LacA-361Y was higher 12.7 and 9.39 times than that of LacA-WT and LacA-301 V, respectively. LacA-WT and mutant enzymes were stability at pH 5–9, retained over 90 % activity for 72 h of incubation at 30 °C. However, LacA-WT showed a little bit more stability than LacA-301 V and LacA-361Y at pH 4.

Conclusions

Our findings demonstrated that the amino acids A301V and F361 play important role in hydrolysis activity of β -galactosidase from B. subtilis. Specially, amino acid F361 had noteworthy effect on both catalytic and thermostability of LacA enzyme, suggesting that F361 is responsible for functional requirement of the GH42 family.

     

Effects of Val34Leu and Val35Leu polymorphism on the enzyme activity of the coagulation factor XIII-A

Change in fibrin stabilizing activity of factor XIII A subunit (FXIII-A) caused by a specific mutation, Val34Leu, is recently implicated to incidences of pathophysiology of thrombosis. In an effort to understand the effect of Val34Leu on enhanced catalytic role of FXIII-A, wild type human factor XIII A (HFXIII-A) and mutant HFXIII-A: HFXIII-A (V34L), HFXIII-A (V35L) and HFXIII-A (V34L/V35L) cDNA were expressed in E.coli system where the purified recombinant FXIII-A (gammaFXIII-A) showed a similar specific transglutaminase activity comparable to the human native FXIII-A from platelet. Using these gammaFXIII-A mutants, the activation kinetics by thrombin and the enzymatic properties of the activated gammaFXIII-A were characterized. gammaFXIII-A (V34L) and gammaFXIII-A (V34L/V35L) mutants were activated by thrombin much faster than those of wild type gammagFXIII-A and V35L variant. However, the activated gammaFXIII-A and mutants showed the identical catalytic efficiency as measured by in vitro assay. These results suggest that ready activation caused by a specific mutation of neighboring thrombin cleavage site(s) in the activation peptide of FXIII-A like V34L resulted in the real-time amount of the activated factor XIII-A that could influence the outcome of fibrin stabilization in vivo such as alpha2-plasmin inhibitor crosslinking to fibrin, a reaction known to be dependent on the initial concentration of active factor-XIII-A.     

A double point mutation in PCL-��1 (Y509A/F510A) enhances Y783 phosphorylation and inositol phospholipid-hydrolyzing activity upon EGF stimulation

Growth factor stimulation induces Y783 phosphorylation of phosphoinositide-specific PLC-γ1, and the subsequent activation of this enzyme in a cellular signaling cascade. Previously, we showed that a double point mutation, Y509A/F510A, of PLC-γ1, abolished interactions with translational elongation factor 1-α. Here, we report that the Y509A/F510A mutant PLC-γ1 displayed extremely high levels of Y783 phosphorylation and enhanced catalytic activity, compared to wild-type PLC-γ1, upon treatment of COS7 cells with EGF. In quiescent COS7 cells, the Y509A/F510A mutant PLC-γ1 exhibited a constitutive hydrolytic activity, whereas the wild-type counterpart displayed a basal level of activity. Upon treatment of COS7 cells with EGF, the Y783F mutation in Y509A/F510A PLC-γ1 (Y509A/F510A/Y783F triple mutant) cells also led to an enhanced catalytic activity, whereas Y783F mutation alone displayed a basal level of activity. Our results collectively suggest that the Y509A/F510A mutant is more susceptible to receptor tyrosine kinase-induced Y783 phosphorylation than is wild-type PLC-γ1, but no longer requires Y783 phosphorylation step for the Y509A/F510A mutant PLC-γ1 activation in vivo.     

CLONING IN Yersinia enterocolitica OF K99 ANTIGEN GENE FROM Escherichia coli

A recombinant plasmid pFS239 containing the geoe coding for K99 antigen of Escherichia coli and wide-host-range plasmid pKT230 has been cloned in E. coli C600. pFS239 has been transferred to Yersinia enterocolitica strains D29, L15 and L15 (pYV15) through triparental mating. In Y. enterocolitica transconjugants the expression of VW antigens and calcium dependence which represent the propertics associated with the virulence plastmid of Y. enterocolitica remains unchanged.