The Conformational Transitions and Dynamics of Burkholderia cepacia Lipase Regulated by Water-Oil Interfaces.

Structural dynamics and conformational transitions are crucial for the activities of enzymes. As one of the most widely used industrial biocatalysts, lipase could be activated by the water-oil interfaces. The interface activations were believed to be dominated by the close-to-open transitions of the lid subdomains. However, the detailed mechanism and the roles of structure transitions are still under debate. In this study, the dynamic structures and conformational transitions of Burkholderia cepacia lipase (LipA) were investigated by combining all-atom molecular dynamics simulations, enhanced sampling simulation, and spectrophotometric assay experiments. The conformational transitions between the lid-open and lid-closed states of LipA in aqueous solution are directly observed by the computational simulation methods. The interactions between the hydrophobic residues on the two lid-subdomains are the driven forces for the LipA closing. Meanwhile, the hydrophobic environment provided by the oil interfaces would separate the interactions between the lid-subdomains and promote the structure opening of LipA. Moreover, our studies demonstrate the opening of the lids structure is insufficient to initiate the interfacial activation, providing explanations for the inability of interfacial activation of many lipases with lid structures.

Quantitative and direct serum albumin detection by label-free SERS using tunable hydroxyapatite nanostructure for prostate cancer detection.

With the aid of good biocompatibility and stability with hydroxyapatite (HAp) in protein separation and adsorption fields, we developed a novel extraction-isolation albumin analysis method by relying on the specific adsorption capacity of HAp, combining with surface-enhanced Raman spectroscopy (SERS) for prostate cancer screening. Two different nanostructures of HAp particles, including the HAp flower and HAp sphere, were synthesized with a hydrothermal method, and the targeted binding and extraction abilities of serum albumin of these two HAp particles were compared. By changing the morphology of the nanostructure, the albumin-adsorption capacity of HAp varied significantly. Compared with spherical HAp particles, HAp flower particles have more albumin binding sites per unit area. Thus, the HAp flower displayed the superior capacity for adsorption-release of albumin, which was further employed for clinical prostate cancer screening. Based on the superior adsorption-extraction ability of albumin of HAp flower, serum albumin was adsorbed and extracted by HAp flower from serum samples of prostate cancer patients (n = 30) and healthy volunteers (n = 30), and mixed with silver colloids to perform SERS spectral analysis. The partial least square-support vector machines (PLS-SVM) model is used to analyze the obtained serum albumin SERS spectra and establish the diagnostic model, the diagnostic accuracy was up to 95.00% for differentiating the normal volunteer from prostate patient groups. The results demonstrate that the PLS-SVM model provides superior performance in the classification of a prostate cancer diagnosis. Due to the advantages of simplicity and rapidness, the HAp flower-adsorbed-released albumin combined with SERS was expected to become a promising tool for prostate cancer detection.

Enzymatic synthesis of 2-phenethyl acetate in water catalyzed by an immobilized acyltransferase from Mycobacterium smegmatis.

Although water is an ideal green solvent for organic synthesis, it is difficult for most biocatalysts to carry out transesterification reactions in water because of the reversible hydrolysis reaction. 3D structural characteristics and the microenvironment of an enzyme has an important effect on its selectivity for the transesterification reaction over the hydrolysis reaction. A novel 2-phenethyl acetate synthesis technology was developed using acyltransferase (EC 3.1.1.2) from Mycobacterium smegmatis (MsAcT) in water. Firstly, MsAcT was entrapped in a tetramethoxysilane gel network and the immobilization process of MsAcT increased its selectivity for the transesterification reaction over the hydrolysis reaction by 6.33-fold. Then, the synthesis technology of 2-phenethyl acetate using the immobilized MsAcT in water was optimized as follows: vinyl acetate was used as acyl donor, the molar ratio of vinyl acetate to 2-phenylethyl alcohol was 2 : 1, and the water content was 80% (w/w). The reaction was carried out at 40 °C for 30 min and conversion rate reached 99.17%. The immobilized MsAcT could be recycled for 10 batches. The synthesis method of 2-phenethyl acetate using MsAcT as a biocatalyst in water is a prospective green process technology.

Phosphorylation Regulation on the Homo-Dimeric Binding of Transactive Response DNA-Binding Protein.

The dimerization of transactive response DNA-binding protein of 43 kDa (TDP-43) is crucial for the RNA metabolism, and the higher-order aggregation of TDP-43 would induce several neurodegenerative diseases. The dimerization and aggregation of TDP-43 are regulated by the phosphorylation on its N-terminal domain (NTD). Understanding the regulation mechanism of TDP-43 NTD dimerization is crucial for the preventing of harmful aggregation and the associated diseases. In this study, the dimerization processes of wild-type (WT), phosphorylated S48 (pS48), and phosphomimic S48E mutation (S48E) of TDP-43 NTD are characterized by the enhanced sampling technology. Our results show that the phosphorylation not only shift the conformation population of bound and unbound state of TDP-43 NTD, but also would regulate the dimerization processes, including increase the binding free-energy barrier. The phosphomimic mutation would also shift the conformational space of TDP-43 NTD dimer to the unbound structures; however, the thermodynamic and kinetic properties of the dimerization processes between the phosphorylated and phosphomimic mutant systems are distinct, which reminds us to carefully study the phosphorylation regulation by using the phosphomimic mutations.

Screening of perhydrolases to optimize glucose oxidase-perhydrolase-in situ chemical oxidation cascade reaction system and its application in melanin decolorization.

A novel glucose oxidase (GOD)-perhydrolase-in situ chemical oxidation (ISCO) cascade reaction system was designed, optimized, and verified the operation feasibility in this research. Among the determined four perhydrolases, acyltransferase from Mycobacterium smegmatis (MsAcT) displayed the highest specific activity for perhydrolysis reaction (76.4 U/mg) and the lowest Km value to hydrogen peroxide (13.9 mmol/L). GOD-MsAcT cascade reaction system also displayed high catalytic efficiency. Under the optimal parameters (50:1 activity unit ratio of GOD to MsAcT, pH 8.0, 50 mmol/L of ß-d-glucose, and 15 mmol/L of glyceryl triacetate), the melanin decolorization rate using GOD-MsAcT-ISCO cascade reaction system reached 86.8 %. Kinetics of GOD-MsAcT-ISCO cascade reaction system for melanin decolorization fitted the kinetic model of Boltzmann sigmoid. As a substitutive skin whitening technology, GOD-MsAcT-ISCO cascade reaction system displayed an excellent application prospect.

Conceptual design of a high-speed electromagnetic switch for a modified flux-coupling-type SFCL and its application in renewable energy system.

The modified flux-coupling-type superconducting fault current (SFCL) is a high-efficient electrical auxiliary device, whose basic function is to suppress the short-circuit current by controlling the magnetic path through a high-speed switch. In this paper, the high-speed switch is based on electromagnetic repulsion mechanism, and its conceptual design is carried out to promote the application of the modified SFCL. Regarding that the switch which is consisting of a mobile copper disc, two fixed opening and closing coils, the computational method for the electromagnetic force is discussed, and also the dynamic mathematical model including circuit equation, magnetic field equation as well as mechanical motion equation is theoretically deduced. According to the mathematical modeling and calculation of characteristic parameters, a feasible design scheme is presented, and the high-speed switch's response time can be less than 0.5 ms. For that the modified SFCL is equipped with this high-speed switch, the SFCL's application in a 10 kV micro-grid system with multiple renewable energy sources are assessed in the MATLAB software. The simulations are well able to affirm the SFCL's performance behaviors.

Cell-bound lipases from Burkholderia sp. ZYB002: gene sequence analysis, expression, enzymatic characterization, and 3D structural model.

BACKGROUND: The whole-cell lipase from Burkholderia cepacia has been used as a biocatalyst in organic synthesis. However, there is no report in the literature on the component or the gene sequence of the cell-bound lipase from this species. Qualitative analysis of the cell-bound lipase would help to illuminate the regulation mechanism of gene expression and further improve the yield of the cell-bound lipase by gene engineering. RESULTS: Three predictive cell-bound lipases, lipA, lipC21 and lipC24, from Burkholderia sp. ZYB002 were cloned and expressed in E. coli. Both LipA and LipC24 displayed the lipase activity. LipC24 was a novel mesophilic enzyme and displayed preference for medium-chain-length acyl groups (C10-C14). The 3D structural model of LipC24 revealed the open Y-type active site. LipA displayed 96 % amino acid sequence identity with the known extracellular lipase. lipA-inactivation and lipC24-inactivation decreased the total cell-bound lipase activity of Burkholderia sp. ZYB002 by 42 % and 14 %, respectively. CONCLUSIONS: The cell-bound lipase activity from Burkholderia sp. ZYB002 originated from a multi-enzyme mixture with LipA as the main component. LipC24 was a novel lipase and displayed different enzymatic characteristics and structural model with LipA. Besides LipA and LipC24, other type of the cell-bound lipases (or esterases) should exist.

[Screening for mutants with thermostabe lipase A from Burkholderia sp. ZYB002].

OBJECTIVE: We improved the thermostability of LipA from Burkholderia cecapia ZYB002 by protein engineering technology to expand the application of lipase LipA. METHOD: On the basis of B-factor value of lipase LipA, series of potential mutation hotspots were selected for iterative saturation mutagenesis and the corresponding small mutation gene libraries were then constructed to screen the hyperthermal variants. RESULTS: From the above mutation libraries, we obtained a series of mutants whose enzyme half-life at 55 degrees C increased by 1.7 to 2.2-fold. CONCLUSION: B-factor iterative test (B-FIT) is feasible to mutate thermostable strains.

[Cloning, expression and characterization of a lipase gene, lipC24, from Burkholderia sp. ZYB002].

OBJECTIVE: We cloned a lipase gene, lipC24, from Burkholderia sp. ZYB002 and characterized the recombinant lipase LipC24. METHOD: Based on the known genomic DNA sequence from Burkholderia cecapia JK321, we designed a pair of specific primers for the lipC24 gene and then obtained the full length of lipC24 gene. The lipC24 gene fragment enconding the mature peptide LipC24 was then subcloned into expression plasmid, pACYC-Duet-lipB, and expressed in E. coli. The recombinant protein, LipC24, was purified to homogeneity by HisTrap HP chromatography column and HiTrap DEAE FF chromatography column. RESULTS: We expressed the lipC24 gene from Burkholderia sp. ZYB002 in E. coli Origami 2(DE3). Nucleotide sequencing revealed that the lipC24 gene had an open reading frame of 1317 bp, and the deduced amino acid sequence of LipC24 corresponded to 438 amino acid residues, including a conserved -G-X1-S-X2-G- motif. The relative molecular weight of the purified LipC24 was about 45 kDa. The purified LipC24 displayed hydrolysis activity to various 4-nitrophenyl esters and substrate preference for the medium chain length 4-nitrophenyl-esters. The optimal temperature was 40°C and the optimal pH was 7.5. The lipase was stable between pH 7.0 and 8.0 for 24 hours. However, the half-life was only 16 min at 40°C. CONCLUSION: The LipC24 was a 45 kDa protein, a mesotherm and neutral lipase.

Production and characteristics of the whole-cell lipase from organic solvent tolerant Burkholderia sp. ZYB002.

The thermostable and organic solvent tolerant whole-cell lipase (WCL) was produced by Burkholderia sp. ZYB002 with broad spectrum organic solvent tolerance. The production medium of the WCL was primarily optimized, which resulted in the maximum activity of 22.8 U/mL and the 5.1-fold increase of the WCL yield. The optimized culture medium was as follows (% w/v or v/v): soybean meal 2, soybean oil 0.5, manganese sulfate 0.1, K(2)HPO(4) 0.1, olive oil 0.5, initial pH 6.0, inoculum density 2, liquid volume 35 mL in 250-mL Erlenmeyer flask, and incubation time 24 h. The biochemical characterization of the WCL from Burkholderia sp. ZYB002 was determined, and the results showed that the optimal pH and temperature for lipolytic activity of the WCL was 8.0 and 65°C, respectively. The WCL was stable at temperature up to 70°C for 1 h and retained 79.2% of its original activity. The WCL was highly stable in the pH range from 3.0 to 8.5 for 6 h. Ca(2+), K(+), Na(+), NO (3) (-) , etc. ions stimulated its lipolytic activity, whereas Zn(2+) ion caused inhibition effect. The WCL was also relatively stable in n-butanol at a final concentration of 50% (v/v) for 24 h. However, the WCL was strongly inhibited in Triton X-100 at a final concentration of 10% (v/v). The WCL with thermal resistance and organic solvent tolerance showed its great potential in various green industrial chemical processes.

Construction of Aspergillus niger lipase mutants with oil-water interface independence.

Based on previous bioinformational analytical results [Shu ZY, et al. Biotechnol Prog 2009;25:409-16], four A. niger lipase (ANL) mutants, ANL-Ser84Gly, ANL-Asp99Pro, ANL-Lys108Glu and ANL-EαH (obtained by replacing the lid domain of ANL with the corresponding domain from A. niger feruloyl esterase), were constructed to screen out ANL mutants with oil-water interface independence. ANL-S84G displayed a pronounced interfacial activation, while ANL-D99P and ANL-K108E displayed no interfacial activation. The specific activity of ANL-S84G towards p-nitrophenyl esters decreased from 29.8% to 76.5% compared with that of ANL, while the specific activity of ANL-D99P towards p-nitrophenyl palmitate increased 2.2-fold. The thermostability of ANL-K108E was almost unchanged, while the thermostability of ANL-S84G and ANL-D99P significantly decreased compared with that of ANL. The construction of oil-water interface-independent ANL mutants would help to further understand the mechanism of lipase interfacial activation.

[Construction of Aspergillus niger lipase mutants with oil-water interface independence].

Based on previous bioinformational analysis results, two Aspergillus niger lipase (ANL) mutants, ANL-Ser84Gly and ANL-Asp99Pro were constructed to screen ANL mutants with oil-water interface independence. ANL-Ser84Gly still displayed a pronounced interfacial activation, while ANL-Asp99Pro displayed no interfacial activation. The specific activity of ANL-Ser84Gly towards p-nitrophenyl palmitate (-myristate, -laurate and -decanoate) decreased by 29.8% (53.1, 60.1 and 77.1, respectively) than that of ANL, while the specific activity of ANL-Asp99Pro towards p-nitrophenyl palmitate increased by 2.2-fold. The mutation in the hinge region at both sides of the lid domain also destabilized various secondary structure factors of ANL-S84G and ANL-D99P, which resulted in a substantial decrease in thermostability. The achievement to construct oil-water interface-independent ANL mutants would help to further understand lipase interfacial activation mechanism.

A rapid and efficient method for directed screening of lipase-producing Burkholderia cepacia complex strains with organic solvent tolerance from rhizosphere.

Lipase from Burkholderia cepacia strain is one of the most versatile biocatalysts and is used widely in many biotechnological application fields including detergent additives, the resolution of racemic compounds, etc. Based on the known whole genomic information of B. cepacia strain, both ampicillin and kanamycin were added to the TB-T medium to screen B. cepacia complex stains from rhizosphere soil samples. The selected colonies from the modified TB-T medium were then qualitatively determined the ability to produce extracellular lipase on the rhodamine B-olive oil agar plates. A total of 35 lipolytic pseudo-B. cepacia complex strains were isolated and the positive rate of lipolytic bacteria was 65%. Among them, 15 pseudo-B. cepacia complex strains showed tolerance to benzene, n-hexane and n-heptane at concentration of 10% (V/V) and were identified by the recA gene sequence. All of the 14 lipolytic bacteria were identified as B. cepacia complex strains except that the recA gene sequence of one lipolytic bacterium, strain ZMB009, was not obtained.

Aspergillus niger lipase: Heterologous expression in Pichia pastoris, molecular modeling prediction and the importance of the hinge domains at both sides of the lid domain to interfacial activation.

Aspergillus niger lipase (ANL) is an important biocatalyst in the food processing industry. However, there is no report of its detailed three-dimensional structure because of difficulties in crystallization. In this article, based on experimental data and bioinformational analysis results, the structural features of ANL were simulated. Firstly, two recombinant ANLs expressed in Pichia pastoris were purified to homogeneity and their corresponding secondary structure compositions were determined by circular dichroism spectra. Secondly, the primary structure, the secondary structure and the three-dimensional structure of ANL were modeled by comparison with homologous lipases with known three-dimensional structures using the BioEdit software, lipase engineering database (http://www.led.uni-stuttgart.de/), PSIPRED server and SwissModel server. The predicted molecular structure of ANL presented typical features of the alpha/beta hydrolase fold including positioning of the putative catalytic triad residues and the GXSXG signature motif. Comparison of the predicted three-dimensional structure of ANL with the X-ray three-dimensional structure of A. niger feruloyl esterase showed that the functional difference of interfacial activation between lipase and esterase was concerned with the difference in position of the lid. Our three-dimensional model of ANL helps to modify lipase structure by protein engineering, which will further expand the scope of application of ANL.

Expressed sequence tag analysis of marine fungus Schizochytrium producing docosahexaenoic acid.

To investigate docosahexaenoic acid (DHA, C22:6n-3) biosynthesis pathway in marine fungus Schizochytrium sp. FJU-512, a cDNA library of the fungus was constructed and analyzed. The titers of primary library were up to 5.0 x 10(6). A total of 4005 ESTs were assembled into 1947 unigenes. Sequences annotation and function analysis were carried out by using Blast, GO and KEGG programs. Compared with other eukaryote genomes, Schizochytrium sp. FJU-512 ESTs shared at least 26.6% genes with Arabidopsis thaliana (E < or = 10(-10)). The cDNA (Contig46, assembled by EH401977 and EH404532) and EH40321 were found to encode serine/threonine protein phosphatase type 1 and cell division control protein 2 which were involved in successive binary cell division. Notably, the key enzymes involved in biosynthesis of fatty acid via polyketide synthases (PKS) such as beta-ketoacyl synthase, beta-ketoacyl reductase, hydroxyacyl dehydrogenase, enoyl-CoA hydratase/isomerase, and enoyl reductase were found in the cDNA library. The results indicated that DHA synthesis in Schizochytrium sp. FJU-512 had undergone PKS pathway.

[Cloning and expression of two elongase genes involved in the biosynthesis of docosahexaenoic acid in Thraustochytrium sp. FJN-10].

Docosahexaenoic acid (DHA C22:6n-3), a typical long chain polyunsaturated fatty acids (PUFAs) has many positive effects on diseases such as artherosclerosis, hypertriglyceridemia, hypertension and cancers. Marine fungi, especially Thraustochytrium spp. producing much DHA can serve as model organisms for explaining the mechanism on the biosynthesis of PUFA. We described two elongase genes (TFD6 and TFD5) involved in the biosynthesis of DHA in Thraustochytrium sp. FJN-10 was cloned by using reverse transcription PCR and rapid amplification of cDNA ends. TFD6 cDNA was 816 bp in length and encoded a protein of 271 amino acids. TFD5 cDNA was 831 bp in length and encoded a protein of 276 amino acids. Transmembrane analysis revealed that TFD6 contained five transmembrane domains while TFD5 contained seven. Tertiary structures of TFD6, TFD5 elongases were predicted by HHMMSTR (Hidden markov model for local sequence-structure) model and Rosetta program. Alignment of TFD6, TFD5 with other elongases showed that both of them shared an HXXHH conserved histidine-rich motif. Phylogenetic analysis showed that TFD6 was the closest to Thraustochytrium 66 elongase, while TFD5 was the closest to Thraustochytrium sp. delta5 elongase. TFD6 and TFD5 were subcloned into the Hind III/Xba I restriction site of pYES2 vector respectively. Recombined plasmids were transformed into Saccharomyces cerevisiae using lithium acetate method. Gas chromatography analysis showed that TFD6 could elongate C18:3n-3 to C20:3n-3 while TFD5 could elongate C20:5n-3 to C22:5n-3.

Aspergillus niger lipase: gene cloning, over-expression in Escherichia coli and in vitro refolding.

From the N-terminal amino acid sequence of the lipase from Aspergillus niger F044, a potential homologous gene A84689 to the lipanl (the gene encoding the lipase from Aspergillus niger F044) was identified. A pair of primers were designed according to the nucleotide sequence of A84689, and the lipanl was cloned by PCR. Nucleotide sequencing revealed that the lipanl has an ORF of 1,044 bp, containing three introns. The deduced amino acid sequence corresponds to 297 amino acid residues. The cloned cDNA fragment encoding the mature lipase from Aspergillus niger F044 was over-expressed in Escherichia coli BL21(De3) and the recombinant protein was refolded in vitro by dilution followed by DEAE Sepharose Fast Flow chromatography.

[Purification and characterization of a lipase from Aspergillus niger F044].

A lipase from Aspergillus niger F044 was purified to homogeneity using ammonium sulfate precipitation, dialysis, DEAE-Sepharose Fast Flow anion exchange chromatography and Sephadex G-75 gel filtration chromatography. This purification protocol resulted in a 73.71-fold purification of lipase with 33.99% final yield, and the relative molecular weight of the enzyme was determined to be approximately 35-40kD using SDS-PAGE. The optimum pH and temperature for lipolytic activity of the lipase was 7.0 and 45 degrees C , respectively. It was extremely stable at 60 degrees C and retained 98.70% of its original activity for 30min. The stability declined rapidly as soon as the temperature rose over 65 degrees C . The lipase was highly stable in the pH range from 2.0 to 9.0 for 4h. Ca2+ and Mg2+ ions stimulated lipolytic activity, whereas Mn2+ , Fe2+ and Zn2+ ions caused inhibition. The values of Km and Vmax calculated from the Lineweaver-Burk plot using pNPP as hydrolysis substrate were 7.37mmol/L and 25.91 micromol/(min x mg), respectively. The N-terminal sequence of the lipase was Ser/Glu/His-Val-Ser-Thr-Ser-Thr-Leu-Asp-Glu-Leu-Gln-Leu-Phe-Ala-Gln, which is highly homogeneity with that of lipase, as reported by Torossian.