A Novel α-Glucosidase Inhibitor Protein from the Rhizomes of <Emphasis Type="Italic">Zingiber ottensii</Emphasis> Valeton

The objective of this study was to investigate a new protein with α-glucosidase inhibitory activity from the rhizomes of Zingiber ottensii. With a simple salting-out technique followed by single-step anion-exchange purification, the protein was successfully purified from the rhizomes. This protein was found to have three likely sub-unit types, 32.5, 15.2, and 13.8 kDa, as revealed by native and reducing SDS-PAGE analysis. Determination of the kinetics of the inhibition of α-glucosidase from Saccharomyces cerevisiae by standard enzymatic methods indicated the maximum percent inhibition; IC₅₀ and K _i of this protein were 77.5%, 30.15 μg/ml, and 140 μmol, while the K _m and V _max were 2.35 μmol and 0.11 mM/min, respectively. The inhibitory action was pH-independent within the pH range 2–10, but was potentially affected by buffer salts, and was relatively temperature-stable between 4–35 °C, with a maximum activity at 65 °C. The amino acid sequence of an internal fragment of this purified Z. ottensii rhizomal protein had a similarity to the sequence from the plant cysteine proteinase family. Although this α-glucosidase inhibitory protein was purified from Z. ottensii rhizomes and preliminarily characterized, further studies are needed prior to firm applications being envisaged.     

Analysis, purification and properties of a 50,000-dalton membrane-associated phosphoprotein from human platelets

Recently, the development of a monospecific antiserum against a 46,000/50,000-dalton membrane protein from human platelets which was stoichiometrically and reversibly phosphorylated in intact human platelets in response to vasodilators was reported. Using this antiserum, the subcellular distribution and the purification of this vasodilator-stimulated phosphoprotein (VASP) from human platelets has now been analysed. The VASP of human platelets is primarily a membrane-associated protein and can be purified to apparent homogeneity by salt extraction and sequential ion-exchange and dye-ligand chromatography with a purification factor of 1200 and a yield of 13%. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis under reducing and non-reducing conditions indicated that purified monomers of this VASP are linked by interchain disulphide bonding.     

Large-scale purification of human granulocyte-macrophage colony-stimulating factor expressed in <Emphasis Type="Italic">Bombyx mori</Emphasis> pupae

Human granulocyte-macrophage colony-stimulating factor (hGM-CSF) acts on many different kinds of cells, including monocytes, macrophages, granulocytes, eosinophils, and multipotential stem cells. To explore further explore pharmaceutical action, we expressed hGM-CSF by the Bombyx mori nucleopolyhedrovirus expression system in silkworm pupae. However, purifying recombinant proteins from silkworm pupae on a large scale has been a big challenge. To establish purification methods suitable for mass production, we tried two crude preparation methods: (NH₄)₂SO₄ fractional precipitation and isoelectric precipitation with a combination of gel filtration andion-exchange chromatography. The isoelectric precipitation method was found to be more efficient. With this method, we eventually obtained approx 11.7 mg of 95% pure product from 1000 g of infected silkworm pupae. The recovery of purified protein was greatly increased, by approx 40%, compared with the other method. The biologic activity of this protein was determined up to 9.0×10⁶ colony-forming units/mg in the final purified product.     

Analysis of subcellular surface structure, function and dynamics

Analytics of single biological cells allows quantitative investigation from a structural, functional and dynamical point of view and opens novel possibilities to an unamplified subcellular analysis. In this article, we report on three different experimental methods and their applications to single cellular systems with a subcellular sensitivity down to the single molecule level. First, the subcellular surface structure of living bacteria (Corynebacterium glutamicum) was investigated with atomic force microscopy (AFM) at the resolution of individual surface layer (S-layer) proteins; discrimination of bacterial strains that lack the expression of hexagonally packed surface layer proteins was possible. Second, quantitative measurement of individual recognition events of membrane-bound receptors on living B-cells was achieved in single cell manipulation and probing experiments with optical tweezers (OT) force spectroscopy. And third, intracellular dynamics of translocating photoactivatable GFP in plant protoplasts (Nicotiana tabacum BY-2) was quantitatively monitored by two-photon laser scanning microscopy (2PLSM).     

Refolding and purification of rhNTA protein by chromatography

RhNTA protein is a new thrombolytic agent which has potential medicinal and commercial value. Protein refolding is a bottleneck for large‐scale production of valuable proteins expressed as inclusion bodies in Escherichia coli. The denatured rhNTA protein was refolded by an improved size‐exclusion chromatography refolding process achieved by combining an increasing arginine gradient and a decreasing urea gradient (two gradients) with a size‐exclusion chromatography refolding system. The refolding of denatured rhNTA protein showed that this method could significantly increase the activity recovery of protein at high protein concentration. The activity recovery of 37% was obtained from the initial rhNTA protein concentration up to 20 mg/mL. After refolding by two‐gradient size‐exclusion chromatography refolding processes, the refolded rhNTA was purified by ion‐exchange and affinity chromatography. The purified rhNTA protein showed one band in SDS‐PAGE and the specific activity of purified rhNTA protein was 110,000 U/mg. Copyright © 2008 John Wiley & Sons, Ltd.     

Using Nearest Feature Line and Tunable Nearest Neighbor methods for prediction of protein subcellular locations

The subcellular location of a protein is closely correlated with it biological function. In this paper, two new pattern classification methods termed as Nearest Feature Line (NFL) and Tunable Nearest Neighbor (TNN) have been introduced to predict the subcellular location of proteins based on their amino acid composition alone. The simulation experiments were performed with the jackknife test on a previously constructed data set, which consists of 2,427 eukaryotic and 997 prokaryotic proteins. All protein sequences in the data set fall into four eukaryotic subcellular locations and three prokaryotic subcellular locations. The NFL classifier reached the total prediction accuracies of 82.5% for the eukaryotic proteins and 91.0% for the prokaryotic proteins. The TNN classifier reached the total prediction accuracies of 83.6 and 92.2%, respectively. It is clear that high prediction accuracies have been achieved. Compared with Support Vector Machine (SVM) and Nearest Neighbor methods, these two methods display similar or even higher prediction accuracies. Hence, we conclude that NFL and TNN can be used as complementary methods for prediction of protein subcellular locations.     

Cloning, Expression, and Identification of a Novel Extracellular Cold-Adapted Alkaline Protease Gene of the Marine Bacterium Strain YS-80-122

As one of the most important groups of industrial enzymes, cold-adapted protease has been studied widely. An extracellular cold-adapted alkaline protease metalloproteinase (MP), produced by a marine bacterium strain YS-80-122, has been purified. The NH₂-amino acid sequence of the purified alkaline protease MP was ANGTSSAFTQ, which was identical to that of the serralysin from Pseudomonas sp. “TAC II 18”. The MP structural gene (lupA gene) was cloned by inverse PCR, and the open reading frame of 1,443 bp encoded a 463 amino acid protein (without signal peptide). Sequence alignment reveals that the alkaline protease MP belongs to the serralysin-type metalloproteases. The recombinant protein LupA was expressed in Escherichia coli, and Western blotting confirmed that the LupA was homologous to the cold-adapted alkaline protease MP.     

Cloning and Expression of Che a 1, the Major Allergen of <Emphasis Type="Italic">Chenopodium album</Emphasis> in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Chenopodium album is a weedy annual plant in the genus Chenopodium. C. album pollen represents a predominant allergen source in Iran. The main C. album pollen allergens have been described as Che a 1, Che a 2, and Che a 3. The aim of this work was to clone the Che a 1 in Escherichia coli to establish a system for overproduction of the recombinant Che a 1 (rChe a 1). In order to clone this allergen, the pollens were subjected to RNA extraction. A full-length fragment encoding Che a 1 was prepared by polymerase chain reaction amplification of the first-strand cDNA synthesized from extracted RNA. Cloning was carried out by inserting the cDNA into the pET21b (+) vector, thereafter the construct was transformed into E. coli Top10 cells and expression of the protein was induced by IPTG. The rChe a 1 was purified using histidine tag in recombinant protein by means of Ni–NTA affinity chromatography. IgE immunoblotting, ELISA, and inhibition ELISA were done to evaluate IgE binding of the purified protein. In conclusion, the cDNA for the major allergen of the C. album pollen, Che a 1, was successfully cloned and rChe a 1 was purified. Inhibition assays demonstrated allergic subjects sera reacted with rChe a 1 similar to natural Che a 1 in crude extract of C. album pollen. This study is the first report of using the E. coli as a prokaryotic system for Che a 1 cloning and production of rChe a 1.     

Isolation,Purification, and Properties of a Novel Small Heat Shock Protein from the Hyperthermophile <Emphasis Type="Italic">Sulfolobus solfataricus</Emphasis>

The isolation, purification, and properties of a putative small heat shock protein (sHsp), named SsHSP14.1, from the hyperthermophilic archaeon Sulfolobus solfataricus have been investigated. The sHsp was successfully expressed and purified from Escherichia coli. In vivo chaperone function of SsHSP14.1 for preventing aggregation of proteins during heating was investigated. It was found that recombinant SsHSP14.1 with a molecular mass of 17.8 kDa prevented E. coli proteins from aggregating in vivo at 50 °C. This result suggested that SsHSP14.1 confers a survival advantage on mesophilic bacteria by preventing protein aggregation at supraoptimal temperatures. In vitro, the purified SsHSP14.1 protein was able to prevent Candida antarctica lipase B from aggregation for up to 60 min at 80 °C. Moreover, the SsHSP14.1 enhanced thermostability of bromelain extending its half-life at 55 °C by 67%.     

PCR-based Gene Synthesis,Molecular Cloning,High Level Expression,Purification, and Characterization of Novel Antimicrobial Peptide,Brevinin-2R,in <Emphasis Type="Italic">Escherichia Coli</Emphasis>

Brevinin-2R, a member of a new family of antimicrobial peptides isolated from the skin of Rana ridibunda, displays antimicrobial activity against bacteria and fungi. In this study, we have used an assembly PCR method for the fast and extremely accurate synthesis of the brevinin-2R gene. A total of six primers were assembled in a single step PCR, and the assembly was then amplified by PCR to produce the final gene. The synthetic gene was cloned into the pET32a (+) vector to allow the expression of brevinin-2R as a Trx fusion protein in Escherichia coli. The results indicated that the expression level of the fusion protein could reach up to 25% of the total cell proteins. The expression products could be easily purified by Ni-NTA chromatography and released from the fusion protein by factor Xa protease. The peptide displayed antimicrobial activity similar to that of the purified brevinin that was reported earlier. This method allows the fast synthesis of a gene that optimized the overexpression in the E. coli system and production of sufficiently large amounts of peptide for functional and structural characterizations.     

Nuclear proteome analysis of undifferentiated mouse embryonic stem and germ cells

Embryonic stem cells (ESCs) and embryonic germ cells (EGCs) provide exciting models for understanding the underlying mechanisms that make a cell pluripotent. Indeed, such understanding would enable dedifferentiation and reprogrammation of any cell type from a patient needing a cell therapy treatment. Proteome analysis has emerged as an important technology for deciphering these biological processes and thereby ESC and EGC proteomes are increasingly studied. Nevertheless, their nuclear proteomes have only been poorly investigated up to now. In order to investigate signaling pathways potentially involved in pluripotency, proteomic analyses have been performed on mouse ESC and EGC nuclear proteins. Nuclei from ESCs and EGCs at undifferentiated stage were purified by subcellular fractionation. After 2‐D separation, a subtractive strategy (subtracting culture environment contaminating spots) was applied and a comparison of ESC, (8.5 day post coïtum (dpc))‐EGC and (11.5 dpc)‐EGC specific nuclear proteomes was performed. A total of 33 ESC, 53 (8.5 dpc)‐EGC, and 36 (11.5 dpc)‐EGC spots were identified by MALDI‐TOF‐MS and/or nano‐LC‐MS/MS. This approach led to the identification of two isoforms (with and without N‐terminal acetylation) of a known pluripotency marker, namely developmental pluripotency associated 5 (DPPA5), which has never been identified before in 2‐D gel‐MS studies of ESCs and EGCs. Furthermore, we demonstrated the efficiency of our subtracting strategy, in association with a nuclear subfractionation by the identification of a new protein (protein arginine N‐methyltransferase 7; PRMT7) behaving as proteins involved in pluripotency.     

Purification and characterization of an exoinulinase from Aspergillus fumigatus

An extracellular exoinulinase was purified from the crude extract of Aspergillus fumigatus by ammonium sulfate precipitation, followed by successive chromatographies on DEAE-Sephacel, Sephacryl S-200, concanavalin A-linked amino-activated silica, and Sepharose 6B columns. The enzyme was purified 25-fold, and the specific activity of the purified enzyme was 171 IU/mg of protein. Gel filtration chromatography revealed a molecular weight of about 200 kDa, and native polyacrylamide gel electrophoresis (PAGE) showed an electrophoretic mobility corresponding to a molecular weight of about 176.5 kDa. Sodium dodecyl sulfate-PAGE analysis revealed three closely moving bands of about 66, 62.7, and 59.4 kDa, thus indicating the heterotrimeric nature of this enzyme. The purified enzyme appeared as a single band on isoelectric focusing, with a pI of about 8.8. The enzyme activity was maximum at pH 5.5 and was stable over a pH range of 4.0–9.5, and the optimum temperature for enzyme activity was 60°C. The purified enzyme retained 35.9 and 25.8% activities after 4 h at 50 and 55°C, respectively. The inulin hydrolysis activity was completely abolished with 1 mM Hg⁺⁺, whereas EDTA inhibited about 63% activity. As compared to sucrose, stachyose, and raffinose, the purified enzyme had lower K _m (0.25 mM) and higher V _max (333.3 IU/mg) values for inulin.     

BOP: A basic phenylalanine‐rich oligo‐peptide located on the surface of glycolate oxidase influences its pI values

Glycolate oxidase (GO) consists of identical subunits and therefore should show one definite pI value, but the isolated GO exhibited a range of pIs. This study investigated the underlying cause of this phenomenon. GO was purified and showed a molecular weight of 40 kDa by SDS‐PAGE. Elution behavior on DEAE‐cellulose chromatography and cellulose acetate membrane electrophoresis indicated that the purified GO was highly basic (pI>10.0). Repeated IEF and cIEF analysis showed that the pI of the purified GO was in the range of 10.0–3.25, either in a smear form or as distinct bands. 2‐DE analysis showed that the 40 kDa subunit of GO displayed variable pIs from 9.6 to 3.65. It was likely that the purified GO was actually a complex consisted of GO and an unknown protein. CE‐SDS, SDS‐cellulose acetate membrane electrophoresis and amino acid compositions indicated that the unknown protein was a highly basic polymer (BP) consisting of basic and phenylalanine‐rich oligo‐peptide (BOP). Many BOPs are located on the surface of the acidic GO via ionic and hydrophobic interactions and formed GO‐BOP complex (GC), resulting in a highly basic GC although GO itself was acidic. This hypothesis was further supported by the facts that anti‐GC serum failed to recognize GO, and GC showed a peak at 257 nm although GO has few phenylalanine residues. Irregular and incomplete disassociation between GO and BOP was observed in IEF and cIEF, resulting in various intermediates with different ratios of GO/BOP, which could be the reason for the range of pIs observed for GO.     

Purification and Kinetic Properties of Human Recombinant Dihydrofolate Reductase Produced in <Emphasis Type="Italic">Bombyx mori</Emphasis> Chrysalides

Recent reports describe the inhibition of human dihydrofolate reductase (hDHFR) by natural tea polyphenols. This finding could explain the epidemiologic data on their prophylactic effects for certain forms of cancer, and it raises the possibility that natural and synthetic polyphenols could be used in cancer chemotherapy. In order to obtain larger quantities of hDHFR to support structural studies, we established and validated a baculovirus system for the expression of this protein in Bombyx mori chrysalides (pupae of the silkworm enclosed in a cocoon). To isolate the expressed protein, whole infected pupae were homogenized, and the expressed protein was purified by affinity chromatography. Here, we demonstrate the efficient expression of recombinant hDHFR in this model and report that this newly expressed protein has high enzymatic activity and kinetic properties similar to those previously reported for recombinant hDHFR expressed in Escherichia coli. The purified protein showed dissociation constants for the binding of natural polyphenols similar to that expressed in E. coli, which ensures its usage as a new tool for further structural studies. Although the hDHFR yield per individual was found to be lower in the chrysalides than in the larvae of B. mori, the former system was optimized as a model for the scaled-up production of recombinant proteins. Expression of proteins in chrysalides (instead of larvae) could offer important advantages from both economic and biosecurity aspects.     

Chitin- and Streptavidin-Mediated Affinity Purification Systems: A Screening Platform for Enzyme Discovery

Affinity purification of recombinant proteins is an essential technique in biotechnology. However, current affinity purification methods are very cost-intensive, and this imposes limits on versatile use of affinity purification for obtaining purified proteins for a variety of applications. To overcome this problem, we developed a new affinity purification system which we call CSAP (chitin- and streptavidin-mediated affinity purification) for low-cost purification of Strep-tag II fusion proteins. The CSAP system is designed to utilize commercially available chitin powder as a chromatography matrix, thereby significantly improving the cost-efficiency of protein affinity purification. We investigated the CSAP system for protein screening in 96-well format as a demonstration. Through the screening of 96 types of purified hemoproteins, several proteins capable of the catalytic diastereodivergent synthesis of cyclopropanes were identified as candidates for an abiotic carbene transfer reaction.     

A highly active fungal β-glucosidase

A highly active thermostable β-glucosidase was purified to homogeneity from a strain ofTrichoderma sp. The enzyme was an extracellular glycoprotein and showed hydrolytic activity toward several β-glucosides. Cellobiose was found to be the substrate of choice for this enzyme. This finding could suggest future technological applications of the purified protein.     

Characterization of Smallest Active Monomeric Lipase from Novel <Emphasis Type="Italic">Rhizopus</Emphasis> Strain: Application in Transesterification

An extracellular lipase-producing fungus was isolated from oil-rich soil. This fungus belongs to the genus Rhizopus and clades with Rhizopus oryzae. Lipase was purified to homogeneity from this novel fungal source using ammonium sulphate precipitation followed by Q-Sepharose chromatography. The extracellular lipase was purified 8.6–fold, and enzymatic properties were studied. The molecular mass of the purified enzyme was estimated to be 17 kD by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and 16.25 kD by matrix-assisted laser desorption ionization/time-of-flight analysis. The native molecular mass was estimated to be 17.5 kD by gel filtration, indicating the protein to be monomer. The optimum pH and temperature for the enzyme catalysis were 7.0 °C and 40 °C, respectively. Enzyme was stable in pH range 6.0–7.0 and retains 95–100% activity when incubated at 50 °C for 1 h. The pI of the purified lipase was 4.2. Enzyme was stable in the organic solvents such as ethanol, hexane and methanol for 2 h. Purified enzyme was used for transesterification of oleic acid in the presence of ethanol for production of oleic acid ethyl ester with a conversion efficiency of 66% after 24 h at 30 °C.     

Interference study should be performed for every protein measurement method used

It is particularly important, when analyzing biological material, for the measurement procedure to be specific to the analyte and not to suffer interference by the matrix effect. Tissue fraction studies also require rapid and accurate methods to estimate the concentration of protein in solutions as well as many measurement methods used in medical laboratories. The design of this study is based on a comparison of the Lowry and the bicinchoninic acid (BCA) methods for the measurement of the total protein concentrations of rat liver subcellular fractions. In our experiment, subcellular fractions enriched in peroxisomes (POs) obtained by differential centrifugation were then further separated by means of density gradient centrifugation. We performed the protein measurement assays on all fractions obtained during the purification steps. The protein contents of the fractions obtained were determined by the two methods. The method comparison statistics were performed by linear Deming regression analysis and Altman and Bland bias plot. The regression equation was unacceptable, indicating that the last three fractions separated by means of Nycodenz discontinuous density gradient centrifugation gave remarkably divergent results. For the Lowry method, the Nycodenz effect could not be eliminated with the use of interference blank. In addition to Nycodenz, the potentially interfering compound used in the isolation procedure as isolation medium was 3-(morpholino)propane sulfonic acid (MOPS). In decreased concentrations of MOPS (10 mM), interference blank should be used for correct measurement with Lowry, but in practical use 10 mM does not provide buffering potency. In the BCA method, interference blank correction seemed to eliminate the measurement error in all concentrations of Nycodenz. There was no MOPS effect on the BCA measurement assay. Referring to deviations as sample-inherent matrix effects, we concluded that not only one, but more measurement methods should be used in order to make a correct protein measurement.     

Purification of glutathione reductase from chicken liver and investigation of kinetic properties

Glutathione reductase was purified from chicken liver and some characteristics of the enzyme were investigated. The purification procedure was composed of four steps: preparation of homogenate, ammonium sulfate precipitation, 2′,5′-ADP Sepharose 4B affinity chromatography, and Sephadex G-200 gel filtration chromatography. Owing to the four consecutive procedures, the enzyme was purified 1714-fold, with a yield of 38%. Specific activity at the final step was 120 enzyme unit (EU)/mg of protein. The purified enzyme showed a single band on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The molecular weight of the enzyme was found to be 100 kDa by Sephadex G-200 gel filtration chromatography, and the subunit molecular weight was found to be 43 kDa by SDS-PAGE. Optimum pH, stable pH, optimum ionic strength, and optimum temperature were 7.0, 7.4, 0.75 M Tris-HCl buffer including 1 mM EDTA, and 50°C, respectively. K _M and V _max values for NADPH and glutathione disulfide (GSSG) substrates were also determined for the enzyme.     

Purification of Bioactive Lipopeptides Produced by Bacillus subtilis Strain BIA

Bacillus subtilis strain BIA was used for the production of bioactive lipopeptides. Different extraction and purification methods were assayed as liquid–liquid extraction, and acid and ammonium sulfate precipitation followed by TLC, SPE, and gel filtration. Active fractions were further purified using RP-HPLC. The molecular mass of the purified product from HPLC was determined through Tris-Tricine SDS-PAGE and MALDI–TOF-MS. The results revealed that Bacillus subtilis strain BIA produced surfactin and iturin like compounds. Coproduction of surfactin and iturin like compounds by this strain is a remarkable trait for a potential biocontrol agent. This paper also includeds techniques that have been developed for the optimal and convenient extraction of bioactive lipopeptides from microbial origin.