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Selective Isolation (selective + isolation)

Distribution by Scientific Domains

Life Sciences	54%
Chemistry	45%

Selected Abstracts

Selective isolation of multiple positively charged peptides for 2-DE-free quantitative proteomics

PROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 16 2006
Aniel Sánchez
Abstract A method for quantitative proteomic analysis based on the selective isolation of multiply charged peptides (RH peptides) containing arginine and histidine residues is described. Two pools of proteins are digested in tandem with lysyl-endopeptidase and trypsin and the primary amino groups of proteolytic peptides are separately labeled with d3 - and d0 -acetic anhydride. This reaction has a dual purpose: (i) to allow the relative protein quantification in two different conditions and (ii) to restrict the positive charges of peptides to the presence of arginine and histidine. The N -acylated peptides are separated by cation-exchange chromatography into two groups, neutral and singly charged peptides (R,+,H,,,1) that are neither retained nor analyzed, whereas the multiply charged peptides (R,+,H>1) are retained into the column and can be eluted in batch or further fractionated using a saline gradient before LC-MS/MS analysis. In silico analysis revealed that the selective isolation of RH peptides considerably simplifies the complex mixture of peptides (three RH peptides/protein) and at the same time they represent 84% of the whole proteomes. The selectivity, and recovery of the method were evaluated with model proteins and with a complex mixture of proteins extracted from Vibrio cholerae. [source]

Highly efficient capture and enumeration of low abundance prostate cancer cells using prostate-specific membrane antigen aptamers immobilized to a polymeric microfluidic device

ELECTROPHORESIS, Issue 18 2009
Udara Dharmasiri
Abstract Prostate tumor cells over-express a prostate-specific membrane antigen (PSMA) that can be used as a marker to select these cells from highly heterogeneous clinical samples, even when found in low abundance. Antibodies and aptamers have been developed that specifically bind to PSMA. In this study, anti-PSMA aptamers were immobilized onto the surface of a capture bed poised within a PMMA, microchip, which was fabricated into a high-throughput micro-sampling unit (HTMSU) used for the selective isolation of rare circulating prostate tumor cells resident in a peripheral blood matrix. The HTMSU capture bed consisted of 51 ultra-high-aspect ratio parallel curvilinear channels with a width similar to the prostate cancer cell dimensions. The surface density of the PSMA-specific aptamers on an ultraviolet-modified PMMA microfluidic capture bed surface was determined to be 8.4×1012,molecules/cm2. Using a linear velocity for optimal cell capture in the aptamer-tethered HTMSU (2.5,mm/s), a recovery of 90% of LNCaP cells (prostate cancer cell line; used as a model in this example) was found. Due to the low abundance of these cells, the input volume required was 1,mL and this could be processed in ,29,min using an optimized linear flow rate of 2.5,mm/s. Captured cells were subsequently released intact from the affinity surface using 0.25%,w/w trypsin followed by counting individual cells using a contact conductivity sensor integrated into the HTMSU that provided high detection and sampling efficiency (,100%) and did not require staining of the cells for enumeration. [source]

Protein engineering and discovery of lipases,

EUROPEAN JOURNAL OF LIPID SCIENCE AND TECHNOLOGY, Issue 1 2010
Robert Kourist
Abstract Lipases are widely used in the modification of fats and oils with applications in the production of structured triacylglycerols, selective isolation or incorporation of specific fatty acids, and in oleochemistry for the synthesis of emollient esters and sugar fatty acid esters. Despite the numerous examples for the effective use of lipases, the biocatalysts often need to be optimized to show the desired specificities, stability, operational properties, etc. Beside rather classical methods such as variation of the solvent system or carrier for immobilization, the use of protein engineering methods to modify the protein on a molecular level is an important tool for the creation of tailor-designed enzymes. Protein design is also complemented with the efficient isolation of novel lipases from the metagenome. This article covers concepts and examples for the discovery of novel lipases and their variants by protein engineering and metagenome techniques. [source]

Identification of the N-termini of NADPH : protochlorophyllide oxidoreductase A and B from barley etioplasts (Hordeum vulgare L.)

FEBS JOURNAL, Issue 4 2009
Matthias Plöscher
The N-termini of the NADPH : protochlorophyllide oxidoreductase (POR) proteins A and B from barley and POR from pea were determined by acetylation of the proteins and selective isolation of the N-terminal peptides for mass spectrometry de novo sequence analysis. We show that the cleavage sites between the transit peptides and the three mature POR proteins are homologous. The N-terminus in PORA is V48, that in PORB is A61, and that in POR from pea is E64. For the PORB protein, two additional N-termini were identified as A62 and A63, with decreased signal intensity of the corresponding N-terminal peptides. The results show that the transit peptide of PORA is considerably shorter than previously reported and predicted by ChloroP. A pentapeptide motif that has been characterized as responsible for binding of protochlorophyllide to the transit peptide of PORA [Reinbothe C, Pollmann S, Phetsarath-Faure P, Quigley F, Weisbeek P & Reinbothe S (2008) Plant Physiol148, 694,703] is shown here to be part of the mature PORA protein. [source]

Bifidobacterium -selective isolation and enumeration from chicken caeca by a modified oligosaccharide antibiotic-selective agar medium

LETTERS IN APPLIED MICROBIOLOGY, Issue 4 2005
S.N. Thitaram
Abstract Aims:, To determine the efficacy and selectivity of an acidified, antibiotic-selective, oligosaccharide-containing media for enumerating Bifidobacterium spp. from chicken caeca samples. Methods and Results:, Transoligosaccharide propionate agar medium (TOS) modified by addition of mupirocin (50 ,g ml,1) and glacial acetic acid (1%, v/v), did not inhibit the growth of bifidobacteria compared with the control media yet inhibited the growth of Lactobacillus acidophilus, Lactobacillus gallinarum, Lactobacillus helveticus and Streptococcus gordonii. Conclusions:, Addition of mupirocin (50 ,g ml,1) and glacial acetic acid (1%, v/v) to TOS (TOS-AM50), is an effective selective medium for isolation and enumeration of Bifidobacterium spp. from chicken caeca samples. Significance and Impact of the Study:, The development of an intestinal bifidobacteria-selective media contributes to the study of probiotics and prebiotics in poultry and potentially other species. [source]

Selective isolation of multiple positively charged peptides for 2-DE-free quantitative proteomics

A method for the selective isolation and enrichment of carrier protein-bound low-molecular weight proteins and peptides in the blood

PROTEOMICS - CLINICAL APPLICATIONS, Issue 2 2007
Serena Camerini
Abstract The low molecular weight (LMW) region of the circulatory proteome, thought to contain a rich source of biomarkers, resides in vivo, in a complexed state with larger, highly abundant resident proteins. Consequently, serum fractionation approaches that deplete the high-abundance proteins under native conditions will remove much of the LMW proteome. We describe a new strategy to systematically collect, isolate and enrich the LMW molecules that would be otherwise eliminated during the depletion of high-abundance circulatory proteins based on continuous elution electrophoresis. We employ strong denaturing conditions to disrupt association with the high-abundance carrier proteins followed by fractionation and removal of SDS. Under denaturation, the LMW molecules were effectively stripped from the highly abundant carrier proteins. We then removed the SDS by ion exchange matrix sequestration and concentrated the fractions. The outcome is a series of SDS-free fractions of LMW molecules. The isolated fractions were then analyzed by enzymatic digestion followed by LC-MS/MS analysis. The yield of multiple peptide hits as well as the total number of identifications significantly increased (50%) compared to unfractionated serum. The method yielded a 30% higher number of low-abundance serum proteins compared to direct sequencing of unfractionated serum. [source]

Mass-directed fractionation and isolation of pharmaceutical compounds by packed-column supercritical fluid chromatography/mass spectrometry

RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 22 2001
Tao Wang
An automated packed-column semi-preparative supercritical fluid chromatography/mass spectrometry (SFC/MS) system incorporating mass-directed fraction collection has been designed and implemented as an alternative to preparative HPLC and preparative HPLC/MS (PrepLC/MS) for the purification of pharmaceutical compounds. The system incorporates a single quadrupole mass spectrometer and a supercritical fluid chromatograph. Separations were achieved using a binary solvent system consisting of carbon dioxide and methanol. Purification of SFC-separated compounds was achieved incorporating mass-directed fraction collection, enabling selective isolation of the target molecular weight compound and eliminating the collection of undesired compounds (e.g., by-products, excess starting materials, etc.). Cross contamination between fractions and recoveries of the system were investigated. Mass spectrometer ionization with basic mobile additives is discussed, and examples of preparative SFC/MS chiral separations are presented. Early experiences suggest SFC will be a powerful and complementary technique to HPLC for the purification of pharmaceutical compounds. Copyright © 2001 John Wiley & Sons, Ltd. [source]

Electro-membrane filtration for the selective isolation of bioactive peptides from an ,s2 -casein hydrolysate

BIOTECHNOLOGY & BIOENGINEERING, Issue 6 2002
Gerrald Bargeman
Abstract For the isolation of the ingredients required for functional foods and nutraceuticals generally membrane filtration has too low a selectivity and chromatography is (too) expensive. Electro-membrane filtration (EMF) seems to be a breakthrough technology for the isolation of charged nutraceutical ingredients from natural sources. EMF combines the separation mechanisms of membrane filtration and electrophoresis. In this study, positively charged peptides with antimicrobial activity were isolated from an ,s2 -casein hydrolysate using batch-wise EMF. ,s2 -Casein f(183,207), a peptide with strong antimicrobial activity, predominated in the isolated product and was enriched from 7.5% of the total protein components in the feed to 25% in the permeate product. With conventional membrane diafiltration using the same membrane (GR60PP), isolation of this and other charged bioactive peptides could not be achieved. The economics of EMF are mainly governed by the energy costs and the capital investment, which is affected by the flux of the desired peptide. A maximum average transport rate of ,s2 -casein f(183,207) during batch-wise EMF of 1.2 g/m2 · h was achieved. Results indicate that an increase in the hydrolysate (feed) concentration, the applied potential difference and the conductivity of the permeate and electrode solutions, and a reduction in the conductivity of the feed result in a higher transport rate of ,s2 -casein f(183,207). This is in line with the expectation that the transport rate is improved when the concentration, the electrical field strength, or the electrophoretic mobility is increased, provided that the electrophoretic transport predominates. The expected energy consumption of the EMF process per gram of peptide transported was reduced by approximately 50% by applying a low overall potential difference and by processing desalinated hydrolysate. Considerable improvements in transport rate, energy efficiency, and process economics seem to be attainable by additional optimization of the process parameters and the EMF module design. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 80: 599,609, 2002. [source]

Rapid and selective isolation of ,-xylosidase through an activity-based chemical approach

BIOTECHNOLOGY JOURNAL, Issue 2 2006
Lee-Chiang Lo Dr.
Abstract ,-Xylosidase is a key enzyme in the xylanolytic system with a great potential in many biotechnological applications, especially in the food as well as the pulp and paper industries. We have developed a chemical approach for the rapid screening and isolation of ,-xylosidase. Activity probe LCL-6X targeting ,-xylosidase was utilized in this study. It carries a ,-xylopyranosyl recognition head, a latent trapping device consisting of a 2-fluoromethylphenoxyl group, and a biotin reporter group. The biotin reporter group serves both as a readout device and as a tool for enriching the labeled proteins. LCL-6X could selectively label a model ,-xylosidase from Trichoderma koningii. All other bystander proteins used in this study, including phosphorylase b, BSA, ovalbumin, carbonic anhydrase, and trypsin inhibitor, gave negligible cross-labeling effect. With the assistance of streptavidin agarose beads and mass spectrophotometry for the recovery and identification of the biotinylated proteins, we demonstrated that LCL-6X could be successfully applied to identify a bi-functional enzyme with ,- L -arabinofuranosidase/,-xylosidase activity from the total protein extract of a Pichia expressing system and a prospective ,-xylosidase in the culture medium of Aspergillus fumigatus. The ,-xylosidase activities from numerous microbes were also screened using the LCL-6X probe. Preliminary results showed significant differences among these microbial sources and some distinct protein bands were observed. Thus, we have successfully developed a novel chemical probe that has potential applications in xylan-related research. [source]

Synthesis of S -Adenosyl- L -homocysteine Capture Compounds for Selective Photoinduced Isolation of Methyltransferases

CHEMBIOCHEM, Issue 2 2010
Christian Dalhoff Dr.
Abstract Understanding the interplay of different cellular proteins and their substrates is of major interest in the postgenomic era. For this purpose, selective isolation and identification of proteins from complex biological samples is necessary and targeted isolation of enzyme families is a challenging task. Over the last years, methods like activity-based protein profiling (ABPP) and capture compound mass spectrometry (CCMS) have been developed to reduce the complexity of the proteome by means of protein function in contrast to standard approaches, which utilize differences in physical properties for protein separation. To isolate and identify the subproteome consisting of S -adenosyl- L -methionine (SAM or AdoMet)-dependent methyltransferases (methylome), we developed and synthesized trifunctional capture compounds containing the chemically stable cofactor product S -adenosyl- L -homocysteine (SAH or AdoHcy) as selectivity function. SAH analogues with amino linkers at the N6 or C8 positions were synthesized and attached to scaffolds containing different photocrosslinking groups for covalent protein modification and biotin for affinity isolation. The utility of these SAH capture compounds for selective photoinduced protein isolation is demonstrated for various methyltransferases (MTases) acting on DNA, RNA and proteins as well as with Escherichia coli cell lysate. In addition, they can be used to determine dissociation constants for MTase,cofactor complexes. [source]