There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

Protein phosphorylation is estimated to affect 30% of the proteome and is a major regulatory mechanism that controls many basic cellular processes. Until recently, our biochemical understanding of protein phosphorylation on a global scale has been extremely limited; only one half of the yeast kinases have known in vivo substrates and the phosphorylating kinase is known for less than 160 phosphoproteins. Here we describe, with the use of proteome chip technology, the in vitro substrates recognized by most yeast protein kinases: we identified over 4,000 phosphorylation events involving 1,325 different proteins. These substrates represent a broad spectrum of different biochemical functions and cellular roles. Distinct sets of substrates were recognized by each protein kinase, including closely related kinases of the protein kinase A family and four cyclin-dependent kinases that vary only in their cyclin subunits. Although many substrates reside in the same cellular compartment or belong to the same functional category as their phosphorylating kinase, many others do not, indicating possible new roles for several kinases. Furthermore, integration of the phosphorylation results with protein-protein interaction and transcription factor binding data revealed novel regulatory modules. Our phosphorylation results have been assembled into a first-generation phosphorylation map for yeast. Because many yeast proteins and pathways are conserved, these results will provide insights into the mechanisms and roles of protein phosphorylation in many eukaryotes.

Global Analysis of Protein Phosphorylation in Yeast

The generation of polymer brushes by surface-initiated controlled radical polymerization (SI-CRP) techniques has become a powerful approach to tailor the chemical and physical properties of interfaces and has given rise to great advances in surface and interface engineering. Polymer brushes are defined as thin polymer films in which the individual polymer chains are tethered by one chain end to a solid interface. Significant advances have been made over the past years in the field of polymer brushes. This includes novel developments in SI-CRP, as well as the emergence of novel applications such as catalysis, electronics, nanomaterial synthesis and biosensing. Additionally, polymer brushes prepared via SI-CRP have been utilized to modify the surface of novel substrates such as natural fibers, polymer nanofibers, mesoporous materials, graphene, viruses and protein nanoparticles. The last years have also seen exciting advances in the chemical and physical characterization of polymer brushes, as well as an ev...

Surface-Initiated Controlled Radical Polymerization: State-of-the-Art, Opportunities, and Challenges in Surface and Interface Engineering with Polymer Brushes

Recovery of gold from secondary sources—A review

Adsorptive removal of bisphenol A (BPA) from aqueous solution: A review.

Leuconostoc mesenteroides subsp. cremoris strain W3, isolated from wine, was previously found to produce a bacteriocin with inhibitory activity towards malolactic bacteria and hence inhibit malolactic fermentation in model wine medium. The bacteriocin, which we termed mesentericin W3, was purified by multistep chromatography and found in a previous study to be similar to mesentericin Y105, albeit with a low recovery (3.2%). In this study, we aimed to achieve large-scale isolation of mesentericin W3 by adsorption of the bacteriocin from culture supernatant onto Micro-Cel (diatomite calcium silicate) and then by subsequent desorption. Water-soluble surfactants including Tween 80, Triton X-100, sodium deoxycholate, sodium dodecyl sulfate (SDS) in distilled water, organic solvents (methanol, ethanol, acetonitrile), and distilled water with a pH range of 2-10 were tested for the desorption of the bacteriocin from Micro-Cel. Mesentericin W3 was successfully desorbed from Micro-Cel with SDS, while other tested reagents were not as successful. The bacteriocin desorbed from Micro-Cel showed the same inhibitory activity as the culture supernatant. The desorbed bacteriocin was applied to an SP Sepharose Fast Flow column for final purification. MALDI-TOF mass spectrometry confirmed the identity of the bacteriocin.

https://journals.tubitak.gov.tr/biology/issues/biy-14-38-5/biy-38-5-8-1312-52.pdf

Large-scale purification of a bacteriocin produced by Leuconostoc mesenteroides subsp. cremoris using diatomite calcium silicate

Several transition metal oxides, such as iron (III), nickel (II) and zirconium (IV) oxides, were examined in detail for the specific enrichment and the purification of phosphopeptides from a digested peptide mixture solution. Phosphopeptide enrichment was performed on the metal oxide particles using a peptide mixture obtained bytryptic digestion of beta-casein. The mixture of protein digests containing bovine serum albumin (BSA): beta-casein digests (100:1 mole ratio) was also used for the phosphopeptide enrichment. Furthermore, non-fat milk digest was examined as a complex biological sample. In each phosphopeptide enrichment process, phosphopeptides were specifically enriched and separated from the non-phosphopeptides. The phosphopeptides were adsorbed onto the metal oxide surface at acidic pH values between 1.0 and 2.0 and, for desorption of phosphopeptides from metal oxide particles, pH values were examined and optimized in the enrichment studies. The analysis of phosphopeptides were carried out by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) using 2,5-dihydroxybenzoic acid matrix containing 1.0% phosphoric acid to obtain intense protonated signals and to overcome degradation of the phosphopeptides by phosphate group loss in mass spectrometric conditions. Moreover, it was demonstrated that the direct detection of phosphopeptides from the surface of the metal oxide particles was possible using MALDI-MS by mixing the phosphopeptide-adsorbed metal oxide particles with MALDI matrix solution in slurry form before the analysis. Thus, the effects of interferences arising from chemical species used in the desorption process was successfully eliminated for the fast and sensitive detection of phosphopeptides in MALDI-MS applications.

Specific enrichment and direct detection of phosphopeptides on insoluble transition metal oxide particles in matrix-assisted laser desorption/ionization mass spectrometry applications

Cationic polymers can bind DNA to form polyplexes, which are noncovalent complexes used for gene delivery into the targeted cells. For more insight on such biologically relevant systems, the noncovalent complexes between the cationic polymer poly(ethylene imine) (PEI) and the nucleotide mimicking dye Cibacron Blue F3G-A (CB) were investigated using mass spectrometry methods. Two PEIs of low molecular weight were utilized (Mn ≈ 423 and 600 Da). The different types of CB anions produced by Na+/H+ exchanges on the three sulfonic acid groups of CB and their dehydrated counterparts were responsible for complex formation with PEI. The CB anions underwent noncovalent complex formation with protonated, but not with sodiated PEI. A higher proportion of cyclic oligomers were detected in PEI423 than PEI600, but both architectures formed association products with CB. Tandem mass spectrometry studies revealed a significantly stronger noncovalent interaction between PEI and dehydrated CB than between PEI and intact CB. Copyright © 2014 John Wiley & Sons, Ltd.

Strong ionic interactions in noncovalent complexes between poly(ethylene imine), a cationic electrolyte, and Cibacron Blue, a nucleotide mimic--implications for oligonucleotide vectors.

Molecularly imprinted, core–shell type boronate affinity sorbents for isolation and detection of sialic acid (SA) isoforms, N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc), were synthesized. The monomer mixture containing a phenylboronic acid functionalized monomer was polymerized on highly porous silica microspheres 5.5 μm in size, in the presence of a SA isomer. The selection of highly porous silica microspheres as the core material eliminated the risk of agglomeration during the formation of polymer shell and resulted in the synthesis of a boronate affinity sorbent with a large surface area available for parking of high number of SA molecules. Neu5Ac was extracted from human serum with high isolation yield and successfully determined in the elution medium by LC-MS/MS. The sorbent is a promising stationary phase for precolumn purification of SA isoforms before LC-MS/MS due to its suitable particle size and high porosity.

Highly Porous, Molecularly Imprinted Core–Shell Type Boronate Affinity Sorbent with a Large Surface Area for Enrichment and Detection of Sialic Acid Isomers

In general, phosphopeptides are specifically adsorbed to the surface of the material at the initial step of phosphopeptide enrichment methods. Thus, nonphosphopeptides can be removed from the media by following the appropriate washing steps. After sufficient washing, the phosphopeptides are eluted from the surface of the material completely for further analysis. Performing the elution of phosphopeptides fully in the enrichment step is very important in terms of determining the whole phosphoproteome profile of a sample by subsequent mass spectrometric analysis. Materials containing anion exchanger groups such as amines on the surface can be used as a selective stationary phase in phosphopeptide enrichment methods. Positively charged groups on the surface of this type of material interact with the phosphate groups of phosphopeptides through electrostatic interactions. Such interactions can be basically manipulated by changing the pH of the medium or replacing the salts present in the solution. Phosp...

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Papers

Large-scale purification of a bacteriocin produced by Leuconostoc mesenteroides subsp. cremoris using diatomite calcium silicate

Specific enrichment and direct detection of phosphopeptides on insoluble transition metal oxide particles in matrix-assisted laser desorption/ionization mass spectrometry applications

Strong ionic interactions in noncovalent complexes between poly(ethylene imine), a cationic electrolyte, and Cibacron Blue, a nucleotide mimic--implications for oligonucleotide vectors.

Highly Porous, Molecularly Imprinted Core–Shell Type Boronate Affinity Sorbent with a Large Surface Area for Enrichment and Detection of Sialic Acid Isomers

Use of Sulfonates as Desorption Agents for Phosphopeptide Elution from an Anion-exchange Material