Development of New Lanthanide(III) Ion-Based Magnetic Affinity Material for Phosphopeptide Enrichment

Lanthanide (III) ion-based magnetic IMAC materials consisting of core-shell-like silica-coated magnetic nanoparticles as supporting material, chelidamic acid as chelating agent, and Ln3+ ions were developed in this study. Magnetic nanoparticles...

Cyanidiophyceae (Rhodophyta) Tolerance to Precious Metals: Metabolic Response to Palladium and Gold

Polyextremophilic red algae, which belong to the class Cyanidiophyceae, are adapted to live in geothermal and volcanic sites. These sites often have very high concentrations of heavy and precious metals. In this study, we assessed the capacity of three strains of Galdieria (G. maxima, G. sulphuraria, and G. phlegrea) and one strain of Cyanidiumcaldarium to tolerate different concentrations of precious metals, such as palladium (Cl4K2Pd) and gold (AuCl4K) by monitoring algal growths in cultures exposed to metals, and we investigated the algae potential oxidative stress induced by the metals. This work provides further understanding of metals responses in the Cyanidiophyceae, as this taxonomic class is developed as a biological refinement tool.

Innovative Electrochemical Sensor Using TiO2 Nanomaterials to Detect Phosphopeptides

Many enrichment techniques for phosphopeptides usually rely on the interaction of phosphate groups with metal ions or metal oxides. Based on this, we innovatively designed and fabricated an electrochemical sensor based on TiO₂ nanoparticles (NPs), which can sensitively and rapidly detect phosphopeptides in protein samples pretreated with AuNPs. When the phosphopeptide solution was pretreated with AuNPs, AuNPs can be linked to the polypeptide chain via the amino group at the tail of the polypeptide chain. When TiO₂ NPs are specifically bound to the phosphate group on the peptide, the modified AuNPs can improve the electron conduction ability of the electrode to detect the phosphopeptides. The designed electrochemical sensor had the advantages of high sensitivity, selectivity, and repeatability, and it showed a wide linear concentration range (1 pg/L to 1 mg/L) and a lower limit of detection (0.24 pg/L) for phosphopeptides. In order to improve the detection capability of the electrochemical sensor, we also synthesized TiO₂ and graphene oxide (GO) composite materials. The influence of the morphology and crystal form of TiO₂ NPs on phosphopeptide detection was studied by changing the feeding ratio and heat treatment temperature. We found that the uniformly dispersed anatase crystal TiO₂ and GO composite-modified electrode showed a lower detection limit (0.37 ag/L). This sensing strategy is expected to provide a novel solution for the direct detection of phosphate groups in polypeptides in complex environments.

Enrichment Strategies in Phosphoproteomics

The comprehensive study of the phosphoproteome is heavily dependent on appropriate enrichment strategies that are most often, but not exclusively, carried out on the peptide level. In this chapter, I give an overview of the most widely used techniques. In addition to dedicated antibodies, phosphopeptides are enriched by their selective interaction with metals in the form of chelated metal ions or metal oxides. The negative charge of the phosphate group is also exploited in a variety of chromatographic fractionation methods that include different types of ion exchange chromatography, hydrophilic interaction chromatography (HILIC), and electrostatic repulsion HILIC (ERLIC) chromatography. Selected examples from the literature will demonstrate how a combination of these techniques with current high-performance mass spectrometry enables the identification of thousands of phosphorylation sites from various sample types.

Enrichment of phosphorylated peptides and proteins by selective precipitation methods

Protein phosphorylation is one of the most prominent post-translational modifications involved in the regulation of cellular processes. Fundamental understanding of biological processes requires appropriate bioanalytical methods for selectively enriching phosphorylated peptides and proteins. Most of the commonly applied enrichment approaches include chromatographic materials including Fe(3+)-immobilized metal-ion affinity chromatography or metal oxides. In the last years, the introduction of several non-chromatographic isolation technologies has increasingly attracted the interest of many scientists. Such approaches are based on the selective precipitation of phosphorylated peptides and proteins by applying various metal cations. The excellent performance of precipitation-based enrichment methods can be explained by the absence of any stationary phase, resin or sorbent, which usually leads to unspecific binding. This review provides an overview of recently published methods for the selective precipitation of phosphorylated peptides and proteins.

Development of the affinity materials for phosphorylated proteins/peptides enrichment in phosphoproteomics analysis

Reversible protein phosphorylation is a key event in numerous biological processes. Mass spectrometry (MS) is the most powerful analysis tool in modern phosphoproteomics. However, the direct MS analysis of phosphorylated proteins/peptides is still a big challenge because of the low abundance and insufficient ionization of phosphorylated proteins/peptides as well as the suppression effects of nontargets. Enrichment of phosphorylated proteins/peptides by affinity materials from complex biosamples is the most widely used strategy to enhance the MS detection. The demand of efficiently enriching phosphorylated proteins/peptides has spawned diverse affinity materials based on different enrichment principles (e.g., electronic attraction, chelating). In this review, we summarize the recent development of various affinity materials for phosphorylated proteins/peptides enrichment. We will highlight the design and fabrication of these affinity materials, discuss the enrichment mechanisms involved in different affinity materials, and suggest the future challenges and research directions in this field.

Ultraviolet matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for phosphopeptide analysis with a solidified ionic liquid matrix

A solidified ionic liquid matrix (SILM) consisting of 3-aminoquinoline, α-cyano-4- hydroxycinnamic acid and ammonium dihydrogen phosphate combines the benefits of liquid and solid MALDI matrices and proves to be well suitable for phosphopeptide analysis using MALDI-MS in the low femtomole range. Desalting and buffer exchange that typically follow after phosphopeptide elution from metal oxide affinity chromatography (MOAC) materials can be omitted. Shifting the pH from acidic to basic during target preparation causes slow matrix crystallization and homogeneous embedding of the analyte molecules, forming a uniform preparation from which (phospho)peptides can be ionized in high yields over long periods of time. The novel combination of MOAC-based phosphopeptide enrichment with SILM preparation has been developed with commercially available standard phosphopeptides and with α-casein as phosphorylated standard protein. The applicability of the streamlined phosphopeptide analysis procedure to cell biological and clinical samples has been tested (i) using affinity-enriched endogenous TRIM28 from cell cultures and (ii) by analysis of a two-dimensional gel-separated protein spot from a bladder cancer sample.

QM/MM MD simulations of La(iii)–phosphopeptide complexes

Hybrid quantum mechanical/molecular mechanical simulations have been used to study the structural and dynamical properties of a La(iii)–phosphopeptide complex.

Recovery of rare earth elements from the sulfothermophilic red alga Galdieria sulphuraria using aqueous acid

The demand for rare earth elements has increased dramatically in recent years because of their numerous industrial applications, and considerable research efforts have consequently been directed toward recycling these materials. The accumulation of metals in microorganisms is a low-cost and environmentally friendly method for the recovery of metals present in the environment at low levels. Numerous metals, including rare earth elements, can be readily dissolved in aqueous acid, but the efficiency of metal biosorption is usually decreased under the acidic conditions. In this report, we have investigated the use of the sulfothermophilic red alga Galdieria sulphuraria for the recovery of metals, with particular emphasis on the recovery of rare earth metals. Of the five different growth conditions investigated where G. sulphuraria could undergo an adaptation process, Nd(III), Dy(III), and Cu(II) were efficiently recovered from a solution containing a mixture of different metals under semi-anaerobic heterotrophic condition at a pH of 2.5. G. sulphuraria also recovered Nd(III), Dy(III), La(III), and Cu(II) with greater than 90% efficiency at a concentration of 0.5 ppm. The efficiency remained unchanged at pH values in the range of 1.5-2.5. Furthermore, at pH values in the range of 1.0-1.5, the lanthanoid ions were collected much more efficiently into the cell fractions than Cu(II) and therefore successfully separated from the Cu(II) dissolved in the aqueous acid. Microscope observation of the cells using alizarin red suggested that the metals were accumulating inside of the cells. Experiments using dead cells suggested that this phenomenon was a biological process involving specific activities within the cells.

PAPE (Prefractionation-Assisted Phosphoprotein Enrichment): A Novel Approach for Phosphoproteomic Analysis of Green Tissues from Plants

Phosphorylation is an important post-translational protein modification with regulatory roles in diverse cellular signaling pathways. Despite recent advances in mass spectrometry, the detection of phosphoproteins involved in signaling is still challenging, as protein phosphorylation is typically transient and/or occurs at low levels. In green plant tissues, the presence of highly abundant proteins, such as the subunits of the RuBisCO complex, further complicates phosphoprotein analysis. Here, we describe a simple, but powerful, method, which we named prefractionation-assisted phosphoprotein enrichment (PAPE), to increase the yield of phosphoproteins from Arabidopsis thaliana leaf material. The first step, a prefractionation via ammonium sulfate precipitation, not only depleted RuBisCO almost completely, but, serendipitously, also served as an efficient phosphoprotein enrichment step. When coupled with a subsequent metal oxide affinity chromatography (MOAC) step, the phosphoprotein content was highly enriched. The reproducibility and efficiency of phosphoprotein enrichment was verified by phospho-specific staining and, further, by mass spectrometry, where it could be shown that the final PAPE fraction contained a significant number of known and additionally novel (potential) phosphoproteins. Hence, this facile two-step procedure is a good prerequisite to probe the phosphoproteome and gain deeper insight into plant phosphorylation-based signaling events.