Prebiotic chemistry: a review of nucleoside phosphorylation and polymerization

The phosphorylation of nucleosides and their polymerization are crucial issues concerning the origin of life. The question of how these plausible chemical processes took place in the prebiotic Earth is still perplexing, despite several studies that have attempted to explain these prebiotic processes. The purpose of this article is to review these chemical reactions with respect to chemical evolution in the primeval Earth. Meanwhile, from our perspective, the chiral properties and selection of biomolecules should be considered in the prebiotic chemical origin of life, which may contribute to further research in this field to some extent

Development of a stable phosphoarginine analog for producing phosphoarginine antibodies

pAIE is designed and synthesized as a stable analog and bioisostere of acid-labile pArg, to produce pArg specific antibodies, facilitating the detection of protein arginine phosphorylation.</p

A Practical Method for Amino Acid Analysis by LC-MS Using Precolumn Derivatization with Urea

Amino acid (AA) analysis is important in biochemistry, food science, and clinical medicine. However, due to intrinsic limitations, AAs usually require derivatization to improve their separation and determination. Here, we present a liquid chromatography-mass spectrometry (LC-MS) method for the derivatization of AAs using the simple agent urea. The reactions proceed quantitatively under a wide range of conditions without any pretreatment steps. Urea-derivatized products (carbamoyl amino acids) of 20 AAs exhibit better separation on reversed-phase columns and increased response in a UV detector compared to underivatized ones. We applied this approach to AA analysis in complex samples using a cell culture media as a model, and it showed potential for the determination of oligopeptides. This fast, simple, and inexpensive method should be useful for AA analysis in complex samples

Cu(II)-Assisted Novel Covalent Warheads for Proteome-wide Cysteine Profiling

In the realm of residue-specific labeling of amino acids within the proteome, cysteine (-SH) emerges as a particularly nucleophilic residue and plays a pivotal role in covalent drug discovery. Despite significant strides in targeting cysteine sites, there remains a substantial expanse of unexplored site space. We discovered that a nucleophilic phenol (DBA)/Cu2+ ‘complex’ serves as a potent warhead for traditionally "inert" cysteines. In the context of a general chemoproteomics profiling, the DBA-1 probe exhibits higher reactivity than IAA toward approximately 45% of quantifiable Cys sites. Dose-dependent profiling experiments suggest that Cu2+ may function not only as an oxidizing agent of phenol but also as a chelating agent of polar residues in proteins. Given its reliance on structural characteristics of proteins for site targeting, this novel (DBA)/Cu2+ ‘complex’ fits the scope of ‘structure-based protein profiling’ (SBPP), highlighting the role of metal ion in the design of effective warheads and the virtue of new proteomic microenvironmental chemistry ‘hunting’

Protein phosphorylation database and prediction tools

AbstractProtein phosphorylation, one of the main protein post-translational modifications, is required for regulating various life activities. Kinases and phosphatases that regulate protein phosphorylation in humans have been targeted to treat various diseases, particularly cancer. High-throughput experimental methods to discover protein phosphosites are laborious and time-consuming. The burgeoning databases and predictors provide essential infrastructure to the research community. To date, &amp;gt;60 publicly available phosphorylation databases and predictors each have been developed. In this review, we have comprehensively summarized the status and applicability of major online phosphorylation databases and predictors, thereby helping researchers rapidly select tools that are most suitable for their projects. Moreover, the organizational strategies and limitations of these databases and predictors have been highlighted, which may facilitate the development of better protein phosphorylation predictors in silico.</jats:p

A sensitive and rapid detection of glutathione based on a fluorescence-enhanced “turn-on” strategy

Fabrication of Au@PLL-AEDP-FITC and its response to GSH.</p