Phosphoproteomics Meets Chemical Genetics: Approaches for Global Mapping and Deciphering the Phosphoproteome

Abstract

Protein kinases are important enzymes involved in the regulation of various cellular processes. To function properly, each protein kinase phosphorylates only a limited number of proteins among the thousands present in the cell. This provides a rapid and dynamic regulatory mechanism that controls biological functions of the proteins. Despite the importance of protein kinases, most of their substrates remain unknown. Recently, the advances in the fields of protein engineering, chemical genetics, and mass spectrometry have boosted studies on identification of bona fide substrates of protein kinases. Among the various methods in protein kinase specific substrate identification, genetically engineered protein kinases and quantitative phosphoproteomics have become promising tools. Herein, we review the current advances in the field of chemical genetics in analog-sensitive protein kinase mutants and highlight selected strategies for identifying protein kinase substrates and studying the dynamic nature of protein phosphorylation.

Design of Micro- and Nanoparticles: Self-Assembly and Application

“…AgNPs undergo preferential binding with the gp120 subunit of the viral envelope glycoprotein. These interaction between AgNPs and glycoproteins inhibit the virus from binding to host cells [84] and AgNPs act as potential antiviral agents against various type of viruses including influenza virus [85,86]. Biologically synthesized AgNPs using plant extracts of Lampranthus coccineus and Malephora lutea exhibited significant antiviral activity against different types of viruses such as HSV-1, HAV-10 and CoxB4 virus [87].…”

Nanostructured Ceria: Biomolecular Templates and (Bio)applications

“…The area of phosphoproteomics is advancing at a rapid pace, in order to gain a better understanding of the biochemical profiling of several pathologies, especially for their early diagnosis [ 84 ]. However, phosphate groups are labile, making the detection of phosphopeptides quite a challenge, for which metal oxide affinity chromatography (MOAC) has offered promising solutions [ 85 ].…”

Chemical Genetic Validation of CSNK2 Substrates Using an Inhibitor-Resistant Mutant in Combination with Triple SILAC Quantitative Phosphoproteomics

“…Those sites which demonstrate reduced phosphorylation relative to control cells not treated with inhibitor are presumed to be substrates. Combination of this method with quantitative phosphoproteomic analysis enables the large-scale identification of putative substrates ( Shah and Kim, 2019 ; Jurcik et al, 2020 ). The success of this approach relies mainly on the availability of specific, potent inhibitors for the kinase of interest.…”