Mechanisms of specificity in protein phosphorylation

Abstract

A typical protein kinase must recognize between one and a few hundred bona fide phosphorylation sites in a background of approximately 700,000 potentially phosphorylatable residues. Multiple mechanisms have evolved that contribute to this exquisite specificity, including the structure of the catalytic site, local and distal interactions between the kinase and substrate, the formation of complexes with scaffolding and adaptor proteins that spatially regulate the kinase, systems-level competition between substrates, and error-correction mechanisms. The responsibility for the recognition of substrates by protein kinases appears to be distributed among a large number of independent, imperfect specificity mechanisms.

SLK-mediated phosphorylation of paxillin is required for focal adhesion turnover and cell migration

“…The composition of focal adhesions has been shown to vary over time depending on its acquired level of maturity. For example, focal complexes, which are integral to the formation of lamellipodial and filopodial extensions, have been shown to express relatively low to non-existent levels of proteins that are more prevalent in stable adhesions such as paxillin and zyxin, respectively [48][49][50]. However, the heterogeneity of the adhesion complex does not end with differential protein composition and localization.…”

“…Phosphorylation plays a major role in propagating the transduction of extracellular stimuli in a sensitive, selective and temporally ordered manner [49,55]. This in turn, functions to activate a diverse cascade of signaling pathways which ultimately culminate in the regulation of global cellular processes [49,[55][56][57].…”

Proteomic analysis of post translational modifications in cyanobacteria

“…Quantitative proteomic approaches are generally subdivided into three categories: in vitro chemical labeling approaches such as isobaric tags for relative and absolute quantification (iTRAQ) and isobaric tandem mass tag (TMT); metabolic labeling strategies, including stable isotope labeling with amino acids in cell culture (SILAC), 15 N labeling; and labelfree approaches. The iTRAQ/TMT labeling techniques have been used in cyanobacteria and proved to be efficient and reliable methods for quantitative proteomics [103][104][105][106].…”

“…However, it works well for mammalian cell lines [113][114][115], but not so effective in autotrophic organisms such as cyanobacteria due to their ability to synthesize all amino acids [116,117]. The second primary method in stable isotope metabolic labeling relies on the introduction of a heavy isotope such as 15 N, often in the form of Na 15 NO 3 or K 15 NO 3 as a nitrogen source, is a powerful tool for the quantitative analysis in plant and bacteria [118,119]. Quantitative proteomics based on "metabolic labeling" has already been successfully used in some cyanobacterial strains [120][121][122].…”

“…The PTM systems are key components of the signal transduction network and play important regulatory roles [14,15]. A large number of PTMs events have already been reported in cyanobacteria, which are extensively involved in cellular processes and metabolic homeostasis (which will be further discussed in Section 2.1).…”