Visualizing Post‐Translational Modifications in Protein Interaction Networks Using PTMOracle

Tay, Aidan P.; Liang, Angelita; Wilkins, Marc R.; Pang, Chi Nam Ignatius

doi:10.1002/cpbi.71

Cited by 4 publications

(4 citation statements)

References 49 publications

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“…Proteins are usually regulated by posttranslational modifications, of which ubiquitylation is the second most common only behind phosphorylation [ 30 ]. Protein ubiquitination dysregulation is one of the causes of colorectal cancer.…”

Section: Discussionmentioning

confidence: 99%

PRDX2 promotes the proliferation of colorectal cancer cells by increasing the ubiquitinated degradation of p53

et al. 2021

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Colorectal cancer is the most common gastrointestinal cancer and causes severe damage to human health. PRDX2 is a member of the peroxiredoxin family reported to have a high level of expression in colorectal cancer. However, the mechanisms by which PRDX2 promotes the proliferation of colorectal cancer are still unclear. Here, the results indicated that PRDX2 expression was upregulated in colorectal cancer and closely correlated with poor prognosis. Functionally, PRDX2 promoted the proliferation of colorectal cancer cells. Mechanistically, PRDX2 could bind RPL4, reducing the interaction between RPL4 and MDM2. These findings demonstrate that the oncogenic property of PRDX2 may be attributed to its regulation of the RPL4-MDM2-p53 pathway, leading to p53 ubiquitinated degradation.

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Section: Discussionmentioning

confidence: 99%

PRDX2 promotes the proliferation of colorectal cancer cells by increasing the ubiquitinated degradation of p53

et al. 2021

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“…Phosphorylated proteins have the broadest interaction spectrum with other modified proteins and are located at the centre of the protein interaction network. [24] Phosphorylation of proteins is also an important and pervasive mechanism that regulates the viability and function of organisms [25] and the mechanism is usually reversible. Besides, phosphorylated proteins play an important role in the transduction of cell signals.…”

Section: Introductionmentioning

confidence: 99%

“…Phosphorylation modification is one of the post‐translational modifications of proteins and is an important PTM in regulating human metabolism. Phosphorylated proteins have the broadest interaction spectrum with other modified proteins and are located at the centre of the protein interaction network [24] . Phosphorylation of proteins is also an important and pervasive mechanism that regulates the viability and function of organisms [25] and the mechanism is usually reversible.…”

Section: Introductionmentioning

confidence: 99%

Electroosmotic Sensing of Uncharged Peptides and Differentiating Their Phosphorylated States Using Nanopores

Si,

Chen,

Zhang

et al. 2024

ChemPhysChem

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The correct characterization and identification of different kinds of proteins is crucial for the survival and development of living organisms, and proteomics research promotes the analysis and understanding of future genome functions. Nanopore technique has been proved to accurately identify individual nucleotides. However, accurate and rapid protein sequencing is difficult due to the variability of protein structures that contains more than 20 amino acids, and it remains very challenging especially for uncharged peptides as they can not be electrophoretically driven through the nanopore. Graphene nanopores have the advantages of high accuracy, sensitivity and low cost in identifying protein phosphorylation modifications. Here, by using all‐atom molecular dynamics simulations, charged graphene nanopores are employed to electroosmotically capture and sense uncharged peptides. By further mimicking AFM manipulation of single molecules, it is also found that the uncharged peptides and their phosphorylated states could also be differentiated by both the ionic current and pulling force signals during their pulling processes through the nanopore with a slow and constant velocity. The results shows ability of using nanopores to detect and discriminate single amino acid and its phosphorylation, which is essential for the future low‐cost and high‐throughput sequencing of protein residues and their post‐translational modifications.

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“…The use of these mass spectrometry toolsets combined with post-translational modification (PTM) analyses, such as phosphorylation, will ultimately move the field toward being able to obtain a comprehensive list of molecular alterations in cellular mechanosensing. 12 Therefore, protein−protein interactions (PPIs) and phosphorylation, one of the main PTMs, 13 will be key indicators of protein activity 13 at the specific time point at which they are analyzed.…”

Section: ■ Introductionmentioning

confidence: 99%

Phosphoproteomic Analysis and Protein–Protein Interaction of Rat Aorta GJA1 and Rat Heart FKBP1A after Secoiridoid Consumption from Virgin Olive Oil: A Functional Proteomic Approach

Pedret

Catalán

Rubió

et al. 2021

J. Agric. Food Chem.

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Protein functional interactions could explain the biological response of secoiridoids (SECs), main phenolic compounds in virgin olive oil (VOO). The aim was to assess protein–protein interactions (PPIs) of the aorta gap junction alpha-1 (GJA1) and the heart peptidyl-prolyl cis-trans isomerase (FKBP1A), plus the phosphorylated heart proteome, to describe new molecular pathways in the cardiovascular system in rats using nanoliquid chromatography coupled with mass spectrometry. PPIs modified by SECs and associated with GJA1 in aorta rat tissue were calpain, TUBA1A, and HSPB1. Those associated with FKBP1A in rat heart tissue included SUCLG1, HSPE1, and TNNI3. In the heart, SECs modulated the phosphoproteome through the main canonical pathways PI3K/mTOR signaling (AKT1S1 and GAB2) and gap junction signaling (GAB2 and GJA1). PPIs associated with GJA1 and with FKBP1A, the phosphorylation of GAB2, and the dephosphorylation of GJA1 and AKT1S1 in rat tissues are promising protein targets promoting cardiovascular protection to explain the health benefits of VOO.

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Visualizing Post‐Translational Modifications in Protein Interaction Networks Using PTMOracle

Cited by 4 publications

References 49 publications

PRDX2 promotes the proliferation of colorectal cancer cells by increasing the ubiquitinated degradation of p53

PRDX2 promotes the proliferation of colorectal cancer cells by increasing the ubiquitinated degradation of p53

Electroosmotic Sensing of Uncharged Peptides and Differentiating Their Phosphorylated States Using Nanopores

Phosphoproteomic Analysis and Protein–Protein Interaction of Rat Aorta GJA1 and Rat Heart FKBP1A after Secoiridoid Consumption from Virgin Olive Oil: A Functional Proteomic Approach

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