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Related Concept Videos

Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

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Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
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Proteomics01:33

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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The addition or removal of phosphate groups from proteins is the most common chemical modification that regulates cellular processes. These modifications can affect the structure, activity, stability, and localization of proteins within cells as well as their interactions with other proteins.
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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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The mammalian target of rapamycin  (mTOR) is a serine/threonine kinase that regulates growth, proliferation, and cell survival in response to hormones, growth factors, or nutrient availability. This kinase exists in two structurally and functionally distinct forms: mTOR complex 1  (mTORC1) and mTOR complex 2  (mTORC2). The first form (mTORC1) is composed of a rapamycin-sensitive Raptor and proline-rich Akt substrate, PRAS40. In contrast,  mTORC2 consists of a...
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Related Experiment Video

Updated: Aug 6, 2025

A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors
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A Mass Spectrometry-Based Approach to Identify Phosphoprotein Phosphatases and their Interactors

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Multi-omics analysis identifies drivers of protein phosphorylation.

Tian Zhang1, Gregory R Keele2, Isabela Gerdes Gyuricza2

  • 1Harvard Medical School, Boston, MA, 02115, USA.

Genome Biology
|March 22, 2023
PubMed
Summary

This study mapped protein phosphorylation regulators across mouse tissues, identifying key factors like PDK1. This multi-omics approach offers a resource for understanding phosphorylation in diverse genetic backgrounds.

Keywords:
Collaborative CrossMedation analysisMulti-omicsPhosphorylationPhosphorylation regulationQuantitative trait loci (QTL)

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Area of Science:

  • Genomics
  • Proteomics
  • Systems Biology

Background:

  • Protein phosphorylation regulates crucial cellular processes like enzyme activation and signaling.
  • Phosphopeptide abundance depends on parent protein levels and site-specific phosphorylation.
  • Understanding phosphorylation is vital for cellular function and disease research.

Purpose of the Study:

  • To quantify phosphopeptides, proteins, and transcripts in mouse tissues.
  • To identify genetic regulators of protein phosphorylation.
  • To explore causal drivers of phosphorylation through genetic mediation analysis.

Main Methods:

  • Quantitative multi-omics analysis (phosphoproteomics, proteomics, transcriptomics).
  • Analysis of heart, liver, and kidney tissues from 58 Collaborative Cross mouse strains.
  • Mapping of phosphorylation quantitative trait loci (phQTL) and genetic mediation analysis.

Main Results:

  • Approximately 700 phQTL were mapped across three tissues.
  • Identified regulators include kinases, phosphatases, and cytokines.
  • Highlighted targets of pyruvate dehydrogenase kinase 1 (PDK1), linked to obesity and type 2 diabetes.

Conclusions:

  • Integrative multi-omics analysis in diverse strains is a powerful tool for identifying phosphorylation regulators.
  • The study provides a valuable data resource for future research on protein phosphorylation.
  • Findings offer insights into the genetic control of phosphorylation and its role in metabolic diseases.