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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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Phosphorylation01:02

Phosphorylation

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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.
During phosphorylation, protein kinases transfer the terminal phosphate group of ATP to specific amino acid side chains of substrate proteins. Serine, threonine, and tyrosine are the most commonly...
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Amplifying Signals via Enzymatic Cascade01:22

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When a ligand binds to a cell-surface receptor, the receptor's intracellular domain changes shape, which may either activate its enzyme function or allow its binding to other molecules. The initial signal is amplified by most signal transduction pathways. This means that a single ligand molecule can activate multiple molecules of a downstream target. Proteins that relay a signal are most commonly phosphorylated at one or more sites, activating or inactivating the protein. Kinases catalyze...
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Receptor Tyrosine Kinases01:26

Receptor Tyrosine Kinases

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Receptor tyrosine kinases or RTKs are membrane-bound receptors that phosphorylate specific tyrosine on protein substrates. RTKs regulate cellular growth, differentiation, survival, and migration. They contain an extracellular ligand binding domain, a transmembrane domain, and a cytosolic tail with intrinsic kinase activity. Several extracellular signaling molecules activate RTKs in one or more ways and relay the signal downstream. Ligands such as platelet-derived growth factor (PDGF) or...
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Transducer Mechanism: Enzyme-Linked Receptors01:27

Transducer Mechanism: Enzyme-Linked Receptors

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Enzyme-linked receptors are cell-surface receptors acting as an enzyme or associating with an enzyme intracellularly. They make excellent drug targets. Drugs can bind to the extracellular ligand-binding domain or directly affect their enzymatic domain and alter their activity.
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Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

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Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
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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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Sequence - dynamics - function relationships in protein tyrosine phosphatases.

Rory M Crean1, Marina Corbella1,2, Ana R Calixto1,3

  • 1Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.

QRB Discovery
|May 1, 2024
PubMed
Summary
This summary is machine-generated.

Protein tyrosine phosphatases (PTPs) activity relies on WPD-loop motion. Simulations reveal significant differences in loop dynamics, not catalysis, offering new drug discovery targets by engineering protein interactions.

Keywords:
empirical valence bondenzyme evolutionloop dynamicsmolecular simulationsprotein tyrosine phosphatases

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Enzymology

Background:

  • Protein tyrosine phosphatases (PTPs) regulate cellular signaling via WPD-loop conformational changes.
  • WPD-loop motion dictates catalytic activity and enzyme turnover rates.

Purpose of the Study:

  • Investigate the dynamic properties of WPD-loops in chimeric PTPs.
  • Understand the molecular basis for WPD-loop population shifts to a wide-open conformation.
  • Explore potential drug discovery strategies targeting the wide-open conformation.

Main Methods:

  • Molecular dynamics simulations of chimeric PTPs (YopH scaffold with PTP1B WPD-loop).
  • Analysis of catalytic step energetics.
  • Detailed interaction network analysis of protein dynamics.

Main Results:

  • Negligible energetic differences in the chemical step of catalysis between variants.
  • Significant differences observed in WPD-loop dynamical properties.
  • Identified molecular interactions driving the population shift to a wide-open conformation.

Conclusions:

  • WPD-loop dynamics, not just chemistry, are critical for PTP function.
  • The wide-open conformation, observed in chimeric PTPs, is a potential drug target.
  • Protein interaction networks can be engineered to modulate WPD-loop dynamics.