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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.
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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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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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PIP-on-a-chip: A Label-free Study of Protein-phosphoinositide Interactions
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Phosphorus binding sites in proteins: structural preorganization and coordination.

Mathias Gruber1, Per Greisen, Caroline M Junker

  • 1The Biomimetic Membrane Group, Department of Physics, Technical University of Denmark , DK 2800 Kongens Lyngby Denmark.

The Journal of Physical Chemistry. B
|January 11, 2014
PubMed
Summary

This study analyzes phosphorus compound binding sites in 8307 protein structures. It reveals characteristic first and second shell residue distributions crucial for stabilizing phosphorus interactions within proteins.

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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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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Phosphorus is essential for cellular structure and function, present in key biomolecules.
  • Understanding phosphorus compound interactions is vital for cell biology.
  • Previous binding analyses were limited to individual phosphate-binding structures.

Purpose of the Study:

  • To characterize the binding sites of phosphorus compounds using a first and second shell approach.
  • To analyze amino acid propensities in phosphorus-binding sites across a large dataset.
  • To investigate the influence of phosphorus compound characteristics and co-bound cations on binding site structure.

Main Methods:

  • Utilized a large dataset of 8307 protein structures from the RCSB Protein Data Bank (PDB).
  • Applied a first shell (direct interactions) and second shell (indirect interactions) analysis framework.
  • Examined amino acid propensities and protein backbone group distributions within binding sites.

Main Results:

  • Identified characteristic first shell residue distributions for phosphorus compound binding.
  • Found that first shell composition is influenced by the phosphorus compound and co-bound cations.
  • Determined that the second shell primarily consists of protein backbone groups, stabilizing the first shell.

Conclusions:

  • The study provides a detailed characterization of phosphorus-binding sites in proteins.
  • First and second shell interactions play distinct but complementary roles in phosphorus compound recognition and stabilization.
  • Co-bound cations significantly influence the structure and composition of phosphorus-binding sites.