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Related Concept Videos

Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

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...
Protein Kinases and Phosphatases02:54

Protein Kinases and Phosphatases

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...
Phosphorylation01:02

Phosphorylation

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...
Phosphorylation01:02

Phosphorylation

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...
ATP Energy Storage and Release01:31

ATP Energy Storage and Release

ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP and inorganic phosphate (Pi), and the free energy released during this process is lost as heat. The energy released by ATP hydrolysis is used to perform work inside the cell and depends on a strategy called energy coupling. Cells couple the exergonic reaction of ATP hydrolysis with endergonic reactions, allowing them to proceed.
One example of energy coupling using ATP involves a...
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

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Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay
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Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay

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Computing the stochastic dynamics of phosphorylation networks.

M N Steijaert1, J H K Van Den Brink, A M L Liekens

  • 1Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands. m.n.steijaert@tue.nl

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|February 23, 2010
PubMed
Summary
This summary is machine-generated.

This study presents a computational approach to model cellular signaling networks with random fluctuations. The methods overcome limitations in simulating stochastic dynamics for finite state space systems like phosphorylation cycles.

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Last Updated: Jun 16, 2026

Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay
12:26

Identification of Cyclin-dependent Kinase 1 Specific Phosphorylation Sites by an In Vitro Kinase Assay

Published on: May 3, 2018

Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation
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Published on: October 4, 2024

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11:13

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Published on: August 29, 2015

Area of Science:

  • Biochemistry
  • Computational Biology
  • Systems Biology

Background:

  • Cells respond to extracellular signals via complex protein interaction networks.
  • Low concentrations of signaling proteins can lead to random fluctuations affecting network dynamics.
  • Stochastic methods are necessary for modeling systems with significant random fluctuations.

Purpose of the Study:

  • To develop and implement computational methods for evaluating the stochastic dynamics of biological signaling networks.
  • To address limitations in numerical evaluation of the Chemical Master Equation for systems with infinite or large state spaces.

Main Methods:

  • Focus on biological networks with finite state spaces, specifically phosphorylation cycles.
  • Utilize parallel computation and memory-efficient algorithms to overcome computational limitations.
  • Implement these methods in a parallel C++ program for evaluating stochastic dynamics.

Main Results:

  • Successfully evaluated the stochastic dynamics of a single phosphorylation cycle.
  • Successfully evaluated the stochastic dynamics of an oscillating MAP-kinase cascade.
  • Demonstrated the effectiveness of the developed computational methods for complex signaling networks.

Conclusions:

  • The developed parallel computation methods efficiently overcome limitations in simulating stochastic dynamics for finite state space biological networks.
  • This approach enables more accurate modeling of cellular signaling pathways influenced by random fluctuations.
  • The implemented C++ program provides a valuable tool for systems biology research.