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Related Concept Videos

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...
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...
The Phosphorus Cycle01:21

The Phosphorus Cycle

Unlike carbon, water, and nitrogen, phosphorus is not present in the atmosphere as a gas. Instead, most phosphorus in the ecosystem exists as compounds, such as phosphate ions (PO43-), found in soil, water, sediment and rocks. Phosphorus is often a limiting nutrient (i.e., in short supply). Consequently, phosphorus is added to most agricultural fertilizers, which can cause environmental problems related to runoff in aquatic ecosystems.

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Related Experiment Video

Updated: May 15, 2026

Chemical Triphosphorylation of Oligonucleotides
13:19

Chemical Triphosphorylation of Oligonucleotides

Published on: June 2, 2022

Revised AMBER parameters for bioorganic phosphates.

T Steinbrecher1, J Latzer, D A Case

  • 1Institute for Physical Chemistry, Kaiserstr 12, University Karlsruhe, KIT, 76131 Karlsruhe, Germany, and Dept. of Chemistry and Chemical Biology, and BioMaPS Institute, 174 Frelinghuysen Road, Rutgers University, Piscataway, NJ 08854.

Journal of Chemical Theory and Computation
|December 25, 2012
PubMed
Summary
This summary is machine-generated.

We developed new AMBER force field parameters for simulating phosphorylated amino acids. These refined parameters improve accuracy for biological simulations, especially those involving multiple protonation states.

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Chemical Triphosphorylation of Oligonucleotides
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Published on: June 2, 2022

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Optimized Procedure for Determining the Adsorption of Phosphonates onto Granular Ferric Hydroxide using a Miniaturized Phosphorus Determination Method
08:21

Optimized Procedure for Determining the Adsorption of Phosphonates onto Granular Ferric Hydroxide using a Miniaturized Phosphorus Determination Method

Published on: May 18, 2018

Area of Science:

  • Computational Chemistry
  • Biomolecular Simulations
  • Molecular Dynamics

Background:

  • Accurate force fields are crucial for reliable biomolecular simulations.
  • Phosphorylation significantly alters amino acid properties, requiring specialized parameters.
  • Existing AMBER force fields may not fully capture phosphorylation energetics.

Purpose of the Study:

  • To develop and validate AMBER force field parameters for phosphorylated serine, threonine, and tyrosine.
  • To improve the accuracy of molecular dynamics simulations involving these modified residues.
  • To enable reliable simulations of biological systems with varying protonation states.

Main Methods:

  • Used RESP fitting for initial atomic partial charges.
  • Refined parameters using a thermodynamic cycle with experimental pKa values and QM/MD calculations.
  • Incorporated a polarization energy term and adjusted Lennard-Jones parameters.
  • Employed thermodynamic integration for solvation free energy calculations.

Main Results:

  • Modified phosphate oxygen radii to balance electrostatic interactions.
  • Achieved thermodynamically consistent parameters for monoanionic phosphorylation.
  • Found that larger, residue-specific radii are needed for dianions.
  • Validated parameter set for improved simulation accuracy.

Conclusions:

  • The refined AMBER force field parameters enhance the simulation of phosphorylated amino acids.
  • Adjustments to van der Waals radii, particularly for phosphate oxygens, are critical.
  • These parameters are valuable for studies involving dynamic protonation states in biological systems.