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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...
13.0K
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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Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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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.
These groups modify specific amino acids in a protein....
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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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Calmodulin-dependent Signaling01:16

Calmodulin-dependent Signaling

5.1K
Calmodulin (CaM) is a calcium-binding protein in eukaryotes that controls various calcium-regulated cellular processes. It has four calcium-binding sites that bind calcium to form the calcium-calmodulin ( Ca2+-CaM) complex. GPCR stimulation increases the calcium levels in the cells that bind to CaM and induces a conformational change.
The Ca2+-CaM complex does not have enzymatic activity by itself. Instead, the complex binds downstream target proteins, including membrane proteins or enzymes,...
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Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

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Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
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Related Experiment Video

Updated: Jun 2, 2025

Oligopeptide Competition Assay for Phosphorylation Site Determination
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MMFuncPhos: A Multi-Modal Learning Framework for Identifying Functional Phosphorylation Sites and Their Regulatory

Juan Xie1, Ruihan Dong2, Jintao Zhu1

  • 1Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.

Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
|January 13, 2025
PubMed
Summary

Researchers developed MMFuncPhos, a deep learning model to identify functional phosphorylation sites. A second model, EFuncType, predicts if phosphorylation upregulates or downregulates enzyme activity, aiding disease research and drug discovery.

Keywords:
drug discoveryenzyme engineeringfunctional phosphorylation sitesmulti‐modal deep learning frameworkphosphorylation regulation typesprecision medicinetransfer learning

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

  • Biochemistry
  • Computational Biology
  • Genomics

Background:

  • Protein phosphorylation is vital for biological processes, but the function of many sites remains unknown.
  • Dysregulation of phosphorylation is linked to numerous diseases, highlighting the need for functional site identification.
  • Current methods for predicting functional phosphorylation sites have limitations.

Purpose of the Study:

  • To develop a deep learning model (MMFuncPhos) for predicting functional phosphorylation sites.
  • To create a novel model (EFuncType) using transfer learning to predict the regulatory effect (upregulation/downregulation) of phosphorylation on enzyme activity.
  • To provide robust computational tools for understanding phosphorylation's role in biological regulation.

Main Methods:

  • Development of MMFuncPhos, a multi-modal deep learning framework for functional phosphorylation site prediction.
  • Application of transfer learning to develop EFuncType for predicting phosphorylation-mediated enzyme activity modulation.
  • Validation of model predictions against experimental findings from recent protein phosphorylation studies.

Main Results:

  • MMFuncPhos demonstrated superior performance compared to existing methods for functional phosphorylation site prediction.
  • EFuncType successfully predicted the regulatory impact of phosphorylation on enzyme activity for the first time.
  • Predictions from both MMFuncPhos and EFuncType showed strong agreement with experimental data.

Conclusions:

  • The developed models, MMFuncPhos and EFuncType, offer significant advancements in predicting functional phosphorylation sites and their regulatory effects.
  • These tools enhance our understanding of phosphorylation-driven biological regulation.
  • The study provides valuable resources for precision medicine, enzyme engineering, and drug discovery efforts.