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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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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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Related Experiment Video

Updated: Oct 28, 2025

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

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

Published on: May 3, 2018

Computational Phosphorylation Network Reconstruction: An Update on Methods and Resources.

Min Zhang¹, Guangyou Duan²

¹Department of Neurology, The First Affiliated Hospital of Shandong First Medical University, Jinan, People's Republic of China.

Methods in Molecular Biology (Clifton, N.J.)

|July 16, 2021

Summary

This summary is machine-generated.

Protein phosphorylation, a key post-translational modification, involves kinases and phosphatases. This study reviews computational methods for inferring these crucial phosphorylation networks.

Keywords:

Kinase–substrate relationship Network reconstruction Phosphatase–substrate relationship Phosphorylation network Posttranslational modification Protein–protein interaction

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Last Updated: Oct 28, 2025

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

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Published on: May 3, 2018

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Identification of Kinase-substrate Pairs Using High Throughput Screening

Identification of Kinase-substrate Pairs Using High Throughput Screening

Published on: August 29, 2015

Area of Science:

Molecular Biology
Systems Biology
Bioinformatics

Background:

Post-translational modifications, particularly protein phosphorylation, are vital for cellular signaling.
Protein kinases and phosphatases regulate cellular information flow through phosphorylation and dephosphorylation cycles.
Understanding protein interactions within phosphorylation networks is crucial for deciphering cellular mechanisms.

Purpose of the Study:

To summarize and discuss computational methods for inferring phosphorylation networks.
To provide an overview of resources available for phosphorylation network analysis.
To highlight the importance of substrate specificity and phosphoproteome data in network inference.

Main Methods:

Review of various statistical learning methods applied to infer phosphorylation networks.
Analysis of approaches utilizing substrate specificity (sequence, structure) for network inference.
Discussion of methods leveraging phosphoproteome data for network reconstruction.

Main Results:

Identified diverse computational approaches for mapping phosphorylation events.
Highlighted the utility of machine learning in predicting kinase-substrate interactions.
Emphasized the role of sequence and structural information in enhancing network inference accuracy.

Conclusions:

Computational methods are essential for elucidating complex phosphorylation networks.
Integrating substrate specificity and phosphoproteome data improves network inference.
Further development of these computational tools will advance our understanding of cell signaling.