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Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...

Ligand Binding and Linkage

Ligand Binding and Linkage

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 the...

Ligand Binding and Linkage

Ligand Binding and Linkage

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 the...

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Related Experiment Video

Updated: May 24, 2026

Identifying the Binding Proteins of Small Ligands with the Differential Radial Capillary Action of Ligand Assay (DRaCALA)

Identifying the Binding Proteins of Small Ligands with the Differential Radial Capillary Action of Ligand Assay (DRaCALA)

Published on: March 19, 2021

The PP1 binding code: a molecular-lego strategy that governs specificity.

Ewald Heroes¹, Bart Lesage, Janina Görnemann

¹Laboratory of Biosignaling and Therapeutics, Department of Cellular and Molecular Medicine, University of Leuven, Leuven, Belgium.

The FEBS Journal

|February 25, 2012

Summary

This summary is machine-generated.

Protein Phosphatase 1 (PP1) interacts with nearly 200 proteins (PIPs) via specific binding motifs. This molecular-lego strategy creates diverse holoenzymes, explaining PP1

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Identifying the Binding Proteins of Small Ligands with the Differential Radial Capillary Action of Ligand Assay (DRaCALA)

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Published on: March 19, 2021

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Published on: April 26, 2013

Area of Science:

Molecular Biology
Biochemistry
Cell Biology

Background:

Ser/Thr protein phosphatase 1 (PP1) is a crucial hub protein with extensive interactions.
PP1-interacting proteins (PIPs) exhibit significant diversity, particularly in the brain, testis, and white blood cells.

Purpose of the Study:

To elucidate the molecular mechanisms underlying the specificity of PP1 interactions.
To understand how the diversity of PP1 interactome contributes to its in vivo functions.

Main Methods:

Analysis of PP1-interacting protein (PIP) binding motifs and their interaction with PP1 surface grooves.
Characterization of the 'PP1 binding code' based on motif variants, number, and combinations.
Investigation of how PIPs modulate PP1 activity and localization.

Main Results:

PIP binding is primarily mediated by short motifs docking to PP1 surface grooves.
A 'molecular-lego strategy' involving diverse combinations of binding motifs creates unique PP1 holoenzymes.
PIPs regulate PP1 by interfering with substrate access or by targeting PP1 to specific subcellular locations.

Conclusions:

The extensive interactome and the 'PP1 binding code' are key to PP1's functional specificity.
The combinatorial nature of PIP binding allows for the generation of holoenzymes with tailored properties.
Understanding PP1-PIP interactions is vital for comprehending cellular regulation and function.