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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...

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...

Allosteric Proteins-ATCase

Allosteric Proteins-ATCase

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 pathway,...

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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Related Experiment Video

Updated: Jun 29, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites.

Alina Rabinovich¹, Victor X Jin, Roman Rabinovich

¹Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA.

Genome Research

|October 7, 2008

Summary

E2F transcription factor binding in vivo is not solely dependent on consensus motifs. Promoter utilization and location, not just DNA sequence, dictate E2F recruitment to target genes.

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Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions

Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions

Published on: October 21, 2016

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Last Updated: Jun 29, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions

Fluorescence Anisotropy as a Tool to Study Protein-protein Interactions

Published on: October 21, 2016

Area of Science:

Molecular Biology
Genetics
Epigenetics

Background:

E2F family proteins are crucial transcription factors regulating cell cycle progression.
Previous studies indicated that many in vivo E2F binding sites lack canonical E2F consensus motifs.
The mechanisms governing E2F specificity at sites with and without consensus motifs remain unclear.

Purpose of the Study:

To investigate how E2F transcription factors are recruited to core promoter regions lacking consensus motifs.
To understand the exclusion of E2F from regions containing consensus motifs.
To elucidate the binding specificity of E2F family members in vivo.

Main Methods:

Chromatin immunoprecipitation coupled with DNA microarray analysis (ChIP-chip) to identify in vivo E2F binding sites.
Development and application of a novel in vivo assay, eChIP, for analyzing transcription factor binding to isolated DNA fragments.
Testing models of E2F recruitment to promoters lacking consensus motifs.

Main Results:

E2F recruitment to in vivo binding sites is primarily determined by the site being within a core promoter and its utilization as a promoter in a specific cell type.
A consensus E2F motif is not sufficient for E2F recruitment in vivo.
E2F transcription factors can bind to isolated DNA regions lacking a consensus motif, and binding can be influenced by regulatory elements beyond the primary motif match.

Conclusions:

E2F binding specificity in vivo is governed by broader genomic context, including promoter function and cellular utilization, rather than solely relying on the presence of consensus DNA motifs.
The study provides evidence for E2F binding to non-consensus sites and highlights the importance of distal regulatory regions in mediating E2F interactions.