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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.
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Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

The Eukaryotic Promoter Region

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The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...

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The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences. The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...

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...

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Related Experiment Video

Updated: Jun 19, 2026

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis

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Published on: June 27, 2020

[Conserved structural features of ETS domain--DNA complexes].

A V Grishin, A V Alekseevskiĭ, S A Spirin

Molekuliarnaia Biologiia

|October 8, 2009

Summary

ETS proteins are key transcription factors regulating animal genes. Their DNA-binding ETS domain uses conserved interactions, including hydrogen bonds and hydrophobic clusters, for stable and specific binding to DNA sequences.

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Last Updated: Jun 19, 2026

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis

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Area of Science:

Molecular Biology
Structural Biology
Genetics

Background:

ETS proteins are crucial transcription factors involved in regulating numerous animal genes.
These proteins share a conserved DNA-binding ETS domain that recognizes the GGA trinucleotide sequence.

Purpose of the Study:

To conduct a comparative analysis of structural features in ETS domain-DNA complexes.
To identify conserved contacts critical for the stability and specificity of protein-DNA interactions.

Main Methods:

Comparative structural analysis of ETS domain-DNA complexes.
Identification of conserved hydrogen bonds, hydrophobic clusters, and water molecules at the protein-DNA interface.

Main Results:

Identified 9 conserved hydrogen bonds with DNA backbone phosphates.
Discovered 2 conserved bidentate hydrogen bonds with DNA major groove atoms.
Found one conserved hydrophobic cluster and 12 conserved water molecules mediating ETS domain-DNA interactions.

Conclusions:

Conserved structural features, including hydrogen bonds and hydrophobic interactions, are vital for ETS protein DNA binding specificity and stability.
The identified interactions provide insights into the molecular mechanisms of ETS transcription factor function.
Results are cataloged in the NPIDB database for protein-DNA complexes.