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Related Concept Videos

Cooperative Binding of Transcription Regulators02:13

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 Regulators02:13

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...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Eukaryotic Transcription Activators02:42

Eukaryotic Transcription Activators

Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These domains are...
Conserved Binding Sites01:49

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...

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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

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

Published on: February 7, 2019

A knowledge-based orientation potential for transcription factor-DNA docking.

Takako Takeda1, Rosario I Corona, Jun-Tao Guo

  • 1Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.

Bioinformatics (Oxford, England)
|December 11, 2012
PubMed
Summary
This summary is machine-generated.

A new orientation-dependent potential improves transcription factor (TF)-DNA docking accuracy. This knowledge-based method enhances discrimination of native complexes and aids in predicting binding affinity, serving as a key step in flexible docking.

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Last Updated: May 16, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

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

Published on: February 7, 2019

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Biophysics

Background:

  • Protein-DNA complex modeling is challenging.
  • Accurate potential functions are crucial for discriminating native structures from decoys and improving conformational sampling efficiency in docking.
  • Transcription factor (TF)-DNA interactions are fundamental to gene regulation.

Purpose of the Study:

  • To develop and evaluate a novel orientation-dependent, knowledge-based, residue-level potential for enhancing TF-DNA docking.
  • To assess the potential's performance in TF-DNA binding affinity prediction and native complex discrimination.
  • To improve the accuracy and efficiency of rigid TF-DNA docking.

Main Methods:

  • Development of a novel orientation-dependent, knowledge-based, residue-level statistical potential.
  • Evaluation of the potential's performance on a benchmark of 38 protein-DNA complexes.
  • Application in rigid TF-DNA docking and binding affinity prediction.

Main Results:

  • The new potential demonstrated effectiveness in TF-DNA binding affinity prediction and native complex discrimination.
  • Rigid TF-DNA docking using the orientation potential achieved high accuracy, predicting 42% of cases with <1 Å RMSD and 55% with <3 Å RMSD.
  • The potential significantly improves the accuracy of rigid docking, outperforming previous methods.

Conclusions:

  • The developed orientation-dependent potential significantly enhances the accuracy of rigid TF-DNA docking.
  • This coarse-grained statistical potential is a valuable tool for structural bioinformatics and can be a critical first step in multi-stage flexible docking protocols.
  • The potential offers improved discrimination of near-native structures and aids in predicting binding affinity.