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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
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Protein Folding

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Related Experiment Video

Updated: Jul 3, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Transition state for protein-DNA recognition.

Diego U Ferreiro1, Ignacio E Sánchez, Gonzalo de Prat Gay

  • 1Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Patricias Argentinas 435, 1405 Buenos Aires, Argentina.

Proceedings of the National Academy of Sciences of the United States of America
|July 31, 2008
PubMed
Summary

Transcriptional regulators directly recognize DNA sequences in a surprising two-state binding process. This direct readout, not nonspecific interactions, forms the bottleneck for protein-DNA complex formation.

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Published on: September 21, 2017

Area of Science:

  • Molecular Biology
  • Biophysics
  • Biochemistry

Background:

  • Transcriptional regulators control gene expression by binding to specific DNA sequences.
  • Understanding the mechanism of protein-DNA recognition is crucial for deciphering gene regulation.

Purpose of the Study:

  • To elucidate the formation of protein-DNA contacts during the two-state recognition pathway of a transcriptional regulator.
  • To identify the rate-limiting step in this direct DNA sequence recognition process.

Main Methods:

  • The study likely involved biophysical techniques to probe protein-DNA interactions and complex formation.
  • Analysis of the transition state and intermediate species in the binding pathway.

Main Results:

  • Direct sequence readout, rather than nonspecific interactions, is established during the transition state.
  • This direct readout constitutes the bottleneck for transcriptional regulator-DNA complex formation.
  • Nonspecific ionic interactions primarily stabilize the final complex, and the transition state interface is hydrated and plastic.

Conclusions:

  • The binding mechanism follows a direct two-state route, differing from previously described multistep pathways.
  • This direct pathway, characterized by a smooth energy landscape, accelerates DNA recognition by transcriptional regulators.