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Related Concept Videos

Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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...
Spin–Spin Coupling: One-Bond Coupling01:17

Spin–Spin Coupling: One-Bond Coupling

Coupling interactions are strongest between NMR-active nuclei bonded to each other, where spin information can be transmitted directly through the pair of bonding electrons. While nuclei polarize their electrons to the opposite spins, the bonding electron pair has opposite spins. Configurations with antiparallel nuclear spins are expected to be lower in energy. When coupling makes antiparallel states more favorable, J is considered to have a positive value. The one-bond coupling constant, 1J,...

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An Optimized Protocol for Electrophoretic Mobility Shift Assay Using Infrared Fluorescent Dye-labeled Oligonucleotides
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Deciphering the Sox-Oct partner code by quantitative cooperativity measurements.

Calista K L Ng1, Noel X Li, Sheena Chee

  • 1Laboratory for Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore.

Nucleic Acids Research
|February 21, 2012
PubMed
Summary
This summary is machine-generated.

Researchers quantified Sox-Oct transcription factor (TF) cooperation, revealing specific TF partnerships that influence cell fate and induced pluripotent stem cell generation. This study offers a new toolset for understanding protein cooperation in genome regulation.

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Published on: November 29, 2016

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Area of Science:

  • Molecular Biology
  • Genetics
  • Cell Biology

Background:

  • Sox and Oct transcription factors (TFs) are crucial for cell fate determination through cooperative binding to enhancers.
  • Understanding the specific interactions between different Sox TFs and Oct4 is essential for deciphering gene regulation.

Purpose of the Study:

  • To develop a biochemical method for quantifying Sox-Oct TF cooperation.
  • To assess the dimerization preferences of 11 Sox TF high-mobility group (HMG) domains with Oct4.
  • To correlate Sox-Oct cooperativity with induced pluripotent stem cell (iPSC) generation efficiency.

Main Methods:

  • Biochemical quantification of Sox-Oct cooperation on canonical and compressed DNA elements.
  • Dimerization preference clustering of 11 Sox TFs with Oct4.
  • Structural modeling and mutational analysis of Sox proteins.
  • Assessment of iPSC generation efficiency.

Main Results:

  • Sox HMG domains exhibit varied propensities to cooperate with Oct4, leading to distinct dimerization preferences.
  • Specific Sox TFs (Sox2, Sox14, Sox21, Sox15, Sry) cooperate on canonical elements but may compete or bind additively on compressed elements.
  • Other Sox TFs (Sox17, Sox4, Sox5, Sox18, Sox8, Sox9) display different cooperation patterns across element types.
  • Sox-Oct cooperativity directly correlates with the efficiency of iPSC generation.

Conclusions:

  • Selective Sox-Oct partnerships play a significant role in genome regulation and cell fate determination.
  • The developed toolset enables further investigation into protein cooperation dynamics on DNA.
  • Understanding these specific TF interactions is key for advancing stem cell biology and regenerative medicine.