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Related Concept Videos

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...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
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...
Ligand Binding and Linkage00:49

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...

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Related Experiment Video

Updated: May 15, 2026

CD Spectroscopy to Study DNA-Protein Interactions
06:48

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

DNA target sequence identification mechanism for dimer-active protein complexes.

Markita P Landry1, Xueqing Zou, Lei Wang

  • 1Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Nucleic Acids Research
|January 1, 2013
PubMed
Summary
This summary is machine-generated.

The protelomerase TelK protein searches DNA as a monomer but dimerizes and condenses DNA, forming a complex. This novel target search mechanism may apply to other dimer-active proteins.

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Protein-DNA Interactions

Background:

  • Sequence-specific DNA-binding proteins require efficient target site localization.
  • The search mechanisms of monomeric proteins are understood, but those of dimeric or oligomeric proteins are not.
  • Protelomerase TelK is a dimer-active recombinase-like protein.

Purpose of the Study:

  • To investigate the target-search mechanism of the dimeric protein TelK using single-molecule techniques.
  • To elucidate how TelK finds its specific DNA target site.

Main Methods:

  • Single-molecule imaging and tracking of TelK on DNA.
  • Theoretical calculations.
  • Molecular dynamics simulations.

Main Results:

  • TelK diffuses as a monomer on non-target DNA.
  • TelK immobilizes and dimerizes even without a DNA target.
  • Dimeric TelK condenses non-target DNA into a nucleoprotein complex.

Conclusions:

  • TelK employs a novel target-search mechanism involving monomeric diffusion followed by dimerization and DNA condensation.
  • This mechanism may be generalizable to other proteins that function as dimers or oligomers.