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Related Concept Videos

Protein-protein Interfaces02:04

Protein-protein Interfaces

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...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

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...
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...
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...
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...

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Updated: May 25, 2026

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain
14:25

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Published on: December 12, 2017

Engineering domain-swapped binding interfaces by mutually exclusive folding.

Jeung-Hoi Ha1, Joshua M Karchin, Nancy Walker-Kopp

  • 1Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210, USA.

Journal of Molecular Biology
|January 17, 2012
PubMed
Summary

Engineered domain swapping creates specific protein assemblies by exchanging segments. This method uses ubiquitin inserted into barnase to induce self-assembly, enabling novel biomaterial and protein complex construction.

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Design and Synthesis of a Reconfigurable DNA Accordion Rack
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Design and Synthesis of a Reconfigurable DNA Accordion Rack

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Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain
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Published on: December 12, 2017

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Area of Science:

  • Protein engineering
  • Biochemistry
  • Structural biology

Background:

  • Domain swapping is a specific protein oligomerization mechanism involving reciprocal exchange of polypeptide segments.
  • It plays roles in protein recognition and offers potential for controlled self-assembly.

Purpose of the Study:

  • To engineer domain-swapped protein interfaces by inserting one protein into a surface loop of another.
  • To utilize the "mutually exclusive folding" design to destabilize monomeric states and promote oligomerization.

Main Methods:

  • Insertion of ubiquitin (Ub) into surface loops of barnase (Bn) to create conformational stress.
  • Analysis of domain-swapped structures using X-ray crystallography.
  • Tuning binding affinity by varying peptide linker lengths.

Main Results:

  • Ubiquitin insertion into barnase surface loops induced domain swapping and oligomerization.
  • X-ray structure revealed strain relief through intermolecular folding, forming domain-swapped polymers.
  • All six insertion constructs demonstrated oligomerization, indicating a consistent domain-swapping event.

Conclusions:

  • Engineered domain swapping via loop insertion is a viable strategy for protein self-assembly.
  • Binding affinity can be modulated by linker length, offering control over the assembly process.
  • These engineered proteins hold potential for creating "smart" biomaterials and assembling complex protein structures.