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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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

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Related Experiment Video

Updated: May 13, 2026

Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

Knotting pathways in proteins.

Joanna I Sułkowska1, Jeffrey K Noel, César A Ramírez-Sarmiento

  • 1Center for Theoretical Biological Physics, Rice University, 6100 Main Street, Houston, TX 77005, U.S.A. jsulkowska@chem.uw.edu.pl

Biochemical Society Transactions
|March 22, 2013
PubMed
Summary

Proteins can navigate complex topological challenges during folding. This review explores theoretical and experimental insights into protein knotting, revealing mechanisms for efficient folding and evolutionary survival.

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Identifying Protein-protein Interaction Sites Using Peptide Arrays
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Area of Science:

  • Biochemistry
  • Structural Biology
  • Biophysics

Background:

  • Proteins must achieve a specific native state for biological function.
  • The discovery of knotted and slipknotted proteins highlights their ability to overcome topological folding barriers.

Purpose of the Study:

  • To review current progress in understanding the protein knotting process.
  • To synthesize theoretical and experimental findings on protein folding topology.

Main Methods:

  • Focus on theoretical approaches for unambiguous knot detection.
  • Inclusion of experimental comparisons to validate theoretical models.
  • Analysis of numerical simulations for folding pathways.

Main Results:

  • Small knotted proteins fold via twisted loop formation and threading mechanisms.
  • Larger, more complex knots increase the likelihood of energy landscape traps.
  • Chaperone assistance is likely crucial for the folding of longer knotted proteins.

Conclusions:

  • Knotted proteins can fold efficiently despite topological complexity.
  • Efficient folding mechanisms allow knotted proteins to persist under evolutionary pressure.
  • Understanding protein knotting is key to comprehending protein function and evolution.