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Related Concept Videos

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...
Conservation of Protein Domains02:26

Conservation of Protein Domains

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 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 Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
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...

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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
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Reassessing a sparse energetic network within a single protein domain.

Celestine N Chi1, Lisa Elfström, Yao Shi

  • 1Department of Medical Biochemistry and Microbiology, Uppsala University Biomedical Centre, Box 582, SE-751 23 Uppsala, Sweden.

Proceedings of the National Academy of Sciences of the United States of America
|March 15, 2008
PubMed
Summary

Statistical coupling in protein sequences does not always indicate energetic coupling or allostery. Residue proximity, not coevolution, better explains allosteric communication in PDZ domains.

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Area of Science:

  • Protein science
  • Molecular biology
  • Biophysics

Background:

  • Allosteric communication is crucial for protein function.
  • Evolutionarily conserved residue networks were previously thought to mediate allostery.
  • PDZ domains provided a model system for studying these networks.

Purpose of the Study:

  • To reassess energetic coupling in conserved residue networks.
  • To determine if statistical coupling predicts energetic coupling and allostery.
  • To investigate the relationship between residue proximity and allosteric communication.

Main Methods:

  • Double mutant cycle analysis.
  • Ligand binding experiments.
  • Protein stability assays.

Main Results:

  • Energetic coupling was not exclusive to coevolved networks.
  • Ligand binding coupling correlated with residue distance, not coevolution.
  • Statistical coupling from sequence analysis did not reliably report energetic coupling.

Conclusions:

  • Coevolved residue networks are not necessarily the primary mediators of allosteric communication.
  • Residue proximity is a stronger predictor of energetic coupling than statistical coupling.
  • Statistical coupling analysis alone may not accurately reflect functional allosteric mechanisms.