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Related Concept Videos

Protein Networks02:26

Protein Networks

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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.
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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...
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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.
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Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Protein Organization01:24

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Updated: Oct 1, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Identifying protein function and functional links based on large-scale co-occurrence patterns.

Zohar Pasternak1,2, Noam Chapnik2, Roy Yosef2

  • 1Division of Identification and Forensic Science, Israel Police, Jerusalem, Israel.

Plos One
|March 3, 2022
PubMed
Summary
This summary is machine-generated.

We developed Cliquely, a novel software tool to uncover protein functions by analyzing co-occurrence patterns. This approach successfully identified known biological networks and discovered new proteins within the type III secretion system (T3SS).

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • The functions of most known proteins remain experimentally uncharacterized.
  • Understanding protein function is crucial for deciphering biological processes and associations.

Purpose of the Study:

  • To develop a computational tool, Cliquely, for exploring protein co-occurrence patterns to infer protein function.
  • To identify functional associations and biological networks within large-scale protein datasets.

Main Methods:

  • Utilized a dataset of over 23 million proteins across 4,742 genomes from Archaea, Bacteria, and Eukarya.
  • Constructed a co-occurrence graph where edge weights represent co-occurrence probabilities.
  • Applied the Bron-Kerbosch algorithm to detect maximal cliques, representing biological networks.

Main Results:

  • Cliquely successfully identified known biological pathways, including nitrogen fixation, glycolysis, and ribosome proteins.
  • The tool identified the virulence-associated type III secretion system (T3SS) network.
  • Added 13 previously uncharacterized proteins to the T3SS network, highlighting novel discoveries.

Conclusions:

  • Cliquely is an effective open-source tool for exploring protein co-occurrence networks to decipher protein function.
  • The software aids in identifying known biological networks and discovering novel protein associations.
  • Enables researchers to investigate protein functional relationships across different domains of life with customizable stringency.