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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.
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,...
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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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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.
The primary structure of a protein is its amino acid sequence....
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Conservation of Protein Domains Over Different Proteins02:26

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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.
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The Protein Data Bank: Current Status and Future Challenges.

Enrique E Abola1, Nancy O Manning1, Jaime Prilusky2

  • 1Department of Chemistry, Brookhaven National Laboratory, Upton, NY 11973 USA.

Journal of Research of the National Institute of Standards and Technology
|January 1, 1996
PubMed
Summary

The Protein Data Bank (PDB), a crucial archive for biological structures, is transitioning to the advanced Three-Dimensional Database of Biomolecular Structures (3DB). This new system offers enhanced knowledge-based archiving and access for the scientific community.

Keywords:
NMRdatabasefederationprotein structurethree-dimensional structurex-ray crystallography

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Biochemistry

Background:

  • The Protein Data Bank (PDB) has served as a primary archive for experimentally determined 3D structures of biological macromolecules for 25 years.
  • The PDB supports a global community of researchers in various life science disciplines.

Purpose of the Study:

  • To announce the transition from the Protein Data Bank (PDB) to the new Three-Dimensional Database of Biomolecular Structures (3DB).
  • To describe the advanced features and architecture of the 3DB system.
  • To inform users about the continuity of service and compatibility during the transition.

Main Methods:

  • The 3DB system integrates object-oriented and relational database technologies.
  • It is designed as a direct-deposition archive.
  • The system will accommodate third-party annotations.

Main Results:

  • The 3DB will continue operations from Brookhaven National Laboratory, ensuring sustained access to structural data.
  • 3DB represents a sophisticated, knowledge-based system for archiving and accessing structural information.
  • The conversion process from PDB to 3DB is designed to be evolutionary, maintaining compatibility with existing software.

Conclusions:

  • The Three-Dimensional Database of Biomolecular Structures (3DB) will supersede the Protein Data Bank (PDB), offering enhanced capabilities.
  • 3DB ensures a seamless transition for the scientific community, preserving data accessibility and software compatibility.