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Related Concept Videos

Protein Organization01:24

Protein Organization

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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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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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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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Protein-protein Interfaces

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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 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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Protein Data Bank Japan: Computational Resources for Analysis of Protein Structures.

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  • 1Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871, Japan.

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Protein Data Bank Japan (PDBj) provides essential tools and archives for macromolecular structure data. New services enhance protein exploration for experimental and computational biologists.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Biophysics

Background:

  • Protein Data Bank Japan (PDBj) is a key resource for 3D macromolecular structure data.
  • PDBj has over two decades of experience in data archiving and distribution.
  • It collaborates globally with other Protein Data Banks.

Purpose of the Study:

  • To highlight PDBj's unique services and tools for exploring protein structures.
  • To introduce novel archives for computational data and raw diffraction images.
  • To showcase new features enhancing data accessibility and analysis for researchers.

Main Methods:

  • Development of unique search, exploration, visualization, and analysis tools.
  • Creation of archives for computational data and raw crystal diffraction images.
  • Introduction of Sequence Navigator Pro and a UniProt-integrated portal.

Main Results:

  • Enhanced capabilities for searching and analyzing protein structures.
  • New archives support computational biology and experimental data.
  • Sequence Navigator Pro and UniProt portal improve experimental design and data integration.

Conclusions:

  • PDBj offers a comprehensive and enhanced service portfolio for structural biologists.
  • New tools facilitate deeper insights into protein structure, dynamics, and function.
  • PDBj continues to be a vital hub for macromolecular structure data and research.