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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.
The primary structure of a protein is its amino acid sequence....
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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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Protein-protein Interfaces02:04

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 Data Bank Japan: Improved tools for sequence-oriented analysis of protein structures.

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Protein Science : a Publication of the Protein Society
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Summary
This summary is machine-generated.

Protein Data Bank Japan (PDBj) offers enhanced tools for exploring 3D macromolecular structures. New features integrate UniProt data, aiding analysis of protein variations, stability, and function for researchers.

Keywords:
BMRBEMDBPDBUniProtprotein structuresequence analyses

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Biochemistry

Background:

  • Protein Data Bank Japan (PDBj) serves as a key repository for 3D macromolecular structure data.
  • PDBj has over two decades of experience in processing and distributing experimental structural data.
  • Global collaboration exists with other Protein Data Bank members for data sharing.

Purpose of the Study:

  • To introduce new services and tools for searching, exploring, visualizing, and analyzing protein structures.
  • To enhance user experience by integrating diverse data resources for a comprehensive protein overview.
  • To support both experimental and computational structural biologists in interpreting protein structure, dynamics, and function.

Main Methods:

  • Development of a UniProt-integrated portal for protein information.
  • Integration of internal and external data resources, including genomic variations.
  • Implementation of services for exploring proteins via experimental and computational approaches.

Main Results:

  • A new portal provides quick overviews of target proteins with recommended structures and integrated data.
  • The portal facilitates identification of genomic variations and their potential impact on protein structure, stability, and dynamics.
  • New services enhance insights for experimental structural biologists to optimize study designs.

Conclusions:

  • PDBj has expanded its service portfolio with innovative tools and integrated data.
  • These enhancements benefit researchers in interpreting protein structures, dynamics, and function.
  • The new features aim to improve the efficiency and depth of structural biology research.