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Related Concept Videos

Protein Families02:47

Protein Families

17.3K
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

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 Organization01:13

Protein Organization

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Overview
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Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
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Gene Families01:57

Gene Families

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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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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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Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
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The young person's guide to the PDB.

Wladek Minor1, Zbigniew Dauter2, Mariusz Jaskolski3,4

  • 1University of Virginia, Charlottesville, VA 22908, USA.

Postepy Biochemii
|January 30, 2017
PubMed
Summary
This summary is machine-generated.

The Protein Data Bank (PDB) now archives over 120,000 macromolecular structures. This educational overview aims to help users understand the complex structural data available in the PDB.

Keywords:
Protein Data Bankdata miningmacromolecular structurestructural biologystructural databasesstructure validation

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Area of Science:

  • Structural biology
  • Biochemistry
  • Molecular biology

Background:

  • The Protein Data Bank (PDB) was established in 1971 with only seven known protein structures.
  • It currently houses over 120,000 experimentally-determined 3D models of macromolecules like ribosomes and viruses.
  • Deposits primarily originate from X-ray crystallography, with significant contributions from NMR spectroscopy and Cryo-Electron Microscopy.

Purpose of the Study:

  • To provide an educational overview of the Protein Data Bank (PDB).
  • To equip users with a foundational understanding of the complex structural information within the PDB.
  • To serve as an initiation for consumers of PDB data.

Main Methods:

  • Overview of macromolecular structure determination techniques.
  • Discussion of data deposition and archival processes within the PDB.
  • Explanation of the types of structural data available (e.g., from X-ray crystallography, NMR, Cryo-EM).

Main Results:

  • The PDB has grown exponentially since its inception.
  • Macromolecular structure determination, while aided by technology, remains a complex scientific endeavor.
  • A diverse range of macromolecules, from small proteins to large complexes, are represented in the PDB.

Conclusions:

  • Understanding PDB data requires basic knowledge of structural biology principles.
  • The PDB is an invaluable resource for researchers in various life science disciplines.
  • This overview serves as a starting point for navigating and interpreting structural data.