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Related Concept Videos

Protein Families02:47

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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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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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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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.
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PDB-2-PBv3.0: An updated protein block database.

Muthuvel Prasath Karuppasamy1, Suresh Venkateswaran2, Parthasarathy Subbiah1

  • 1Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India.

Journal of Bioinformatics and Computational Biology
|May 15, 2020
PubMed
Summary
This summary is machine-generated.

The updated PDB-2-PBv3.0 database now offers protein block (PB) sequences for over 147,000 protein structures. This expanded resource includes interaction data and supports chains with missing atoms, enhancing protein structure analysis.

Keywords:
Protein blockslocal protein structuresprotein data bankprotein molecular functions

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • The Protein Data Bank (PDB) is a crucial resource for protein structure data.
  • Protein blocks (PB) have practical applications in various biological studies.
  • The PDB database continuously grows, necessitating updated resources for PB sequences.

Purpose of the Study:

  • To update and expand the PDB-2-PB database with comprehensive PB sequences and dihedral angles.
  • To include protein interaction data with nucleic acids and functional classifications.
  • To enhance usability through improved download functionalities and support for incomplete protein structures.

Main Methods:

  • Extraction of PB sequences and dihedral angles from PDB structures.
  • Integration of protein-nucleic acid interaction data from NDB and PDB.
  • Development of enhanced search and download features for multiple PB records.

Main Results:

  • The PDB-2-PBv3.0 database contains PB sequences for 147,602 PDB structures (400,355 protein chains) as of October 2019.
  • A significant increase of 2-fold in structures and 4-fold in chains compared to the previous version (PDB-2-PBv1.0).
  • Inclusion of PB information for protein chains with missing atom records, and integrated DNA/RNA interaction data.

Conclusions:

  • PDB-2-PBv3.0 is a substantially expanded and improved resource for protein block analysis.
  • The database facilitates research by providing comprehensive data and user-friendly access.
  • This updated resource supports a wider range of structural biology and bioinformatics applications.