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Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

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Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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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 chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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Disordered Residues and Patterns in the Protein Data Bank.

Mikhail Yu Lobanov1, Ilya V Likhachev1,2, Oxana V Galzitskaya1,3

  • 1Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290 Moscow, Russia.

Molecules (Basel, Switzerland)
|April 2, 2020
PubMed
Summary

Researchers developed a new library of protein disordered patterns and residues from the Protein Data Bank (PDB). This resource aids in analyzing protein structures and predicting residue disorder.

Keywords:
disordered residueshomo-repeatsidentitylow complexity regionsprotein structure

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein Data Bank (PDB) contains vast structural information.
  • Identifying disordered regions is crucial for understanding protein function and dynamics.
  • Existing methods for analyzing protein disorder patterns have limitations.

Purpose of the Study:

  • To create a comprehensive library of disordered patterns and residues.
  • To develop novel computational methods for identifying and analyzing protein disorder.
  • To provide a user-friendly resource for researchers studying protein structure and function.

Main Methods:

  • Clustering of Protein Data Bank (PDB) chains based on sequence identity.
  • Identification and marking of disordered residues within protein structures.
  • Development of a new procedure for discovering and categorizing disordered patterns.
  • Creation of a library comprising unique patterns, two-amino-acid patterns, and homo-repeats.

Main Results:

  • A new, updated library of disordered patterns and residues is now available.
  • The library includes three distinct sets of patterns: unique, two-amino-acid, and homo-repeats.
  • The developed database enables various analyses, including homologue searching, statistical analysis of disordered residues, and pattern searching.

Conclusions:

  • The new library of disordered patterns enhances the accuracy of predicting structured and unstructured protein regions.
  • This resource facilitates deeper insights into protein disorder and its implications.
  • The database offers multiple functionalities for researchers, including interactive 3D structure visualization.