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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 Folding01:25

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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.
Protein Structure Is Critical to Its Biological Function
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Protein Networks02:26

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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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Conservation of Protein Domains Over Different Proteins02:26

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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 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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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Computational Identification of Potential Shape-Shifting Proteins from Structures.

Francisco M Pérez-Canales1, Enrique Alanís-Domínguez1, Ana M Rojas2

  • 1CABD-CSIC, Computational Biology and Bioinformatics Group, Seville, Spain.

Methods in Molecular Biology (Clifton, N.J.)
|November 1, 2025
PubMed
Summary

Identifying protein shape-shifters, which adopt multiple structures for distinct functions, is challenging. This study introduces a computational method to screen databases for these versatile proteins, advancing our understanding of protein dynamics.

Keywords:
Fold-switchingFunctionShape-shifting proteinsStructural alignment

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Area of Science:

  • Biochemistry and Structural Biology
  • Computational Biology and Bioinformatics

Background:

  • The conventional paradigm posits a single protein structure dictates its function.
  • Proteins known as 'shape-shifters' and intrinsically disordered proteins (IDPs) challenge this by exhibiting multiple functional states or folding upon binding.
  • Identifying these dynamic proteins is crucial but hindered by limited structural data and predictive method limitations.

Purpose of the Study:

  • To develop and present a computational protocol for identifying potential shape-shifting proteins.
  • To address the limitations in current methods for detecting proteins with conformational variability.
  • To facilitate the discovery of proteins that deviate from the 'one structure-one function' model.

Main Methods:

  • Integration of both structural and sequence data for protein analysis.
  • Development of a computational protocol to screen large structural databases.
  • Application of the protocol to identify proteins with significant conformational variability within the Protein Data Bank (PDB).

Main Results:

  • A computational protocol was successfully developed to identify potential shape-shifting proteins.
  • The method enables the screening of the Protein Data Bank (PDB) for proteins exhibiting conformational flexibility.
  • This approach provides a new avenue for discovering proteins that do not adhere to the traditional structure-function paradigm.

Conclusions:

  • The developed computational protocol offers a viable method for identifying shape-shifting proteins.
  • This work expands the understanding of protein functionality beyond the 'one structure-one function' principle.
  • The findings pave the way for further research into the biological roles and mechanisms of dynamic proteins.