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Related Concept Videos

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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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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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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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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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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Paramagnetic Relaxation Enhancement for Detecting and Characterizing Self-Associations of Intrinsically Disordered Proteins
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PUNCH: An Interactive Web Server for Predicting Intrinsically Disordered Regions in Protein Sequences.

Di Meng1, Gianluca Pollastri1

  • 1School of Computer Science, University College Dublin, Ireland.

Journal of Molecular Biology
|March 26, 2025
PubMed
Summary
This summary is machine-generated.

PUNCH is a new web server for fast and accurate prediction of intrinsically disordered regions (IDRs) in proteins. It offers a user-friendly interface and reliable results for diverse protein sequences.

Keywords:
bioinformaticsconvolutional neural networkintrinsically disordered regionsprotein predictionweb server

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Intrinsically disordered regions (IDRs) are crucial for protein function but challenging to predict.
  • Accurate prediction of IDRs is essential for understanding protein structure-function relationships.

Purpose of the Study:

  • To introduce PUNCH, a novel, freely accessible web server for rapid and accurate prediction of IDRs in protein sequences.
  • To provide researchers with a streamlined tool for IDR prediction using the PUNCH2-Light predictor.

Main Methods:

  • Development of the PUNCH web server utilizing a high-performance computational framework and the PUNCH2-Light predictor.
  • Validation of PUNCH's performance against established benchmarking datasets, including CAID2, Disorder_PDB, and Disorder_NOX.

Main Results:

  • PUNCH demonstrates competitive speed and accuracy in predicting IDRs across diverse protein sequences.
  • The server shows particular strength in the Disorder_PDB dataset and provides reliable predictions for the Disorder_NOX dataset, even with low sequence similarity.

Conclusions:

  • PUNCH offers a valuable and accessible resource for researchers in structural biology and bioinformatics.
  • The web server effectively addresses the challenge of predicting intrinsically disordered regions in proteins.