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Related Concept Videos

Intrinsically Disordered Proteins02:18

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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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The ER is the hub of protein synthesis in a cell. It has robust systems to quality control protein folding and also for degradation of terminally misfolded proteins. Under normal conditions, a small proportion of misfolded proteins that cannot be salvaged need to be transported to the cytoplasm by the ER-associated degradation or ERAD pathways. However, if the ERAD cannot handle the misfolded proteins, the cell activates the unfolded protein response or UPR to adjust the protein folding...
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Analyzing Protein Disorder with IUPred2A.

Gábor Erdős1, Zsuzsanna Dosztányi1

  • 1Department of Biochemistry, MTA-ELTE Momentum Bioinformatics Research Group, ELTE Eötvös Loránd University, Budapest, Hungary.

Current Protocols in Bioinformatics
|April 3, 2020
PubMed
Summary

This article provides instructions for using IUPred2A, a tool for predicting intrinsically disordered proteins and regions. It covers online and local usage, interpretation of results, and analysis of conditionally disordered segments.

Keywords:
binding sitesbioinformaticscontext dependent disorderintrinsically disordered proteinsredox regulation

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Computational Biology

Background:

  • Intrinsically disordered regions (IDRs) lack stable 3D structures but are crucial for biological functions.
  • Predicting IDRs and conditionally disordered regions presents computational challenges due to their dynamic nature and environmental sensitivity.
  • Various prediction methods exist, but user-friendly tools with comprehensive guidance are essential for researchers.

Purpose of the Study:

  • To provide detailed instructions for using the IUPred2A prediction tool.
  • To demonstrate how to analyze intrinsically disordered proteins and conditionally disordered regions.
  • To guide users in interpreting prediction results in various biological contexts.

Main Methods:

  • Utilizing the IUPred2A online server for disorder propensity analysis.
  • Employing ANCHOR2 for predicting disordered binding regions.
  • Performing local installations and using the REST API for programmatic access.
  • Analyzing redox-sensitive disordered regions.

Main Results:

  • Demonstrated practical application of IUPred2A through online and local protocols.
  • Provided clear guidelines for interpreting disorder predictions.
  • Illustrated methods for analyzing specific types of disordered regions, including binding and redox-sensitive ones.

Conclusions:

  • IUPred2A is a versatile and widely used tool for identifying disordered proteins and regions.
  • The provided protocols facilitate the application and interpretation of disorder predictions in research.
  • Understanding disordered regions is critical for advancing biological insights.