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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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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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Amyloid fibrils are aggregates of misfolded proteins.  Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils. 
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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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Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
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MobiDB: intrinsically disordered proteins in 2021.

Damiano Piovesan1, Marco Necci1, Nahuel Escobedo2

  • 1Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58/B, Padua 35121, Italy.

Nucleic Acids Research
|November 25, 2020
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Summary
This summary is machine-generated.

MobiDB version 4 enhances intrinsically disordered protein data with new annotations and an improved interface. This update offers advanced search, visualization, and data access for researchers studying protein disorder.

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Area of Science:

  • Biochemistry and Bioinformatics
  • Structural Biology

Background:

  • Intrinsically disordered proteins (IDPs) play crucial roles in cellular functions but present unique challenges for structural and functional annotation.
  • Existing databases often lack comprehensive data on the dynamic nature and diverse functions of IDPs.

Purpose of the Study:

  • To report the recent developments and improvements in MobiDB version 4, focusing on enhanced data accessibility and annotation of intrinsically disordered proteins.
  • To introduce a redesigned user interface, advanced search capabilities, and an improved API for programmatic access to MobiDB data.

Main Methods:

  • Implementation of a new database schema for increased flexibility and simplified maintenance.
  • Development of a re-designed website with enhanced visualization tools, including customizable feature viewers and residue contact map graphs.
  • Integration of novel annotations for binding modes, disorder-to-order transitions, liquid-liquid phase separation, and post-translational modifications.

Main Results:

  • MobiDB version 4 offers a more effective search engine and advanced API for programmatic data retrieval.
  • New visualization tools and a simplified interface facilitate faster searches and customized dataset downloads in various formats (TSV, Fasta, JSON).
  • The database now includes detailed annotations on binding modes, phase separation, and post-translational modifications for disordered proteins.

Conclusions:

  • MobiDB version 4 significantly improves data accessibility and provides state-of-the-art knowledge on intrinsically disordered proteins.
  • The enhanced features cater to both computational and experimental users, facilitating deeper insights into protein disorder.
  • The updated database structure and interface streamline data management and user interaction for IDP research.