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Related Concept Videos

Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

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...
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

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...
Protein Organization01:24

Protein Organization

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.
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Uncertainty analysis in protein disorder prediction.

Mohamed F Ghalwash1, A Keith Dunker, Zoran Obradović

  • 1Center for Data Analytics and Biomedical Informatics, Computer and Information Sciences Department, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA. mohamed.ghalwash@temple.edu

Molecular Biosystems
|November 22, 2011
PubMed
Summary

Predicting intrinsically disordered proteins (IDPs) is challenging. This study introduces a meta-predictor that effectively measures prediction uncertainty, improving accuracy and balancing sensitivity and specificity for disorder prediction.

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Area of Science:

  • Proteomics and structural genomics
  • Computational biology
  • Biophysics

Background:

  • Accurate prediction of intrinsically disordered proteins (IDPs) remains a significant challenge.
  • Existing IDP predictors often lack reliability when used individually, as they ignore model uncertainty.
  • Understanding protein disorder is crucial for structural genomics.

Purpose of the Study:

  • To develop an empirical method for quantifying uncertainty in intrinsically disordered protein (IDP) predictions.
  • To improve the accuracy and reliability of IDP prediction by integrating multiple models.
  • To analyze the impact of sequence variations on predicted protein disorder.

Main Methods:

  • Training a set of prediction models for intrinsically disordered proteins (IDPs).
  • Developing meta-predictors that combine outputs from multiple individual models.
  • Assessing prediction uncertainty by analyzing variations within reference models and data.
  • Evaluating the effect of mutations on predicted disorder using homologous sequences.

Main Results:

  • The best meta-predictor achieved performance comparable to or exceeding individual models.
  • Meta-predictors demonstrated improved balance in sensitivity and specificity compared to single models.
  • Mutations in homologous sequences frequently shifted predicted disordered residues to ordered, but rarely vice versa.
  • Disorder tendencies appear more sensitive to mutations than structure tendencies.

Conclusions:

  • Integrating multiple models (meta-prediction) is crucial for robust intrinsically disordered protein (IDP) prediction.
  • Protein disorder is less conserved and more sensitive to sequence changes than protein structure.
  • The developed meta-predictors offer improved and more balanced disorder prediction capabilities.