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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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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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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.
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
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Predicting substitutions to modulate disorder and stability in coiled-coils.

Yasaman Karami1,2, Paul Saighi3, Rémy Vanderhaegen3

  • 1CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Sorbonne Université, 75005, Paris, France. yasaman.karami@pasteur.fr.

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|December 22, 2020
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Summary

We developed a computational method to quantify protein coiled-coil disorder and guide protein design. This framework helps modulate protein stability and flexibility by analyzing molecular dynamics simulations.

Keywords:
Coiled-coilMolecular dynamicsProtein disorderProtein dynamicsProtein stabilityProtein structure

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Area of Science:

  • Computational biology
  • Protein structure and dynamics
  • Bioinformatics

Background:

  • Coiled-coils are protein structural motifs, but can exhibit local mobility and intrinsic disorder.
  • Intrinsically disordered regions are crucial for protein function but challenging to characterize.
  • Quantifying disorder in protein regions computationally is an ongoing challenge.

Purpose of the Study:

  • To develop a computational framework for quantifying coiled-coil disorder in solution.
  • To enable the design of protein substitutions that modulate coiled-coil disorder and stability.
  • To apply the framework to viral phosphoprotein multimerization domains (PMDs).

Main Methods:

  • Analysis of conformational ensembles from short all-atom Molecular Dynamics (MD) simulations.
  • Application to tetrameric left-handed coiled-coils of Measles virus (MeV) and Nipah virus (NiV) PMDs.
  • Derivation of design rules for substitutions based on impact on coiled-coil stability.

Main Results:

  • Quantified C-terminus disorder in MeV and NiV PMDs using short MD simulations.
  • Established a conceptual framework for rational design of substitutions.
  • Identified rules to control MeV PMD stability and cohesiveness.
  • Designed substitutions to increase or decrease tetramer stability/flexibility.

Conclusions:

  • The developed method serves as a platform for designing substitutions to regulate protein flexibility and stability.
  • This approach aids in understanding and engineering coiled-coil behavior.
  • Facilitates rational design of protein structural properties.