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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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Protein Diffusion in the Membrane01:24

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Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...
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Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

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The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...
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Protein Folding01:25

Protein Folding

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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.
Protein Structure Is Critical to Its Biological Function
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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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Ligand Binding Sites02:40

Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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Updated: Jun 18, 2025

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
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Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

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Diffusing protein binders to intrinsically disordered proteins.

Caixuan Liu1,2, Kejia Wu1,2,3, Hojun Choi1,2

  • 1Department of Biochemistry, University of Washington, Seattle, WA, USA.

Biorxiv : the Preprint Server for Biology
|July 29, 2024
PubMed
Summary
This summary is machine-generated.

Researchers developed a new method using RFdiffusion to create high-affinity protein binders for intrinsically disordered proteins (IDPs) and regions (IDRs). This breakthrough enables therapeutic and diagnostic tools targeting these flexible molecules.

Keywords:
Amyloid fibril dissociationIntrinsically disordered proteinRFdiffusionRosettadeep learningdiagnosticsintrinsically disordered regionprotein design

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Paramagnetic Relaxation Enhancement for Detecting and Characterizing Self-Associations of Intrinsically Disordered Proteins
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Area of Science:

  • Biochemistry
  • Structural Biology
  • Protein Engineering

Background:

  • Intrinsically disordered proteins (IDPs) and regions (IDRs) lack stable structures, posing challenges for therapeutic and diagnostic development.
  • Existing methods for generating specific binders to IDPs/IDRs are limited, hindering their application.
  • High-affinity and specific binders are crucial for unlocking the therapeutic and diagnostic potential of IDPs/IDRs.

Purpose of the Study:

  • To develop a general methodology for generating protein binders targeting intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs).
  • To demonstrate the capability of RFdiffusion in designing binders that recognize IDPs/IDRs across various conformations.
  • To validate the functional utility of designed binders in therapeutic and diagnostic contexts.

Main Methods:

  • Utilized RFdiffusion, a computational protein design tool, starting from the target IDP/IDR sequence.
  • Employed conformational sampling for both the target IDP/IDR and the potential binding protein.
  • Generated and characterized binders for specific IDPs (Amylin, C-peptide, VP48) and IDRs (G3bp1, IL2RG, prion).

Main Results:

  • Successfully generated binders to Amylin, C-peptide, and VP48 with dissociation constants (Kds) in the 3-100 nM range.
  • Developed binders for IDRs G3bp1, IL2RG, and prion, exhibiting affinities of 10-100 nM by targeting beta-strand conformations.
  • Demonstrated functional activity: Amylin binder inhibited fibril formation and aided detection; IL2RG binder colocalized with the receptor in cells.

Conclusions:

  • RFdiffusion provides a versatile platform for designing high-affinity binders to intrinsically disordered proteins and regions.
  • The developed binders show promise for therapeutic interventions, such as inhibiting amyloid formation and modulating cellular signaling.
  • This approach significantly advances the ability to target flexible proteins, opening new avenues for diagnostics and therapeutics.