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Intrinsically Disordered Proteins

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 Proteins

Intrinsically Disordered Proteins

Conservation of Protein Domains Over Different Proteins

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...

Protein Folding

Protein Folding

Protein Folding

Protein Folding

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
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...

Noncovalent Attractions in Biomolecules

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Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
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Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

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Binding Thermodynamics to Intrinsically Disordered Protein Domains.

Arne Schön¹, Ernesto Freire^2,3

¹Department of Biology, The Johns Hopkins University, Baltimore, MD, USA.

Methods in Molecular Biology (Clifton, N.J.)

|July 23, 2020

Summary

This study explores how protein binding thermodynamics differ when intrinsically disordered regions either fold upon binding or remain unstructured. Understanding these differences is key for analyzing protein interactions and drug development.

Keywords:

Calorimetry Folding upon binding HIV IDP ITC Interactions Protein folding gp120

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Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions

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Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy

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Published on: April 28, 2011

Area of Science:

Biochemistry
Structural Biology
Molecular Interactions

Background:

Many proteins contain intrinsically disordered regions (IDRs) that participate in crucial binding interactions.
Binding to IDRs often necessitates a transition from disordered to ordered states, coupling binding with folding.
The thermodynamics of these coupled events are critical for understanding protein function.

Purpose of the Study:

To differentiate the thermodynamic profiles of binding coupled to folding versus binding independent of folding in the same protein.
To provide a protocol for analyzing these distinct binding mechanisms.
To use the HIV-1 envelope glycoprotein gp120 as a model system.

Main Methods:

Investigating the binding thermodynamics of intrinsically disordered protein domains.
Comparing binding events that induce protein structuring with those that do not.
Utilizing the HIV-1 envelope glycoprotein gp120 and its binding partners (CD4, MAb 17b, MAb b12).

Main Results:

Demonstrated distinct thermodynamic signatures for binding coupled to folding versus binding independent of folding.
Showcased how different ligands binding to gp120 elicit varied structural responses and thermodynamic outcomes.
Highlighted the role of protein structure dynamics in molecular recognition.

Conclusions:

The thermodynamic analysis of protein-ligand interactions must account for whether binding is coupled to folding.
Understanding these differences is crucial for characterizing the function of intrinsically disordered proteins.
This approach provides insights into the mechanisms of viral glycoproteins like gp120.