Related Experiment Video
Updated: Jun 13, 2025
06:48
Author Spotlight: Evaluation of Protein-Condensate Dynamics in Live Human Cells
Published on: January 5, 2024
3.4K
Conformational fluidity of intrinsically disordered proteins in crowded environment: a molecular dynamics simulation
Carolyn Shult1, Keegan Gunderson1, Stephen J Coffey1
1Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, USA.
Journal of Biomolecular Structure & Dynamics
|September 17, 2024
Summary
Intrinsically disordered proteins (IDPs) gain structural stability from molecular crowders. This study shows polymer crowders enhance IDP flexibility and function through enthalpic and entropic effects.
Area of Science:
- Biochemistry
- Structural Biology
- Biophysics
Background:
- Intrinsically disordered proteins (IDPs) lack stable 3D structures, complicating studies of their function and dynamics.
- Understanding IDP behavior in crowded cellular environments is crucial for elucidating their biological roles.
Purpose of the Study:
- To investigate the impact of molecular crowding on the conformational flexibility of intrinsically disordered proteins.
- To compare the effects of polymer crowders versus monomeric crowders on IDP dynamics.
Main Methods:
- Molecular dynamics simulations were performed on two IDPs and two control folded proteins.
- Simulations were conducted in both the presence and absence of molecular crowders (polymers and monomers).
Main Results:
- Molecular crowders, particularly polymer crowders, were found to stabilize intrinsically disordered proteins.
- Stabilization effects were attributed to significant enthalpic and entropic contributions from polymer crowders.
- Crowding induced a diverse ensemble of dynamic protein scaffolds, enhancing functional capabilities.
Conclusions:
- Molecular crowding plays a significant role in modulating the conformational ensemble and stability of IDPs.
- Polymer crowders offer a more pronounced stabilizing effect on IDPs compared to monomeric crowders.
- These findings provide insights into how IDPs maintain function within the crowded intracellular environment.
Related Concept Videos
02:18Intrinsically Disordered Proteins
17.7K
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...
17.7K
01:25Protein Folding
7.8K
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...
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
7.8K
03:00Molecular Chaperones and Protein Folding
17.8K
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...
The...
17.8K
01:24Protein Diffusion in the Membrane
4.3K
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...
4.3K
00:52¹H NMR of Conformationally Flexible Molecules: Temporal Resolution
815
At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
815
01:19Protein Dynamics in Living Cells
2.1K
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
2.1K