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Related Concept Videos

Protein Folding01:22

Protein Folding

Overview
Protein Folding01:25

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...
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Molecular Chaperones and Protein Folding03:00

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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...
Molecular Chaperones and Protein Folding03:00

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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.
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The Unfolded Protein Response01:37

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The ER is the hub of protein synthesis in a cell. It has robust systems to quality control protein folding and also for degradation of terminally misfolded proteins. Under normal conditions, a small proportion of misfolded proteins that cannot be salvaged need to be transported to the cytoplasm by the ER-associated degradation or ERAD pathways. However, if the ERAD cannot handle the misfolded proteins, the cell activates the unfolded protein response or UPR to adjust the protein folding...

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding.

Rudesh D Toofanny1, Amanda L Jonsson, Valerie Daggett

  • 1Department of Bioengineering, University of Washington, Seattle, Washington, USA.

Biophysical Journal
|June 2, 2010
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Summary

The Dynameomics project developed a new 1D reaction coordinate (RXN) to accurately track protein unfolding. This method overcomes limitations of previous approaches, enabling better analysis of protein conformational states.

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Area of Science:

  • Structural biology
  • Computational biophysics
  • Protein dynamics

Background:

  • Analyzing protein unfolding requires a reliable reaction coordinate (RXN).
  • Existing properties like native contacts and radius of gyration suffer from degeneracy, limiting accuracy.
  • The Dynameomics project aims to simulate and analyze protein unfolding pathways.

Purpose of the Study:

  • To develop a robust, multidimensional-embedded 1D RXN coordinate for protein unfolding.
  • To accurately capture the complex nature of protein conformational changes during unfolding.
  • To enable high-throughput assignment and comparison of protein conformational states.

Main Methods:

  • Utilized 15 physical properties to construct a novel 1D RXN coordinate.
  • Performed molecular dynamics simulations for 188 proteins in explicit water (22.9 μs total).
  • Calculated unfolding RXN coordinates and identified distinct protein states (native, transition, intermediate, denatured).

Main Results:

  • Successfully calculated unfolding RXN coordinates for 188 proteins.
  • Demonstrated the ability to readily identify native, transition, intermediate, and denatured states.
  • Created a global native ensemble effective for new protein folds.
  • Enabled high-throughput assignment of conformational states.

Conclusions:

  • The new RXN coordinate accurately represents protein unfolding.
  • This method facilitates comparison of protein properties across diverse folds.
  • It provides a powerful tool for characterizing individual protein unfolding pathways.