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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...
Protein Folding01:22

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Molecular Chaperones and Protein Folding03:00

Molecular Chaperones and Protein Folding

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

Molecular Chaperones and Protein Folding

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...
Amyloid Fibrils03:03

Amyloid Fibrils

Amyloid fibrils are aggregates of misfolded proteins.  Under most circumstances, misfolded proteins are either refolded by chaperone proteins or degraded by the proteasome. However, in the case of a mutation or a disease, these proteins can accumulate to form large clusters and often further assemble to form elongated fibers, called fibrils. 
Amyloid deposits were observed as early as 1639 in the liver and the spleen.   In 1854, Rudolph Virchow performed iodine staining, normally used to...

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Microfluidic Mixers for Studying Protein Folding
12:42

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Published on: April 10, 2012

Topological solitons and folded proteins.

Maxim Chernodub1, Shuangwei Hu, Antti J Niemi

  • 1Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200 Tours, France. chernodub@lmpt.univ-tours.fr

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|September 28, 2010
PubMed
Summary

Protein loops are modeled as topological solitons, bridging alpha-helices and beta-strands. This new approach accurately reproduces protein secondary structures, offering insights into protein dynamics.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Protein loops connect secondary structural elements like alpha-helices and beta-strands.
  • Understanding loop structure and dynamics is crucial for protein function.
  • Current models may not fully capture the topological nature of protein loops.

Purpose of the Study:

  • To propose a novel theoretical framework for describing protein loops.
  • To model protein loops using topological domain-wall solitons.
  • To validate the model by applying it to known protein structures.

Main Methods:

  • Developing an energy function that supports soliton solutions for protein loops.
  • Utilizing numerical methods to construct soliton solutions.
  • Applying the model to specific protein structures from the Protein Data Bank (e.g., 1VII, 2EB8, 3EBX).

Main Results:

  • Protein loops can be effectively represented as topological domain-wall solitons.
  • The model successfully reproduces secondary structural motifs (alpha-helix-loop-alpha-helix, beta-sheet-loop-beta-sheet).
  • High accuracy (around 1.0 Å RMSD for Cα atoms) was achieved, nearing experimental limits.

Conclusions:

  • Topological solitons provide a powerful new description for protein loops.
  • This approach accurately models the conformational states of protein loops.
  • The findings offer a novel perspective on protein structural dynamics and modeling.