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Related Concept Videos

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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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...
Protein Organization01:13

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Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
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Folding pathways and rates for the three-stranded beta-sheet peptide Beta3s using discrete path sampling.

Joanne M Carr1, David J Wales

  • 1University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

The Journal of Physical Chemistry. B
|July 1, 2008
PubMed
Summary

Discrete path sampling revealed the folding mechanism of the Beta3s peptide. The peptide folds via C-terminal hairpin formation and N-terminal strand docking, consistent with experimental data.

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular dynamics

Background:

  • Understanding peptide folding is crucial for protein science.
  • Antiparallel beta-sheets are common structural motifs in proteins.

Purpose of the Study:

  • To investigate the folding mechanism of a three-stranded antiparallel beta-sheet peptide, Beta3s.
  • To determine the folding time and pathway using computational methods.

Main Methods:

  • Discrete path sampling method applied to the Beta3s peptide.
  • Utilized an empirical potential and implicit solvent model.
  • Employed a coarse-graining scheme to group local minima.

Main Results:

  • Calculated folding time agreed with other simulations and experimental upper bounds.
  • Identified the most significant discrete paths for folding.
  • Observed early C-terminal hairpin formation followed by N-terminal strand docking.

Conclusions:

  • The discrete path sampling method is effective for studying peptide folding.
  • The folding mechanism of Beta3s involves a specific sequence of structural events.
  • Computational findings align with experimental observations, validating the model.