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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

Protein Folding

Overview
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...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...

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Related Experiment Video

Updated: May 9, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
10:50

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

Published on: September 15, 2010

Consensus for the Fip35 folding mechanism?

Ganna Berezovska1, Diego Prada-Gracia, Francesco Rao

  • 1Freiburg Institute for Advanced Studies, School of Soft Matter Research, Freiburg im Breisgau, Germany.

The Journal of Chemical Physics
|July 26, 2013
PubMed
Summary

Protein folding mechanisms were analyzed using atomistic simulations. A network-based approach revealed two distinct folding pathways for the Fip35 WW-domain, each involving an intermediate state.

Area of Science:

  • Computational biology
  • Biophysics
  • Protein dynamics

Background:

  • All-atom simulations now enable studying reversible protein folding.
  • Interpreting atomistic folding mechanisms, like for the Fip35 WW-domain, remains challenging despite extensive simulation data.
  • Contradictory interpretations exist for the Fip35 WW-domain folding pathways.

Purpose of the Study:

  • To elucidate the folding mechanism of the Fip35 WW-domain using a novel network-based analysis.
  • To identify and characterize the predominant folding pathways and intermediate states.
  • To reconcile conflicting interpretations of existing simulation data.

Main Methods:

  • Network-based analysis of local fluctuations in folding order parameters.
  • Utilized 100 μs all-atom simulation trajectories of the Fip35 WW-domain.

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Last Updated: May 9, 2026

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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  • Compared results with reaction coordinate optimization, Markov-state-models, and other simulation schemes.

    • Main Results:

    • Identified two major folding pathways for the Fip35 WW-domain.
    • One pathway is approximately four times more populated than the other.
    • Each pathway proceeds through a distinct intermediate state where one hairpin forms a native configuration.

    Conclusions:

    • The Fip35 WW-domain folds via multiple pathways.
    • The presence of hairpin-based intermediates is a key feature of these pathways.
    • Results strongly support a multiple pathway scenario with intermediates, validated by multiple computational approaches.