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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

Protein Folding

Overview
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...
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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Related Experiment Video

Updated: Jun 1, 2026

Microfluidic Mixers for Studying Protein Folding
12:42

Microfluidic Mixers for Studying Protein Folding

Published on: April 10, 2012

Folding of small proteins using constrained molecular dynamics.

Gouthaman S Balaraman1, In-Hee Park, Abhinandan Jain

  • 1Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA.

The Journal of Physical Chemistry. B
|May 20, 2011
PubMed
Summary
This summary is machine-generated.

Constrained molecular dynamics (MD) simulations enhance protein folding conformational searches, yielding more native-like structures than all-atom MD. This method offers a computationally efficient approach for protein structure prediction and refinement.

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Last Updated: Jun 1, 2026

Microfluidic Mixers for Studying Protein Folding
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Published on: April 10, 2012

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

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OaAEP1-Mediated Enzymatic Synthesis and Immobilization of Polymerized Protein for Single-Molecule Force Spectroscopy
08:34

OaAEP1-Mediated Enzymatic Synthesis and Immobilization of Polymerized Protein for Single-Molecule Force Spectroscopy

Published on: February 5, 2020

Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Protein folding is computationally expensive using all-atom molecular dynamics (MD) simulations due to long timescales.
  • Constrained MD methods offer a more efficient alternative for simulating protein folding.
  • Predicting protein structures and refining existing ones are crucial in structural biology.

Purpose of the Study:

  • To compare the effectiveness of constrained MD versus all-atom MD in protein folding simulations.
  • To evaluate the enrichment of "native-like" structures using constrained MD.
  • To investigate the utility of a generalized "freeze and thaw" constrained MD method.

Main Methods:

  • Developed a generalized constrained MD method allowing "freeze and thaw" of torsional degrees of freedom.
  • Applied all-torsion constrained MD with replica exchange in implicit solvent.
  • Studied small proteins with diverse secondary structures (α-helix, β-turn, mixed motif).
  • Investigated hierarchical constrained MD by freezing partially formed helical regions.

Main Results:

  • Constrained MD replica exchange demonstrated a broader conformational search than all-atom MD.
  • Near-native structures were significantly enriched using the constrained MD approach.
  • Hierarchical constrained MD simulations showed superior sampling of near-native structures compared to all-torsion simulations.
  • Results align with the zipping-and-assembly protein folding model.

Conclusions:

  • Constrained MD, particularly with replica exchange, is a powerful and efficient tool for protein folding simulations.
  • Hierarchical "freeze and thaw" strategies in constrained MD enhance the sampling of biologically relevant conformations.
  • This approach significantly improves protein structure prediction and refinement efficiency.