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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...
Protein Diffusion in the Membrane01:24

Protein Diffusion in the Membrane

Proteins show rotational as well as lateral diffusion across the membrane. The lateral diffusion of proteins was confirmed through the cell fusion experiment where mouse and human cells were fused, resulting in hybrid cells. When the human and mouse cells fused, the specific membrane proteins on human and mouse cells were marked with the red and green-fluorescent markers, respectively. Initially, the red and green fluorescence was located on the respective hemisphere of the cell. As time...

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Related Experiment Video

Updated: Jun 18, 2026

Microfluidic Mixers for Studying Protein Folding
12:42

Microfluidic Mixers for Studying Protein Folding

Published on: April 10, 2012

Proteins fold by subdiffusion of the order parameter.

Amandeep K Sangha1, T Keyes

  • 1Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.

The Journal of Physical Chemistry. B
|November 12, 2009
PubMed
Summary

Protein folding dynamics deviate from standard diffusion models due to subdiffusion. A novel fractal Smoluchowski equation theory accurately predicts folding pathways, offering a faster simulation method for slow protein folding.

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High-Resolution Neutron Spectroscopy to Study Picosecond-Nanosecond Dynamics of Proteins and Hydration Water

Published on: April 28, 2022

Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Dynamics

Background:

  • Standard diffusion models, like the Smoluchowski equation (SE), often fail to accurately describe complex biological processes such as protein folding.
  • The order parameter in protein folding dynamics has been observed to follow subdiffusion, a behavior not captured by normal diffusion models.

Purpose of the Study:

  • To investigate the limitations of existing diffusion models in describing chymotrypsin inhibitor 2 (CI2) protein folding.
  • To propose and validate a new theoretical framework, the fractal SE theory, to accurately model protein folding dynamics.
  • To develop an accelerated computational method for simulating slow protein folding processes.

Main Methods:

  • Utilized a C(alpha) model for chymotrypsin inhibitor 2 (CI2) protein folding simulations.
  • Developed a new, constraint-free method to determine the order-parameter-dependent diffusion constant.
  • Employed statistical temperature molecular dynamics (STMD) for enhanced free energy sampling.
  • Validated the fractal SE theory against long-time folding dynamics simulations.

Main Results:

  • Demonstrated that standard Smoluchowski equation and normal-diffusion continuous time random walk models are inadequate for CI2 protein folding.
  • Established that subdiffusion of the order parameter is the reason for the failure of conventional models.
  • Showed that the proposed fractal SE theory accurately predicts folding pathways and dynamics.
  • Confirmed quantitative agreement between fractal SE theory predictions and simulated long-time folding dynamics.

Conclusions:

  • The fractal Smoluchowski equation provides a more accurate description of protein folding dynamics than traditional diffusion models.
  • The fractal SE theory, validated by simulations, can be used to study protein folding pathways.
  • This approach offers a potential accelerated algorithm for simulating protein folding, especially for systems with slow dynamics.