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Related Concept Videos

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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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.
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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.
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Single-Molecule Tracking Microscopy - A Tool for Determining the Diffusive States of Cytosolic Molecules
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Coordinate-dependent diffusion in protein folding.

Robert B Best1, Gerhard Hummer

  • 1Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom. rbb24@cam.ac.uk

Proceedings of the National Academy of Sciences of the United States of America
|January 19, 2010
PubMed
Summary
This summary is machine-generated.

Protein folding dynamics are modeled by diffusion, but the diffusion coefficient (D) varies with position. This study reveals how D changes, impacting single-molecule experiments and protein folding speed limit estimations.

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Thermodynamics of Membrane Protein Folding Measured by Fluorescence Spectroscopy
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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Dynamics

Background:

  • Protein folding dynamics are often modeled using diffusion on low-dimensional free-energy surfaces.
  • Interpreting simulations and experiments is complicated by position-dependent diffusion coefficients (D).
  • The dependence of D on the folding coordinate can vary, affecting analysis.

Purpose of the Study:

  • To explore the position dependence of the diffusion coefficient (D) in protein folding.
  • To connect this dependence to internal friction and its consequences for single-molecule experiments.
  • To develop methods for analyzing protein folding dynamics and interpreting experimental data.

Main Methods:

  • Investigated the position dependence of D using various reaction coordinates.
  • Analyzed the relationship between D, internal friction, and protein internal friction.
  • Developed a transformation to obtain reaction coordinates with position-invariant D.

Main Results:

  • Found a significant decrease in D from unfolded to folded states for Cartesian coordinates used in single-molecule experiments.
  • Observed that D is nearly independent of Q (fraction of native contacts), unlike Cartesian coordinates.
  • Demonstrated a transformation relating position-dependent free energies and diffusion coefficients for different reaction coordinates.

Conclusions:

  • The study provides insights into the position dependence of diffusion coefficients during protein folding.
  • Developed methods to obtain position-invariant D, aiding in the interpretation of protein folding speed limits.
  • Suggests new avenues for designing single-molecule experiments to directly probe the position dependence of D.