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Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Published on: January 16, 2016
Protein translocation through a tunnel induces changes in folding kinetics: a lattice model study
Lydia M Contreras Martínez1, Francisco J Martínez-Veracoechea, Prabhas Pohkarel
1School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA.
Biotechnology and Bioengineering
|March 11, 2006
Summary
Ribosomal tunnel confinement accelerates protein folding for well-designed proteins by promoting compact unfolded states. However, this effect is diminished for poorly designed proteins and depends on tunnel width.
Area of Science:
- Biophysics
- Computational Biology
- Protein Folding
Background:
- Protein folding is crucial for cellular function.
- The ribosomal exit tunnel's role in protein folding is under investigation.
- Nascent polypeptide compaction within the tunnel may influence folding kinetics.
Purpose of the Study:
- To investigate the impact of confinement within a channel on protein folding kinetics.
- To explore how tunnel width affects the folding of well-designed versus poorly designed proteins.
- To understand the role of ribosomal exit tunnels in co-translational and post-translational folding.
Main Methods:
- Kinetic Monte Carlo simulations.
- Minimalist on-lattice protein model.
- Exploration of various channel geometries and widths.
Main Results:
- Tunnel confinement accelerates folding for well-designed proteins by favoring compact unfolded states near the transition state.
- Poorly designed proteins, with compact misfolded states, are less affected by tunnel confinement.
- The beneficial effect of confinement is dependent on tunnel width: too narrow hinders transition state access, too wide has no effect.
Conclusions:
- Ribosomal exit tunnel confinement can enhance protein folding efficiency for certain proteins.
- Tunnel geometry and protein design influence the extent of folding acceleration.
- These findings suggest a significant role for co-translational effects in protein folding within the cellular environment.
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