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A Didactic Model of Macromolecular Crowding Effects on Protein Folding

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  • Douglas Tsao
  • Allen P Minton
  • Nikolay V Dokholyan

Abstract

A didactic model is presented to illustrate how the effect of macromolecular crowding on protein folding and association is modeled using current analytical theory and discrete molecular dynamics. While analytical treatments of crowding may consider the effect as a potential of average force acting to compress a polypeptide chain into a compact state, the use of simulations enables the presence of crowding reagents to be treated explicitly. Using an analytically solvable toy model for protein folding, an approximate statistical thermodynamic method is directly compared to simulation in order to gauge the effectiveness of current analytical crowding descriptions. Both methodologies are in quantitative agreement under most conditions, indication that both current theory and simulation methods are capable of recapitulating aspects of protein folding even by utilizing a simplistic protein model.

Suggested Citation

  • Douglas Tsao & Allen P Minton & Nikolay V Dokholyan, 2010. "A Didactic Model of Macromolecular Crowding Effects on Protein Folding," PLOS ONE, Public Library of Science, vol. 5(8), pages 1-8, August.
    • Handle: RePEc:plo:pone00:0011936
    DOI: 10.1371/journal.pone.0011936
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    References listed on IDEAS

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    1. Sean R McGuffee & Adrian H Elcock, 2010. "Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm," PLOS Computational Biology, Public Library of Science, vol. 6(3), pages 1-18, March.
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