A didactic model of macromolecular crowding effects on protein folding

Douglas Tsao, Allen P. Minton, Nikolay V. Dokholyan

Research output: Contribution to journalArticle

16 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere11936
JournalPloS one
Volume5
Issue number8
DOIs
StatePublished - Oct 15 2010

Fingerprint

Protein folding
protein folding
Protein Folding
toys
Play and Playthings
Statistical mechanics
molecular dynamics
Molecular Dynamics Simulation
gauges
Thermodynamics
thermodynamics
Gages
Molecular dynamics
polypeptides
methodology
Association reactions
Peptides
Proteins
proteins

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

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A didactic model of macromolecular crowding effects on protein folding. / Tsao, Douglas; Minton, Allen P.; Dokholyan, Nikolay V.

In: PloS one, Vol. 5, No. 8, e11936, 15.10.2010.

Research output: Contribution to journalArticle

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