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Journal of Chemical Physics / Volume 131 / Issue 3 / ARTICLES / Biological Molecules, Biopolymers, and Biological Systems

J. Chem. Phys. 131, 035101 (2009); doi:10.1063/1.3170984 (7 pages)

Nearly symmetrical proteins: Folding pathways and transition states

Marco Zamparo and Alessandro Pelizzola

Dipartimento di Fisica, CNISM Unità di Torino and INFN, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy

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(Received 21 December 2008; accepted 12 June 2009; published online 15 July 2009)

The folding pathways of the B domain of protein A have been the subject of many experimental and computational studies. Based on a statistical mechanical model, it has been suggested that the native state symmetry leads to multiple pathways, highly dependent on temperature and denaturant concentration. Experiments, however, have not confirmed this scenario. By considering four nearly symmetrical proteins, one of them being the above molecule, here we show that, if contact energies are properly taken into account, a different picture emerges from kinetic simulations of the above-mentioned model. This is characterized by a dominant folding pathway, which is consistent with the most recent experimental results. Given the simplicity of the model, we also report on a direct sampling of the transition state.

© 2009 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. THE MODEL
  3. FOLDING PATHWAYS
  4. TRANSITION STATE ENSEMBLE
  5. CONCLUSIONS

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KEYWORDS and PACS

Keywords

biothermics, molecular biophysics, proteins, statistical mechanics

PACS

  • 87.14.E-

    Proteins

  • 87.15.Cc

    Folding: thermodynamics, statistical mechanics, models, and pathways

  • 87.15.La

    Mechanical properties

  • 87.15.Zg

    Phase transitions

  • 87.19.Pp

    Biothermics and thermal processes in biology

ARTICLE DATA

Permalink
http://link.aip.org/link/doi/10.1063/1.3170984

PUBLICATION DATA

ISSN:

0021-9606 (print)  
1089-7690 (online)

Publisher:

$abstract.society.value is a Member of CrossRef American Institute of Physics

For access to fully linked references, you need to log in.
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