Multiple folding pathways of the SH3 domain

Jose M. Borreguero, Feng Ding, Sergey V. Buldyrev, H. Eugene Stanley, Nikolay V. Dokholyan

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36 Scopus citations

Abstract

Experimental observations suggest that proteins follow different folding pathways under different environmental conditions. We perform molecular dynamics simulations of a model of the c-Crk SH3 domain over a broad range of temperatures, and identify distinct pathways in the folding transition. We determine the kinetic partition temperature-the temperature for which the c-Crk SH3 domain undergoes a rapid folding transition with minimal kinetic barriers-and observe that below this temperature the model protein may undergo a folding transition by multiple folding pathways via only one or two intermediates. Our findings suggest the hypothesis that the SH3 domain, a protein fold for which only two-state folding kinetics was observed in previous experiments, may exhibit intermediate states under conditions that strongly stabilize the native state.

Original languageEnglish (US)
Pages (from-to)521-533
Number of pages13
JournalBiophysical journal
Volume87
Issue number1
DOIs
StatePublished - Jul 2004

All Science Journal Classification (ASJC) codes

  • Biophysics

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    Borreguero, J. M., Ding, F., Buldyrev, S. V., Stanley, H. E., & Dokholyan, N. V. (2004). Multiple folding pathways of the SH3 domain. Biophysical journal, 87(1), 521-533. https://doi.org/10.1529/biophysj.104.039529