Native-like mean structure in the unfolded ensemble of small proteins. Journal Article uri icon



  • The nature of the unfolded state plays a great role in our understanding of proteins. However, accurately studying the unfolded state with computer simulation is difficult, due to its complexity and the great deal of sampling required. Using a supercluster of over 10,000 processors we have performed close to 800 micros of molecular dynamics simulation in atomistic detail of the folded and unfolded states of three polypeptides from a range of structural classes: the all-alpha villin headpiece molecule, the beta hairpin tryptophan zipper, and a designed alpha-beta zinc finger mimic. A comparison between the folded and the unfolded ensembles reveals that, even though virtually none of the individual members of the unfolded ensemble exhibits native-like features, the mean unfolded structure (averaged over the entire unfolded ensemble) has a native-like geometry. This suggests several novel implications for protein folding and structure prediction as well as new interpretations for experiments which find structure in ensemble-averaged measurements.

publication date

  • October 11, 2002

has restriction

  • closed

Date in CU Experts

  • September 4, 2015 2:15 AM

Full Author List

  • Zagrovic B; Snow CD; Khaliq S; Shirts MR; Pande VS

author count

  • 5

Other Profiles

International Standard Serial Number (ISSN)

  • 0022-2836

Additional Document Info

start page

  • 153

end page

  • 164


  • 323


  • 1