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

Overview

abstract

  • 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

Full Author List

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

Other Profiles

Additional Document Info

start page

  • 153

end page

  • 164

volume

  • 323

issue

  • 1