Unknown

Dataset Information

0

Minimal folding pathways for coarse-grained biopolymer fragments.


ABSTRACT: The minimal folding pathway or trajectory for a biopolymer can be defined as the transformation that minimizes the total distance traveled between a folded and an unfolded structure. This involves generalizing the usual Euclidean distance from points to one-dimensional objects such as a polymer. We apply this distance here to find minimal folding pathways for several candidate protein fragments, including the helix, the beta-hairpin, and a nonplanar structure where chain noncrossing is important. Comparing the distances traveled with root mean-squared distance and mean root-squared distance, we show that chain noncrossing can have large effects on the kinetic proximity of apparently similar conformations. Structures that are aligned to the beta-hairpin by minimizing mean root-squared distance, a quantity that closely approximates the true distance for long chains, show globally different orientation than structures aligned by minimizing root mean-squared distance.

SUBMITTER: Mohazab AR 

PROVIDER: S-EPMC2599856 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature

altmetric image

Publications

Minimal folding pathways for coarse-grained biopolymer fragments.

Mohazab Ali R AR   Plotkin Steven S SS  

Biophysical journal 20080926 12


The minimal folding pathway or trajectory for a biopolymer can be defined as the transformation that minimizes the total distance traveled between a folded and an unfolded structure. This involves generalizing the usual Euclidean distance from points to one-dimensional objects such as a polymer. We apply this distance here to find minimal folding pathways for several candidate protein fragments, including the helix, the beta-hairpin, and a nonplanar structure where chain noncrossing is important  ...[more]

Similar Datasets

| S-EPMC3362049 | biostudies-literature
| S-EPMC196869 | biostudies-literature
| S-EPMC3910140 | biostudies-literature
| S-EPMC5551056 | biostudies-literature
| S-EPMC4249799 | biostudies-literature
| S-EPMC5385882 | biostudies-literature
| S-EPMC4109841 | biostudies-literature
| S-EPMC1301808 | biostudies-other
| S-EPMC3128589 | biostudies-literature
| S-EPMC4838351 | biostudies-literature