A comprehensive multidimensional-embedded, one-dimensional reaction coordinate for protein unfolding/folding.

ABSTRACT: The goal of the Dynameomics project is to perform, store, and analyze molecular dynamics simulations of representative proteins, of all known globular folds, in their native state and along their unfolding pathways. To analyze unfolding simulations, the location of the protein along the unfolding reaction coordinate (RXN) must be determined. Properties such as the fraction of native contacts and radius of gyration are often used; however, there is an issue regarding degeneracy with these properties, as native and nonnative species can overlap. Here, we used 15 physical properties of the protein to construct a multidimensional-embedded, one-dimensional RXN coordinate that faithfully captures the complex nature of unfolding. The unfolding RXN coordinates for 188 proteins (1534 simulations an

SUBMITTER: Toofanny RD 

PROVIDER: S-EPMC2877366 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature