Polymer uncrossing and knotting in protein folding, and their role in minimal folding pathways.

ABSTRACT: We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost chain, and calculating the minimal uncrossing cost that would have been required to avoid such events. A depth-first tree search algorithm is applied to find minimal transformations to fold [Formula: see text], [Formula: see text], [Formula: see text], and knotted proteins. In all cases, the extra uncrossing/non-crossing distance is a small fraction of the total distance travelled by a ghost chain. Different structural classes may be distinguished by the amount of extra uncrossing distance, and the effectiveness of such discrimination is compared with other o

SUBMITTER: Mohazab AR 

PROVIDER: S-EPMC3554774 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature