Catch bond-like kinetics of helix cracking: network analysis by molecular dynamics and milestoning.

ABSTRACT: The first events of unfolding of secondary structure under load are considered with Molecular Dynamics simulations and Milestoning analysis of a long helix (126 amino acids). The Mean First Passage Time is a non-monotonic function of the applied load with a maximum of 3.6 ns at about 20 pN. Network analysis of the reaction space illustrates the opening and closing of an off-pathway trap that slows unfolding at intermediate load levels. It is illustrated that the nature of the reaction networks changes as a function of load, demonstrating that the process is far from one-dimensional.

SUBMITTER: Kreuzer SM 

PROVIDER: S-EPMC3716791 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature