Force and Stress along Simulated Dissociation Pathways of Cucurbituril-Guest Systems.

ABSTRACT: The field of host-guest chemistry provides computationally tractable yet informative model systems for biomolecular recognition. We applied molecular dynamics simulations to study the forces and mechanical stresses associated with forced dissociation of aqueous cucurbituril-guest complexes with high binding affinities. First, the unbinding transitions were modeled with constant velocity pulling (steered dynamics) and a soft spring constant, to model atomic force microscopy (AFM) experiments. The computed length-force profiles yield rupture forces in good agreement with available measurements. We also used steered dynamics with high spring constants to generate paths characterized by a tight control over the specified pulling distance; these paths were then equilibrated via umbrella samplin

SUBMITTER: Velez-Vega C 

PROVIDER: S-EPMC3383817 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature