Stress-induced shape transitions in polymers using a new approach to steered molecular dynamics

Tertiary folds are structurally stable, yet present a notable degree of plasticity. This duality is a key feature to understanding biological function and activity. Recent experiments using atomic force microscopy allow one to assess folding stability by directly measuring conformational changes in a single biomolecule. Experimental data can be complemented by the microscopic detail provided by computer simulations of mechanical unfolding. In this work, we present a simple computational alternative to study stress-induced transitions in chain molecules. In our approach to steered molecular dynamics, a soft perturbation is introduced by performing regular pull/push events localized on two bonds at the chain's ends, followed by constrained dynamics with two anchored atoms. We test the procedure on a hydrocarbon chain, and then illustrate its potential by studying the stretching of an alpha-helix. Shape transitions are monitored in terms of molecular size and chain entanglements. We find that extensive distorsions of the helix can proceed at essentially constant molecular size. The results highlight the importance of using complementary shape descriptors to understand the behaviour of stressed chain molecules.