Steered molecular dynamics simulations of force-induced protein domain unfolding

Steered molecular dynamics (SMD), a computer simulation method for studying force-induced reactions in biopolymers, has been applied to investigate the response of protein domains to stretching apart of their terminal ends. The simulations mimic atomic force microscopy and optical tweezer experiments, but proceed on much shorter time scales. The simulations on different domains for 0.6 nanosecond each reveal two types of protein responses: the first type, arising in certain beta-sandwich domains, exhibits nanosecond unfolding only after a force above 1,500 pN is applied; the second type, arising in a wider class of protein domain structures, requires significantly weaker forces for nanosecond unfolding. In the first case, strong forces are needed to concertedly break a set of interstrand hydrogen bonds which protect the domains against unfolding through stretching; in the second case, stretching breaks backbone hydrogen bonds one by one, and does not require strong forces for this purpose. Stretching of beta-sandwich (immunoglobulin) domains has been investigated further revealing a specific relationship between response to mechanical strain and the architecture of beta-sandwich domains.