Steered molecular dynamics simulation of conformational changes of immunoglobulin domain I27 interprete atomic force microscopy observations Original Research Article

Atomic force microscopy and steered molecular dynamics investigations of the response of so-called mechanical proteins like titin, tenascin or their individual immunoglobulin and fibronectin type III domains have lead to qualitative insights about the relationship between the β sandwich domain architecture and the function of this class of proteins. The proteins, linear segments of up to hundreds of domains, through strain induced shape changes, unfolding and refolding, maintain order and elasticity in cellular systems over a nearly tenfold length scale. In this paper we develop a steered molecular dynamics description of the response of the titin immunoglobulin domain I27 at the onset of domain unfolding in quantitative agreement with AFM observations. We show that if forces stronger than 50 pN are applied to the terminal ends the two hydrogen bonds between the antiparallel A and B β strands break with a concomitant 6–7 Å elongation of the protein. If forces strong enough to unfold the domain are applied, the protein is halted in this initial extension until the set of all six hydrogen bonds connecting strands A′ and G break simultaneously. This behavior is accounted for by a barrier separating folded and unfolded states, the shape of which is consistent with AFM and chemical denaturation data. We also demonstrate that steered molecular dynamics simulations which induce unfolding through slow pulling (speed 0.1 Å/ps) predict unfolding forces that are within a factor of two within force values extrapolated from AFM observations.