Multiple Unfolding Intermediates Obtained by Molecular Dynamic Simulations under Stretching for Immunoglobulin-Binding Domain of Protein G

Open Biochem J. 2009 Nov 23:3:66-77. doi: 10.2174/1874091X00903010066.


We have studied the mechanical properties of the immunoglobulin-binding domain of protein G at the atomic level under stretching at constant velocity using molecular dynamics simulations. We have found that the unfolding process can occur either in a single step or through intermediate states. Analysis of the trajectories from the molecular dynamic simulations showed that the mechanical unfolding of the immunoglobulin-binding domain of protein G is triggered by the separation of the terminal beta-strands and the order in which the secondary-structure elements break is practically the same in two- and multi-state events and at the different extension velocities studied. It is seen from our analysis of 24 trajectories that the theoretical pathway of mechanical unfolding for the immunoglobulin-binding domain of protein G does not coincide with that proposed in denaturant studies in the absence of force.

Keywords: Molecular dynamics; denaturant unfolding pathway; ensemble of transition states; explicit model of water.; intermediate state; mechanical unfolding pathway.