Hierarchy of structure loss in MD simulations of src SH3 domain unfolding

To complement experimental studies of the src SH3 domain folding, we studie d 30 independent, high-temperature, molecular dynamics simulations of src S H3 domain unfolding. These trajectories were observed to differ widely from each other. Thus, rather than analyzing individual trajectories, we sought to identify the recurrent features of the high-temperature unfolding proce ss. The conformations from all simulations were combined and then divided i nto groups based on the number of native contacts. Average occupancies of e ach side-chain hydrophobic contact and hydrogen bond in the protein were th en determined. In the symmetric funnel limit, the occupancies of all contac ts should decrease in concert with the loss in total number of native conta cts. If there is a lack of symmetry or hierarchy to the unfolding process, the occupancies of some contacts should decrease more slowly, and others mo re rapidly. Despite the heterogeneity of the individual trajectories, the e nsemble averaging revealed an order to the unfolding process: contacts betw een the N and C-terminal strands are the first to disappear, whereas contac ts within the distal beta-hairpin and a hydrogen-bonding network involving the distal loop beta-turn and the diverging turn persist well after the maj ority of the native contacts are lost. This hierarchy of events resembles b ut is somewhat less pronounced than that observed in our experimental studi es of the folding of src SH3 domain. (C) 1999 Academic Press.