Simulations of the T <-> R conformational transition in aspartate transcarbamylase

Aspartate transcarbamylase (ATCase) from Escherichia coli is one of the bes t known allosteric enzymes. In spite of numerous experiments performed by b iochemists, no consensus model for the cooperative transition between the t ensed (T) and the relaxed (R) forms exists. It is hypothesized, however; th at changes in the quaternary structure play a key role in the allosteric pr operties of oligomeric proteins such as ATCase. Previous normal mode calcul ations of the two states of ATCase illustrated the type of motions that cou ld be important in initiating the transition. In this work four pathways fo r the transition were calculated using the targeted molecular dynamics (TMD ) method without constraint on the symmetry of the system. The most importa nt quaternary structure changes are the relative rotation and translation o f the catalytic trimers and the rotations of the regulatory dimers. The sim ulations show that these quaternary changes start immediately and finish wh en about 70% of the transition is completed whereas there are tertiary chan ges throughout the transition. In agreement,vith the work of Lipscomb et al ., it was found that the relative translation between the catalytic trimers appears to play a central role in allowing the transition to occur: In all the simulations differences are observed in the opening and closing behavi ours of the domains in the catalytic and regulatory chains that could provi de a structural interpretation for the results of certain site-directed mut agenesis experiments. Overall the motions of the subunits are concerted eve n though the constraint imposed on the TMD method does not explicitly requi re that this be so.