Pathways for conformational change in seryl-tRNA synthetase from Thermus thermophilus

Seryl t-RNA synthetase of the bacterium Thermus thermophilus contains a long arm, consisting of an antiparallel coiled coil, that is involved in binding of tRNA. Two crystallographic structures exist for this protein, in which the arm is in different conformations. Here, we use computational methods employing an empirical potential energy function to investigate the flexibility of the long arm. A conformational pathway is calculated between the 2 crystallographic structures using a method based on molecular dynamics simulation. The pathway is analyzed in terms of sequential phi and psi backbone angle changes. Several transient phi and psi displacements are present along the pathway that are not visible in the end states and may be required for transition between them. Energy maps are constructed by rotating the arm around its principal axes of inertia and energy minimizing. The map identifies 2 regions of relatively low energy which might be accessible to the arm.