Molecular-dynamics simulation of domain movements in aspartate aminotransferase

Mitochondrial aspartate aminotransferase is a homodimeric protein with 2 x 402 amino acid residues. The enzyme in solution undergoes ligand-induced and syncatalytic conformational changes which appear to correspond to shifts in the equilibrium between the crystallographically defined open and closed conformation. In the closed conformation, the small domain of each subunit has rotated as a rigid body by 13 degrees and 14 degrees towards the large coenzyme-binding domain and has closed the active-site pocket. Molecular dynamics simulations at 300 K of 120-ps duration were started from the crystal structures of the unliganded pyridoxal form (open form) of the dimeric enzyme and the 2-methylaspartate-liganded closed form in which the 2-methyl group had been removed. Both structures contained the crystal water molecules and were placed in a 5-A shell of water. The rms fluctuations of the individual C alpha atoms during the simulations agreed well with the corresponding B factors of the crystal structures. Superposition of the initial structures and the average structures of the last 20 ps showed in both simulations extensive C alpha deviations in the case of the whole subunit but much smaller changes in the individual large and small domains, indicating a movement of the two domains relative to each other. In the simulation of the open form, superposition of the large domains made evident a displacement of the small domain towards its position in the closed crystal structure, which can be described by a rotation of the small domain by about 13 degrees around the twofold symmetry (z) axis. A significantly less extensive rearrangement of parts of the small domain, i.e. a rotation of about 5 degrees around the z axis, was observed in the simulation of the substrate-liganded enzyme (closed form) which, in contrast to the open form, showed only small conformational changes around the active site. In both simulations an additional rotation of the small domain by 9 degrees around the x axis occurred. The actual domain movement is estimated to occur in a time range at least two orders of magnitude larger than the simulation time of 120 ps. Apparently, the surface tension of the unrestrained nonspherical shell of water accelerates the simulated conformational change which, however, quite closely imitates the geometric features of the extensive movement of the small domains (each approximately 130 residues).