MOLECULAR-DYNAMICS SIMULATION OF DOMAIN MOVEMENTS IN ASPARTATE-AMINOTRANSFERASE

Mitochondrial aspartate aminotransferase is a homodimeric protein with 2X402 amino acid residues. The enzyme in solution undergoes ligand-in duced and syncatalytic conformational changes which appear to correspo nd to shifts in the equilibrium between the crystallographically defin ed 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 th e active-site pocket. Molecular dynamics simulations at 300 K of 120-p s duration were started from the crystal structures of the unliganded pyridoxal form (open form) of the dimeric enzyme and the 2-methylaspar tate-liganded closed form in which the 2-methyl group had been removed . Both structures contained the crystal water molecules and were place d in a 5-Angstrom shell of water. The rms fluctuations of the individu al C alpha atoms during the simulations agreed well with the correspon ding B factors of the crystal structures. Superposition of the initial structures and the average structures of the last 20 ps showed in bot h simulations extensive C alpha deviations in the case of the whole su bunit but much smaller changes in the individual large and small domai ns, indicating a movement of the two domains relative to each other. I n the simulation of the open form, superposition of the large domains made evident a displacement of the small domain towards its position i n the closed crystal structure, which can be described by a rotation o f the small domain by about 13 degrees around the twofold symmetry (z) axis. A significantly less extensive rearrangement of parts of the sm all domain, i.e. a rotation of about 5 degrees around the z axis, was observed in the simulation of the substrate-liganded enzyme (closed fo rm) which, in contrast to the open form, showed only small conformatio nal 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 le ast two orders of magnitude larger than the simulation time of 120 ps. Apparently, the surface tension of the unrestrained nonspherical shel l of water accelerates the simulated conformational change which, howe ver, quite closely imitates the geometric features of the extensive mo vement of the small domains (each approximate to 130 residues).