LOW-FREQUENCY DOMAIN MOTIONS IN THE CARBOXY-TERMINAL FRAGMENT OF L7 L12 RIBOSOMAL-PROTEIN STUDIED WITH MOLECULAR-DYNAMICS TECHNIQUES - ARE THESE MOVEMENTS MODEL-INDEPENDENT/

A large-amplitude and low-frequency (5-cm(-1)) domain-domain motion is found to occur in two molecular dynamics simulations of the carboxy t erminal fragment of the L7/L12 ribosomal protein of E. coli. These sim ulations were carried out at constant energy with the CHARMM program p ackage (ref 1), with two different electrostatic protocols: one in whi ch a ''smoothed'' 9-Angstrom cutoff is used and another one in which a ll atom-atom interactions are taken into account. Our results are in a greement with those obtained previously from the analysis of simulatio ns performed with another electrostatic protocol, another kind of traj ectory initialization, another kind of statistical ensemble, another p rogram package, etc. (refs 2-4). This ensemble of results suggests tha t the low-frequency domain-domain motion we observe is unlikely to be an artifact due to the particularities of the protocols used to perfor m all of these simulations. It is much more Likely to be a dynamical c haracteristic of the particular fold of the carboxy terminal fragment of the L7/L12 ribosomal protein.