Journal of Physical Chemistry, Vol.99, No.15, 5698-5704, 1995
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 terminal fragment of the L7/L12 ribosomal protein of E. coli. These simulations were carried out at constant energy with the CHARMM program package (ref 1), with two different electrostatic protocols : one in which a "smoothed" 9-Angstrom cutoff is used and another one in which all atom-atom interactions are taken into account. Our results are in agreement with those obtained previously from the analysis of simulations performed with another electrostatic protocol, another kind of trajectory initialization, another kind of statistical ensemble, another program package, etc. (refs 2-4). This ensemble of results suggests that the low-frequency domain-domain motion we observe is unlikely to be an artifact due to the particularities of the protocols used to perform all of these simulations. It is much more Likely to be a dynamical characteristic of the particular fold of the carboxy terminal fragment of the L7/L12 ribosomal protein.