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Biophys J, December 2000, p. 2902-2908, Vol. 79, No. 6
and
*Department of Chemistry and Chemical Biology, Harvard University,
Cambridge, Massachusetts 02138 USA; Neotrope Research,
Pelham, Massachusetts 01002 USA; and Laboratoire de
Chimie Biophysique, Institut le Bel, Université Louis
Pasteur, 67000 Strasbourg, France
A constant-energy molecular dynamics simulation is used
to monitor protein motion at zero-total angular momentum. With a simple protein model, it is shown that overall rotation is possible at zero-total angular momentum as a result of flexibility. Since the
rotational motion is negligible on a time scale of 1000 reduced time
units, the essentially rotation-free portion of the trajectory provides
an unbiased test of the common approximate methods for separating
overall rotation from internal motions by optimal superposition. Removing rotation by minimizing the root-mean-square deviation (RMSD)
for the entire system is found to be more appropriate than using the
RMSD for only the more rigid part of the system. The results verify the
existence of positive cross-correlation in the motions of atoms
separated by large distances.
Biophys J, December 2000, p. 2902-2908, Vol. 79, No. 6
© 2000 by the Biophysical Society 0006-3495/00/12/2902/07 $2.00
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