Are there non-trivial dynamic cross-correlations in proteins?

The analysis of internal motion in ensembles of flexible molecules in coordinate space requires the removal of overall motion by a least-squares fitting procedure of the Cartesian coordinates. It has been demonstrated that the choice of the atom set used for fitting influences the picture of the internal motion of BPTI. We have performed essential dynamics analyses of a 1 ns molecular dynamics trajectory of the single-stranded DNA-binding protein from the Pf3 phage using either all alpha-carbon atoms or the least mobile ones for fitting the trajectory prior to the analysis. We found that covariances of atoms separated by long distances were significantly reduced in the latter case; the overall overlap of essential spaces was still high. In the second part we present a method that does not introduce any bias caused by overall motion: principal component analysis in distance space. Non-trivial dynamic cross-correlations were preserved in distance space, which answers the question posed in the title in the affirmative. However, cross-correlations were throughout smaller than those detected by standard essential dynamics analyses. (C) 1998 Academic Press Limited.