Additional file 5.
Gaussian Network Model Analysis. The yeast RNAP elongation complex (PDB #2E2H) was subjected to Gaussian Network Model simulation (ignm.ccbb.pitt.edu; 6Å cut-off) to assess the distribution of forces within intact RNAPs. Slow-mode motions (rank 4, 6 and 8) affect particularly the center of the Bridge Helix (as indicated by green/gold color-coding), whereas the N- and C-terminal region remain immobile. The slow modes identify predominantly the response of individual domains to mechanical forces exerted on them from other structures during the simulation. It should be noted that such simulations do not take the chemical nature of residues into account and would therefore not be able to detect the intrinsic kinking properties of the BH-HN and the BH-HC regions.
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Weinzierl BMC Biology 2010 8:134 doi:10.1186/1741-7007-8-134