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. 2006 May 12;91(3):948–956. doi: 10.1529/biophysj.105.080259

FIGURE 4.

FIGURE 4

Essential modes of YopH visualized by projecting the MD trajectory onto the eigenvector and superimposing the minimum and maximum structures from MD simulations. (A) The first essential mode shows the opening-closure of the WPD loop and correlated internal motions with loop L2 and loop L6. (B) The second essential mode shows the dominant open conformation with correlated motions between the WPD loop and loop L4. (C) Cartoon representations of helix α4 and the following loop L6 associated with the open (gray and yellow) and closed (blue and green) conformations in the first essential mode.