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. Author manuscript; available in PMC: 2011 Sep 17.
Published in final edited form as: J Mol Biol. 2010 Jul 23;402(2):475–489. doi: 10.1016/j.jmb.2010.07.035

Figure 5.

Figure 5

HQBM simulations of ubiquitin. a) The RMSD of the ubquitin backbone atoms as a function of time for simulations in which bias potentials with a force constant α of 20 kcal / (mol ·Å4) (circles), 50 kcal / (mol ·Å4) (triangles) and 100 kcal / (mol ·Å4) (diamonds) was applied. b) Snapshots taken at the indicated time points during a HQBM trajectory in which a bias potential with a force constant of 20 kcal / (mol ·Å4) was applied. α helices are shown in yellow and β strands are shown in blue. For clarity, some C-terminal residues were omitted from partially unfolded structures.