Figure 4.

Modification of catB flexibility at different pH conditions and upon heparin binding A) Visualization of backbone flexibility colored according to residue RMS fluctuation values during the 40 ns MD of the apo form of catB in different pH conditions. The black arrows indicate the catalytic residue C29. B) The same as A but for the complexes catB-heparin. The disaccharide is represented by sticks and its position corresponds to the binding site (L or R) occupied. C) Time-evolution of RMSD clusters of catB backbone conformations (using a clustering criteria of 1 Å RMSD). Each system is colored differentially according to the legend D) Backbone RMSD distributions for each simulation. Colors definitions were applied as in C.

Costa et al. BMC Genomics 2010 11(Suppl 5):S5   doi:10.1186/1471-2164-11-S5-S5