... running on a Linux PC clus-ter, was used for the MD simulations and analysis of thetrajectories.Using the gromacs utilities, the ED analysis was carriedout in to separate the motions of the examined ... DK9 mutant and 6.86 inWT thrombin. Because previous studies have assignedthis group to the active site His57 side chain [3–5], thisfinding suggests that Lys9 deletion allosterically affectsthe ... experimentaldata using the grafit program (Erithacus Software Ltd,Staines, UK).Binding of sodium ionSteady-state fluorescence titration measurements were car-ried out using 500 nm WT and mutant thrombin,...