The sequences of the protease domain of the tick-borne encephalitis (TBE) virus 
NS3 protein have two amino acid substitutions, 16 R→K and 45 S→F, in the highly 
pathogenic and poorly pathogenic strains of the virus, respectively. Two models 
of the NS2B-NS3 protease complex for the highly pathogenic and poorly pathogenic 
strains of the virus were constructed by homology modeling using the crystal 
structure of West Nile virus NS2B-NS3 protease as a template; 20 ns molecular 
dynamic simulations were performed for both models, the trajectories of the 
dynamic simulations were compared, and the averaged distance between the two 
models was calculated for each residue. Conformational differences between two 
models were revealed in the identified pocket. The different conformations of 
the pocket resulted in different orientations of the NS2B segment located near 
the catalytic triad. In the model of the highly pathogenic TBE virus the 
identified pocket had a more open conformation compared to the poorly pathogenic 
model. We propose that conformational changes in the active protease center, 
caused by two amino acid substitutions, can influence enzyme functioning and the 
virulence of the virus.