Comparative molecular dynamics simulation studies of salmon and bovine trypsins in aqueous solution

The flexibility and conformational behaviour of salmon and bovine trypsins were modelled with a 300 ps molecular dynamics simulation in aqueous solution. Trajectories from both trypsins were analysed to eventually detect differences in mobility that could explain observed variations in stability and activity. The simulations were performed at 300 K with all the acidic groups deprotonated and the basic groups protonated. The radius of gyration, the overall r.m.s. deviation from the starting structure as a function of time, together with the r.m.s. deviation from the starting structures as a function of residue number, demonstrated that the simulations were stable and representative of the X-ray structures of both enzymes. Isotropic Debye-Waller factors were calculated from the fluctuations for main-chain atoms and were in good agreement with experimental values. The overall dynamic properties of the two enzymes were similar. Based on the present 300 ps molecular dynamics simulation, it cannot be concluded that either of the two enzymes is more 'flexible' than the other. However, there are clearly differences in mobility on a more detailed level and for particular regions.