COMPARATIVE MOLECULAR-DYNAMICS SIMULATION STUDIES OF SALMON AND BOVINE TRYPSINS IN AQUEOUS-SOLUTION

The flexibility and conformational behaviour of salmon and bovine tryp sins were modelled with a 300 ps molecular dynamics simulation in aque ous solution, Trajectories from both trypsins were analysed to eventua lly detect differences in mobility that could explain observed variati ons in stability and activity, The simulations were performed at 300 K with all the acidic groups deprotonated and the basic groups protonat ed. The radius of gyration, the overall r.m.s. deviation from the star ting structure as a function of time, together with the r.m.s. deviati on from the starting structures as a function of residue number, demon strated that the simulations were stable and representative of the X-r ay structures of both enzymes, Isotropic Debye-Waller factors were cal culated from the fluctuations for main-chain atoms and were in good ag reement with experimental values, The overall dynamic properties of th e two enzymes were similar, Based on the present 300 ps molecular dyna mics simulation, it cannot be concluded that either of the two enzymes is more 'flexible' than the other, However, there are clearly differe nces in mobility on a more detailed level and for particular regions.