The different protonation state of amino group can bring quite different catalytic mechanism in enzymatic process.Herein,based on state-of-the-art ab initio QM/MM MD simulations,the catalytic mechanisms and free energy profile of glucosamine 6-phosphate deaminase from Streptococcus mutans(SmuNagB)and hydroxynitrile lyases from Hevea brasiliensis(HbHNL)have been determined to explain the phenomenon.For SmuNagB,the deprotonation amino group of substrate will give rise to a concerted ring-opening process while the protonated amino will lead to a stepwise reaction.The free energy barrier for the rate-determining step in the low-energy stepwise reaction is 17.9 kcal mol-1.For HbHNL,the different protonation state of Lys236 exhibits quite different catalytic process,which may be caused by the distinctive driving force.The protonation Lys236 play an important role in catalytic process through the analysis of two protonation models and mutant systems.The protonation model has been predicted to more favorable than deprotonation model dynamically.Our predictions for both enzyme systems are consistent with the experimental studies[1~2].Such remarkable effects of the protonation state of amino group on the catalytic mechanism and the reaction energetics may be applied to the other enzymatic systems.