Abstract: The degrading serine proteases derived from nematophagous fungi are known as one of the most important virulence determinants during infection processes.The previous studies have shown that degradation of alkaline degrading serine protease was more effective than neutral ones,the structural dynamics mechanism underlying this phenomenon remains to be elucidated.To obtain detailed information about the differences of structural dynamics features and catalytic properties of alkaline and neutral degrading serine proteases,molecular dynamics (MD) simulations,essential dynamics (ED) analysis,and metadynamics simulations were performed on the alkaline serine protease PR1and neutral serine protease PII.The results revealed that during the dynamic simulations PR1 had higher global conformational stability,more ruggedness of free energy landscape surface and higher minimum free energy.The global dynamic features revealed that the global structural stability of PR1 was higher than PII.Comparative analysis between the dynamic geometrical properties demonstrated that the binding sites of PII had more RMSF,Rg,SASA and less NHB,NNC than that in PR1,which revealed that the flexibility of the binding sites was higher in PR1 than that in PII.Further essential dynamics analysisrevealed that the large concerted motions of PR1 mainly concentrated in regions of substrate-binding site,which could be beneficial for improving catalytic abilities.Therefore,it was concluded that the differences of structural dynamics features betweenPR1and PIImakesPR1have higher catalytic efficiency than that of neutral serine proteases PII.