碱性和中性食线虫真菌丝氨酸蛋白酶动力学行为差异研究

Study on the differences of the structural dynamic features of alkaline and neutral serine proteases from nematophagous fungi

食线虫真菌丝氨酸蛋白酶被认为是病原真菌感染线虫最重要的毒力因子之一.研究表明,碱性体壁降解丝氨酸蛋白酶比中性蛋白酶具有更强的催化活性和杀线虫活性.研究选取中性丝氨酸蛋白酶PII和碱性丝氨酸蛋白酶PR1为研究对象,通过分子动力学模拟、元动力学模拟和本质动力学分析等手段研究二者的结构动力学差异及对催化能力的影响.研究结果表明,模拟过程中PII比PR1具有更高的全局构象柔性; PII较PR1具有更为粗糙的自由能表面和更高的自由能最小化值,说明PR1比PII具备更高的热稳定性和全局结构稳定性.对于两者底物结合区域柔性的比较结果表明,PR1的底物结合区域比PII具备更高的RMSF、Rg和SASA,同时具备更少NHB和NNC,说明PR1底物结合部位具有更强的构象柔性.通过对二者的模拟平衡轨迹进行本质动力学分析表明,PII和PR1具有不一样的主要运动模式,PII的大尺度协同运动主要为分子表面环区的运动,而PR1的大尺度协同运动则是底物结合区域与功能相关的协同运动.以上动力学行为的差异可能使得碱性丝氨酸蛋白酶PR1较中性丝氨酸蛋白酶PII具备更强的催化活性和杀线虫活性.

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.