Molecular dynamics simulations of the plant-specific insert monomer at pH 7.4

This study examines the underlying mechanics driving tertiary structure and quaternary conformational changes in silico of the saposin-like domain, the plant-specific insert, of a potato (Solanum tuberosum) aspartic protease as a function of pH. Umbrella sampling was used to determine the free energy change of dissociation of the plant-specific insert at acidic and neutral pH and revealed that a lower barrier to dissociation exists at neutral pH as compared to acidic pH. Furthermore, principal component analysis was used to characterize tertiary structure conformational changes at active (pH4.5)and neutral pH of monomeric plant-specific insert. The results indicate that the plant-specific insert may adopt a tertiary structure similar to the characteristic saposin-fold at neutral pH and suggests a potential new structural motif among saposin-like proteins at pH 4.5.本研究以马铃薯（Solanum tuberosum）天冬氨酸蛋白酶（aspartic protease）的植物特异性插入片段（plant-specific insert）——鞘脂激活蛋白样结构域（saposin-like domain）为研究对象，探究其在pH依赖条件下计算机模拟（in silico）中的三级结构与四级构象变化的内在机制。本研究采用伞形采样（Umbrella Sampling）方法，测定了植物特异性插入片段在酸性与中性pH条件下的解离自由能变化，结果显示相较于酸性pH环境，中性pH下其解离能垒更低。此外，本研究通过主成分分析（Principal Component Analysis）表征了单体形式植物特异性插入片段在活性pH（pH4.5）与中性pH条件下的三级结构构象变化。研究结果表明，植物特异性插入片段在中性pH条件下可呈现出与典型鞘脂激活蛋白折叠（saposin-fold）相似的三级结构，同时提示在pH4.5条件下，鞘脂激活蛋白样蛋白家族中可能存在一种全新的潜在结构基序。