Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, Towson, Maryland 21252, United States.
Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States.
J Chem Inf Model. 2021 Jan 25;61(1):400-407. doi: 10.1021/acs.jcim.0c01201. Epub 2020 Dec 23.
Renin is a pepsin-like aspartyl protease and an important drug target for the treatment of hypertension; despite three decades' research, its pH-dependent structure-function relationship remains poorly understood. Here, we employed continuous constant pH molecular dynamics (CpHMD) simulations to decipher the acid/base roles of renin's catalytic dyad and the conformational dynamics of the flap, which is a common structural feature among aspartyl proteases. The calculated p's suggest that catalytic Asp38 and Asp226 serve as the general base and acid, respectively, in agreement with experiment and supporting the hypothesis that renin's neutral optimum pH is due to the substrate-induced p shifts of the aspartic dyad. The CpHMD data confirmed our previous hypothesis that hydrogen bond formation is the major determinant of the dyad p order. Additionally, our simulations showed that renin's flap remains open regardless of pH, although a Tyr-inhibited state is occasionally formed above pH 5. These findings are discussed in comparison to the related aspartyl proteases, including β-secretases 1 and 2, cathepsin D, and plasmepsin II. Our work represents a first step toward a systematic understanding of the pH-dependent structure-dynamics-function relationships of pepsin-like aspartyl proteases that play important roles in biology and human disease states.
肾素是一种胃蛋白酶样天冬氨酸蛋白酶，是治疗高血压的重要药物靶点；尽管已经进行了三十年的研究，但它的 pH 依赖的结构-功能关系仍未得到很好的理解。在这里，我们采用连续恒 pH 分子动力学（CpHMD）模拟来破译肾素催化二联体的酸碱作用以及瓣的构象动力学，这是天冬氨酸蛋白酶的共同结构特征。计算出的 p 值表明，催化天冬氨酸 38 和天冬氨酸 226 分别作为广义碱和酸，与实验结果一致，并支持肾素的中性最适 pH 是由于底物诱导的天冬氨酸二联体 p 位移的假设。CpHMD 数据证实了我们之前的假设，即氢键的形成是二联体 p 顺序的主要决定因素。此外，我们的模拟表明，肾素的瓣始终保持开放状态，尽管在 pH 值高于 5 时偶尔会形成 Tyr 抑制状态。这些发现与相关的天冬氨酸蛋白酶进行了比较，包括β-分泌酶 1 和 2、组织蛋白酶 D 和血浆酶 II。我们的工作代表了朝着系统理解在生物学和人类疾病状态中发挥重要作用的胃蛋白酶样天冬氨酸蛋白酶的 pH 依赖的结构-动力学-功能关系迈出的第一步。
