Electrostatic modulation of protein dynamics and interactions (Supplement for Equipment Purchase)

项目摘要/摘要 这项更新建议旨在继续开发和应用连续恒定pH分子 动力学(CpHMD)工具，以促进对蛋白水解酶、激酶和钠/质子的分子理解。 分别与阿尔茨海默病、癌症和高血压有关的转运蛋白。这样做的目的是 建议1)进一步开发、加速和推广CPhMD；2)发现静电调制器 3)阐明了钠/质子的作用机制。 反搬运者。 开发一种pH恒定器来适当地控制溶液的pH值一直是MD社区的一个长期目标。 我们最近开发的基于PME的全原子CpHMD使我们离目标更近了一步。在目标1中，我们将添加 一种可极化的力量fi将CpHMD的精度提高到一个新的水平。我们将在其他环境中实现CPhMD 支持替代隐式溶剂模型并强制fi域的包。我们将在GPU上实现代码 允许进行常规微秒级模拟的平台。新的事态发展将推动当前的 分子动力学模拟、变换pKA计算和质子中介过程的研究。 由于缺乏工具，质子化状态和pH效应是基于结构的药物设计中被忽视的一个方面 和理解。我们最近发现了-分泌酶(A)的pH调节动力学-活性关系 阿尔茨海默病的主要药物靶点)，并表明fi不能在小分子结合中依赖pH。在AIM 我们将继续研究与-分泌酶相关的天冬氨酸蛋白酶，并解决具有挑战性的问题。 关于激酶的激活和选择性抑制。 传统的基于静态结构计算的fi质子态MD不能可靠地识别质子态MD。 确定质子结合残基，阐明质子偶联构象动力学。我们最近开发了 膜混合溶剂CpHMD，它允许质子通道(M2)的fi第一个恒定pH模拟，a 钠/质子逆向转运体(NAHA)和EfflUX泵(AcrB)。在目标3中，我们计划应用此工具和新工具 在目标1中开发，以进一步了解NhaA中的钠-质子交换过程并阐明 另一种钠-质子逆向转运蛋白的独特机制。这些研究将进一步验证CpHMD和 使其成为研究质子偶联跨膜蛋白的有力工具。 总而言之，拟议的项目将推动分子模拟当前预测能力的边界， 改变质子介导过程的研究，并产生新的见解，以加速药物发现靶向 阿尔茨海默病、癌症和高血压。

Project Summary/Abstract This renewal proposal seeks to continue the development and application of continuous constant pH molecular dynamics (CpHMD) tools to advance molecular understanding of proteases, kinases and sodium/proton an- tiporters which are involved in Alzheimer's disease, cancer and hypertension, respectively. The objectives of this proposal are to 1) further develop, accelerate and disseminate CpHMD; 2) discover electrostatic modulators of aspartyl proteases and kinases towards selective inhibition; and 3) elucidate the mechanisms of sodium/proton antiporters. Development of a pH stat to properly control solution pH has been a long-standing goal in the MD community. Our recent development of PME-based all-atom CpHMD brought us closer to the goal. In Aim 1, we will add a polarizable force field to take the accuracy of CpHMD to the next level. We will implement CpHMD in other packages to enable alternative implicit-solvent models and force fields. We will implement the code on the GPU platform to allow routine microsecond-scale simulations. The new developments will push the boundary of current MD simulations, transforming pKa calculations and studies of proton-mediated processes. Protonation states and pH effects are a neglected aspect in structure-based drug design due to the lack of tools and understanding. We recently discovered a pH-regulated dynamics-activity relationship for -secretase (a major Alzheimer's drug target) and demonstrated significant pH dependence in small-molecule binding. In Aim 2, we will continue the study of -secretase related aspartyl proteases, and we will tackle challenging questions regarding kinase activation and selective inhibition. Conventional fixed-protonation-state MD with static-structure-based electrostatic calculations cannot reliably iden- tify proton-binding residues and elucidate proton-coupled conformational dynamics. We recently developed the membrane hybrid-solvent CpHMD, which allowed the first constant pH simulations of a proton channel (M2), a sodium/proton antiporter (NhaA) and an efflux pump (AcrB). In Aim 3, we plan to apply this and the new tools developed in Aim 1 to gain further insights into the sodium-proton exchange process in NhaA and to elucidate the distinctive mechanism of another sodium-proton antiporter. These studies will further validate CpHMD and establish it as a powerful tool for studies of proton-coupled transmembrane proteins. In summary, the proposed project will push the boundary of the current predictive power of molecular simulations, transform studies of proton-mediated processes, and generate new insights to accelerate drug discovery targeting Alzheimer's disease, cancer and hypertension.