Solution pH is a critical environmental factor for chemical and biological processes. Over the last decade, significant efforts have been made in the development of constant pH molecular dynamics (pHMD) techniques for gaining detailed insights into pH-coupled dynamical phenomena. In this article, we review the advancement of this field in the past five years, placing a special emphasis on the development of the all-atom continuous pHMD technique. We discuss various applications, including the prediction of pKa shifts for proteins, nucleic acids and surfactant assemblies, elucidation of pH-dependent population shifts, protein–protein and protein–RNA binding, as well as the mechanisms of pH-dependent self-assembly and phase transitions of surfactants and peptides. We also discuss future directions for the further improvement of the pHMD techniques.

中文翻译：

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恒pH分子动力学研究进展及应用

溶液 pH 值是化学和生物过程的关键环境因素。在过去的十年中，在开发恒定 pH 分子动力学 (pHMD) 技术方面做出了重大努力，以获得对 pH 耦合动力学现象的详细了解。在本文中，我们回顾了过去五年该领域的进展，特别强调了全原子连续 pHMD 技术的发展。我们讨论了各种应用，包括预测蛋白质、核酸和表面活性剂组装的 pKa 变化，阐明 pH 依赖性种群变化、蛋白质-蛋白质和蛋白质-RNA 结合，以及 pH 依赖性自组装的机制和表面活性剂和肽的相变。我们还讨论了进一步改进 pHMD 技术的未来方向。