论文标题
天冬氨酸残基在硫氧还蛋白中的PKA转移的计算研究：构型采样和溶剂模型的作用
Computational Study of pKa shift of Aspartate residue in Thioredoxin: Role of Configurational Sampling and Solvent Model
论文作者
论文摘要
炼金术自由能计算广泛用于预测PKA，并在生物分子系统中使用结合自由能计算。这些计算是使用自由能扰动（FEP）或热力学整合（TI）进行的。已经做出了许多努力来提高此类计算的准确性和效率，尤其是通过增强构象采样。在本文中，我们使用一种技术，通过用于炼金术转化的集体变量的温度加速来增强构象采样，并将其应用于硫氧还蛋白中埋藏的ASP 26残基的PKA预测。我们讨论了PKA计算中增强采样的重要性。还介绍了溶剂模型在计算的PKA值中的效果。
Alchemical free energy calculations are widely used in predicting pKa, and binding free energy calculations in biomolecular systems. These calculations are carried out using either Free Energy Perturbation (FEP) or Thermodynamic Integration (TI). Numerous efforts have been made to improve the accuracy and efficiency of such calculations, especially by boosting conformational sampling. In this paper, we use a technique that enhances the conformational sampling by temperature acceleration of collective variables for alchemical transformations and applies it to the prediction of pKa of the buried Asp 26 residue in thioredoxin protein. We discuss the importance of enhanced sampling in the pKa calculations. The effect of the solvent models in the computed pKa values is also presented.
