论文标题
基于分子的准化学理论的流行隐式溶剂模型与全原子模拟结果的多肽的水合自由能
Hydration free energies of polypeptides from popular implicit solvent models versus all-atom simulation results based on molecular quasichemical theory
论文作者
论文摘要
大分子的水合自由能是了解其在构象和聚集状态的分布的核心特性。在全原子模拟中计算大分子的水合自由能一直是一个挑战,需要使用模型,其中在没有明确说明溶剂自由度的情况下捕获溶剂的效果。随着分子准化学理论(QCT)的发展,这种情况发生了变化,这种方法可以计算出全原子模拟中大分子溶质中大原子模拟中大分子的水合自由能。该理论还提供了一个严格且物理上透明的框架,以概念化和建模分子溶液中的相互作用,从而提供了一个方便的框架来研究隐式 - 溶剂模型中的假设。在这项研究中,我们使用分子QCT与EEF1,Absinth和GB/SA隐式溶剂模型的预测进行比较,用于涵盖一系列链长和构象的多聚甘氨酸和聚丙氨酸溶质。在这三种型号中,GB/SA最能捕捉自由能的广泛趋势。我们将群体添加的EEF1和Absinth模型的缺陷记录到其对溶质组之间水合合作的评价不足;从这个角度看,尽管在连续介电框架内,但GB/SA的表现更好归因于其对水合的集体特性的处理。我们强调了验证各个物理成分的重要性,这些物理成分输入了蛋白质溶液热力学的隐式溶剂模型。
The hydration free energy of a macromolecule is the central property of interest for understanding its distribution over conformations and its state of aggregation. Calculating the hydration free energy of a macromolecule in all-atom simulations has long remained a challenge, necessitating the use of models wherein the effect of the solvent is captured without explicit account of solvent degrees of freedom. This situation has changed with developments in the molecular quasi-chemical theory (QCT), an approach that enables calculation of the hydration free energy of macromolecules within all-atom simulations at the same resolution as is possible for small molecule solutes. The theory also provides a rigorous and physically transparent framework to conceptualize and model interactions in molecular solutions, and thus provides a convenient framework to investigate the assumptions in implicit-solvent models. In this study, we compare the results using molecular QCT versus predictions from EEF1, ABSINTH, and GB/SA implicit-solvent models for poly-glycine and poly-alanine solutes covering a range of chain lengths and conformations. Among the three models, GB/SA does best in capturing the broad trends in hydration free energy. We trace the deficiencies of the group-additive EEF1 and ABSINTH models to their under-appreciation of the cooperativity of hydration between solute groups; seen in this light, the better performance of GB/SA can be attributed to its treatment of the collective properties of hydration, albeit within a continuum dielectric framework. We highlight the importance of validating the individual physical components that enter implicit solvent models for protein solution thermodynamics.