J Phys Chem B. 2018 Aug 23;122(33):7997-8005. doi: 10.1021/acs.jpcb.8b05359. Epub 2018 Aug 14.
Increasing demand for hybrid materials that merge the synthetic and biological areas in drug industries requires in-depth knowledge of the individual components and their contributions to these complexes. Coarse-grained (CG) models developed for proteins and polymers exist, yet there is a lack of understanding of the cross interactions when these two groups of materials integrate to build a complex. In this work, we characterized the nonbonded interactions between poly(ethylene glycol) (PEG) and amino acids in a Martini CG model utilizing state-of-the-art quantum mechanics calculations of interaction energies. The parameter set proposed, was validated by assessing the polymer density in the vicinity of individual amino acids obtained from available all-atomistic molecular dynamic simulations of plasma proteins. Our results revealed the necessity of protein-polymer interaction parameterization at the CG level to avoid overestimation of polymer association when employing other PEG models within the Martini framework.
在药物行业中，对融合了合成和生物领域的混合材料的需求不断增加，这需要深入了解各个组件及其对这些复合物的贡献。已经存在针对蛋白质和聚合物的粗粒 (CG) 模型，但当这两组材料融合构建复合物时，对于它们之间的交叉相互作用缺乏了解。在这项工作中，我们利用最先进的量子力学计算相互作用能，对马蒂尼 CG 模型中聚乙二醇 (PEG) 和氨基酸之间的非键相互作用进行了表征。所提出的参数集通过评估从等离子体蛋白的全原子分子动力学模拟中获得的单个氨基酸附近聚合物密度来进行验证。我们的结果表明，在 CG 水平上对蛋白质-聚合物相互作用进行参数化是必要的，以避免在马蒂尼框架内使用其他 PEG 模型时高估聚合物的缔合。
