Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
Intercollegiate Faculty of Biotechnology of UG and MUG, ul. Abrahama 58, 80-307 Gdańsk, Poland.
J Chem Inf Model. 2023 Apr 10;63(7):2147-2157. doi: 10.1021/acs.jcim.2c01472. Epub 2023 Mar 29.
In computational studies of glycosaminoglycans (GAGs), a group of anionic, periodic linear polysaccharides, so far there has been very little discussion about the role of solvent models in the molecular dynamics simulations of these molecules. Predominantly, the TIP3P water model is commonly used as one of the most popular explicit water models in general. However, there are numerous alternative explicit and implicit water models that are neglected in the computational research of GAGs. Since solvent-mediated interactions are particularly important for GAG dynamic and structural properties, it would be of great interest for the GAG community to establish the solvent model that is suited the best in terms of the quality of theoretically obtained GAG parameters and, at the same time, would be reasonably demanding in terms of computational resources required. In this study, heparin (HP) was simulated using five implicit and six explicit solvent models with the aim to find out how different solvent models influence HP's molecular descriptors in the molecular dynamics simulations. Here, we initiate the search for the most appropriate solvent representation for GAG systems and we hope to encourage other groups to contribute to this highly relevant subject.
在糖胺聚糖（GAGs）的计算研究中，GAGs 是一组带负电荷的、周期性的线性多糖，到目前为止，关于溶剂模型在这些分子的分子动力学模拟中的作用，讨论得非常少。主要是，TIP3P 水模型通常被用作最流行的通用显式水模型之一。然而，在 GAG 的计算研究中，有许多其他的显式和隐式水模型被忽略了。由于溶剂介导的相互作用对 GAG 的动态和结构性质特别重要，对于 GAG 社区来说，确定最适合的溶剂模型将是非常有趣的，这方面的标准是从理论上获得的 GAG 参数的质量，同时在所需的计算资源方面也有合理的要求。在这项研究中，使用了五种隐式和六种显式溶剂模型来模拟肝素（HP），目的是找出不同的溶剂模型如何在分子动力学模拟中影响 HP 的分子描述符。在这里，我们开始寻找最适合 GAG 系统的溶剂表示法，并希望鼓励其他小组为这一高度相关的课题做出贡献。
