Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans

• Published in: Journal of chemical information and modeling Vol. 63; no. 7; pp. 2147 - 2157
• Main Authors: Marcisz, Mateusz, Samsonov, Sergey A.
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 10.04.2023
• Subjects: Computational Biochemistry; Fluid dynamics; Glycosaminoglycans; Glycosaminoglycans - chemistry; Heparin; Models, Molecular; Molecular Conformation; Molecular dynamics; Molecular Dynamics Simulation; Physical simulation; Polysaccharides; Solvents; Solvents - chemistry
• ISSN: 1549-9596; 1549-960X; 1549-960X
• DOI: 10.1021/acs.jcim.2c01472

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.