Benchmarking Water Models in Molecular Dynamics of Protein-Glycosaminoglycan Complexes.

ABSTRACT: Glycosaminoglycans (GAGs) made of repeating disaccharide units intricately engage with proteins, playing a crucial role in the spatial organization of the extracellular matrix (ECM) and the transduction of biological signals in cells to modulate a number of biochemical processes. Exploring protein-GAG interactions reveals several challenges for their analysis, namely, the highly charged and periodic nature of GAGs, their multipose binding, and the abundance of the interfacial water molecules in the protein-GAG complexes. Most of the studies on protein-GAG interactions are conducted using the TIP3P water model, and there are no data on the effect of various water models on the results obtained in molecular dynamics (MD) simulations of protein-GAG complexes. Hence, it is essential to perform

SUBMITTER: Anila S 

PROVIDER: S-EPMC10934818 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature