Multiscale modeling of glycosaminoglycan structure and dynamics: current methods and challenges. (June 2018)

• Record Type: Journal Article
• Authors: Almond, Andrew
• Is Part Of: Current opinion in structural biology. Volume 50(2018)
• Page Start: 58
• Page End: 64
• Publication Date: 2018-06
• Subjects: Molecular biology -- Periodicals; 570
• DOI: 10.1016/j.sbi.2017.11.008
• Languages: English
• ISSNs: 0959-440X

Abstract

Graphical abstract: Highlights: Methods established for modeling oligosaccharides, polysaccharides and protein interactions. Molecular mechanics force-fields now extended to most glycosaminoglycans. Realistic dynamic predictions from enhanced sampling and microsecond simulations. Docking protocols for predicting interactions, binding sites and poses. Coarse graining an emerging route to macroscopic experimental interpretation. Abstract : Glycosaminoglycans are long unbranched and complex polysaccharides that are an essential component of mammalian extracellular matrices. Characterization of their molecular structure, dynamics and interactions are essential to understand important biological phenomena in health and disease, and will lead to novel therapeutics and medical devices. However, this has proven to be a challenge experimentally and theoretical techniques are needed to develop new hypotheses, and interpret experiments. This review aims to examine the current theoretical (rather than experimental) methods used by researchers to investigate glycosaminoglycan structure, dynamics and interactions, from the monosaccharide to the macromolecular scale. It will consider techniques such as quantum mechanics, molecular mechanics, molecular dynamics, coarse graining and docking.