Chapter 11:Strategies for Building Protein–Glycosaminoglycan Interaction Networks Combining SPRi, SPR, and BLI

Sulfated glycosaminoglycans (GAGs) are complex, linear polysaccharides that are covalently linked to proteins to form proteoglycans. They are located in the extracellular matrix and at the cell surface and interact with many proteins. More than 400 interactions have been reported for heparin/heparan sulfate and these interactions are involved in numerous biological processes such as development, angiogenesis, tumor growth, host–pathogen interactions and inflammation, extracellular matrix (ECM) assembly, cell–matrix interactions and signaling. The building of GAG–protein interaction networks is required to determine how these individual interactions influence each other in vivo, are coordinated in biological processes, and are altered in diseases. This chapter reports the roadmap designed to build and analyze these interaction networks. New interactions were identified by surface plasmon resonance imaging (SPRi) using a Biacore Flexchip system and were combined with data manually curated from the literature to build a GAG–protein network. The values of equilibrium dissociation constants and of association and dissociation rates, calculated by SPR and biolayer interferometry (BLI), were integrated into the network. The network was then analyzed in silico to determine the biological processes and pathways associated with GAG partners.