Cell-surface carbohydrates play important roles in numerous biological processes through their interactions with various proteinbinding partners. These interactions are made possible by the vast structural diversity of carbohydrates and the diverse array of carbohydrate presentations on the cell surface. Among the most complex and important carbohydrates are glycosaminoglycans (GAGs), which display varied stereochemistry, chain lengths, and patterns of sulfation. GAG-protein interactions participate in neuronal development, angiogenesis, spinal cord injury, viral invasion, and immune response. Unfortunately, little structural information is available for these complexes; indeed, for the highly sulfated chondroitin sulfate motifs, CS-E and CS-D, there are no structural data. We describe here the development and validation of the GAG-Dock computational method to predict accurately the binding poses of protein-bound GAGs. We validate that GAG-Dock reproduces accurately (<1-Ă
rmsd) the crystal structure poses for four known heparin-protein structures. Further, we predict the pose of heparin and chondroitin sulfate derivatives bound to the axon guidance proteins, protein tyrosine phosphatase Ï (RPTPÏ), and Nogo receptors 1-3 (NgR1-3). Such predictions should be useful in understanding and interpreting the role of GAGs in neural development and axonal regeneration after CNS injury.docking | chondroitin sulfate | heparin | axonal growth | RPTPÏ G lycans and proteins are important partners in the regulation of fundamental biological processes such as the immune response, signal transduction, development, and pathogen invasion (1). An understanding of the wide array of glycan-protein interactions is critical to mapping the biological functions of glycans and will pave the way for the development of new therapies that target glycan-protein interactions that contribute to diseases such as cancer and autoimmune and neurodegenerative disorders (2). Glycosaminoglycans (GAGs) are a prototypical example: they are known to interact with more than 300 secreted or membranebound proteins and thereby regulate a broad range of phenomena, including cell proliferation, migration, differentiation, morphogenesis, blood coagulation, angiogenesis, axon guidance, and response to CNS injury (3, 4). The GAG family of polysaccharides, which includes heparan sulfate (HS) and chondroitin sulfate (CS), is composed of alternating uronic acid and hexosamine units. The polysaccharides can vary in length, net charge, and the pattern and degree of sulfation (Fig. 1). Recent studies have shown that the biological activity of GAGs is often dependent on their sulfation sequence, with specific, highly sulfated sequences directing interactions with growth factors and other signaling proteins (5-8). Despite the importance of GAG-protein interactions, there is remarkably little structural information about these complexes. This is largely a result of the inherent structural complexity and heterogeneity of GAGs, which makes it difficult to obtain sufficient q...