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Fig. 3 | Journal of Biomedical Science

Fig. 3

From: Dissecting the conformation of glycans and their interactions with proteins

Fig. 3

Modeling of structures and molecular interactions for the complex between N-glycosylated SPARC and collagen. a The Fut8 target protein, SPARC, is a collagen-binding matricellular protein. Surface representation of the crystal structure of human SPARC includes the follistatin-like (FS) domain (cyan) and the C-terminal extracellular calcium-binding (EC) domain (yellow) bound to collagen peptide (red) [Protein Data Bank (PDB; http://www.rcsb.org), code 2 V53]. N-glycosylation at site N116 of SPARC is highlighted in blue, and collagen binding residues of SPARC are highlighted in green. Another structural model of SPARC protein, 1BMO, contains the peptide fragment AA 204 to 223, which was lacking in the model of PDB 2 V53. b The 1BMO model did not form a complex with collagen. Its AA 257 to 264 sequence displayed a unique loop conformation. When SPARC complexed with collagen in 2 V53, the AA 257 to 264 segment was folded to form a helix structure. c Modeller software was used to generate a new SPARC model, using 2 V53 and 1BMO as templates. The complex type N-glycan moiety was then attached to the side chain of N116 of SPARC using doGlycans software. The conformation of glycosylated SPARC protein was then optimized using molecular dynamics simulation software, e. g., Gromacs. Finally, Modeller software was used to model the molecular interactions between the glycosylated SPARC and collagen molecule

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