Molecular dynamics insights into glycosaminoglycan effects on the extracellular domains of syndecan 2 and 4 dimers

The four mammalian syndecans (1-4) are transmembrane proteoglycans, which all bear three heparan sulfate chains covalently attached to their core protein. They contribute to cell signaling, and play a role in numerous diseases. The syndecans dimerize via their transmembrane domains, and their cytoplasmic domains form a compact intertwined dimer. This computational study aims at building models of the dimers of the extracellular domain of syndecans 2 and 4, and to determine if and how the glycosaminoglycan (GAG) chains attached to their core proteins affect the dimer structural and dynamic properties. The GAGosylation was mimicked by adding three heparin hexadecasaccharide chains to each extracellular domain. The initial conformations of the dimers, and specifically the distances between the C-termini of the extracellular domains, were defined using our SAXS experimental data and literature data. The four generated models (i.e., dimers of the extracellular domains of syndecans 2 and 4 with or without GAG chains) were then subjected to multiple independent microsecond-scale molecular dynamics simulations in implicit solvent, and their trajectories were analyzed. The structural and dynamic descriptors calculated from the ensembles of the four models followed unimodal distributions. No well-defined conformational states were observed. GAGosylation increased the compactness of the dimer of extracellular domain of syndecan 2, but not of the dimer of syndecan 4. Our computational approach provides novel structural insights into syndecan 2 and 4 dimers and the structural role of GAGs on conformations of proteoglycan core proteins, which remains challenging to investigate experimentally, and even more challenging when attached to disordered core proteins such as those of syndecans.