Extended disorder at the cell surface: The conformational landscape of the ectodomains of syndecans

Abstract

Highlights The syndecan ectodomains are flexible random-coil intrinsically disordered proteins. Their extended conformations have the same size as their cell surface partners. Their binding-motifs to cells and receptors are not accessible in all conformations. Only some of conformations of the ectodomains may be biologically active. The syndecan-4 ectodomain forms a disulfide-bonded dimer with extended conformations.

Interplay of heparan sulfate chains with the core proteins of syndecans 2 and 4

“…The radius of gyration ( Rgyr ) was calculated to evaluate the effect of the HS chains on the compactness of the extracellular domains of syndecans. It ranged from ~20 to 45 Å for the non‐GAGosylated and GAGosylated forms of the extracellular domain of syndecan‐2 (Supporting Information: Figure ), compared to an average value of 42.90 Å determined by SAXS 5 . The radius of gyration of the extracellular domain of syndecan‐4 ranged from 25 to 55 Å for its non‐GAGosylated form, compared to an average value of 41.53 Å determined by SAXS, 5 and from 20 to 45 Å for its GAGosylated form (Supporting Information: Figure ).…”

“…to 55 Å for its non-GAGosylated form, compared to an average value of 41.53 Å determined by SAXS, 5 and from 20 to 45 Å for its GAGosylated form (Supporting Information: Figure S4). These large variations were expected given that the syndecan extracellular domains are mostly disordered, unfolded, proteins.…”

“…Three heparan sulfate (HS) chains are covalently attached to the extracellular domain of the four mammalian syndecans, and chondroitin sulfate (CS) chains are also attached to syndecans 1 and 3 1 . We have recently shown using circular dichroism (CD), small‐angle X‐ray scattering (SAXS), and native mass spectrometry that the extracellular domains of the four human syndecans are intrinsically disordered, flexible and adopt a wide range of conformations including minor globular conformations and extended conformations 5 . These experiments were carried out with the protein moiety of the syndecans extracellular domains without their glycosaminoglycan (GAG) chains.…”

“…We have first generated coarse-grained models of the extracellular domains of syndecans 2 and 4 based on the experimental SAXS data we collected. 5 The best models were then used for MD simulations in absence or presence of three HS chains to investigate their influence on the conformational diversity, flexibility, compactness and secondary structure of the core proteins of syndecans 2 and 4. Since the valency of HS chains is important for cell adhesion mediated by syndecan-4, 8 we have also explored the effect of the number and the location of HS chains by generating three singlechain and three two-chain variants for each syndecan (one HS chain and two HS chains attached to different serine residues on the core proteins respectively), and performed MD simulations for all these variants.…”

Structural and dynamical insights into SilE silver binding from combined analytical probes

“…However, the observed ATDs can be understood as an indirect mapping of the conformational space sampled by the complexes in solution. 24,25 Following this line, each gas phase conformer corresponds to the end point of a distinct portion of the solution-phase conformational space, after conformational relaxation. The observed changes can then be attributed to a modification in the solution-phase conformational space of SilE upon silver binding.…”