Midkine Interaction with Chondroitin Sulfate Model Synthetic Tetrasaccharides and Their Mimetics: The Role of Aromatic Interactions

Abstract

Midkine (MK) is a neurotrophic factor that participates in the embryonic central nervous system (CNS) development and neural stem cell regulation, interacting with sulfated glycosaminoglycans (GAGs). Chondroitin sulfate (CS) is the natural ligand in the CNS. In this work, we describe the interactions between a library of synthetic models of CS-types and mimics. We did a structural study of this library by NMR and MD (Molecular Dynamics), concluding that the basic shape is controlled by similar geometry of the glycosidic linkages. Their 3D structures are a helix with four residues per turn, almost linear. We have studied the tetrasaccharide-midkine complexes by ligand observed NMR techniques and concluded that the shape of the ligands does not change upon binding. The ligand orientation into the complex is very variable. It is placed inside the central cavity of MK formed by the two structured beta-sheets domains linked by an intrinsically disordered region (IDR). Docking analysis confirmed the participation of aromatics residues from MK completed with electrostatic interactions. Finally, we test the biological activity by increasing the MK expression using CS tetrasaccharides and their capacity in enhancing the growth stimulation effect of MK in NIH3T3 cells.

The Interaction between Chondroitin Sulfate and Dermatan Sulfate Tetrasaccharides and Pleiotrophin

“…In a previous work [12], we compared the NOE growing curves from the transfer NOESY sample with a similar model but without protein and showed the clear effect of the correlation time between both samples. As previously reported for MK [10], the ligands do not modify their 3D structures when they are complexed with PTN. See Supplementary Material and Figure 2.…”

“…In this work, we describe the interaction between these tetrasaccharides and PTN using Fluorescence Polarization and NMR ligand-observed methods. synthesis methods [9,10]. The first series is formed by CS type E, 1, type T, 2, and hybrid CS/DS, 3, with an iduronate residue at the non-reducing terminal [9,10].…”

“…synthesis methods [9,10]. The first series is formed by CS type E, 1, type T, 2, and hybrid CS/DS, 3, with an iduronate residue at the non-reducing terminal [9,10]. This series is followed by another with two benzyl moieties in position 3 of the Uronic acid ring, 4-6.…”

“…We have prepared six tetrasaccharides models of CS and hybrid sequences CS/DS (Chondroitin Sulfate/Desmatan Sulfate) carrying iduronate residues at the non-reducing end using chemical synthesis methods [ 9 , 10 ]. The first series is formed by CS type E, 1 , type T, 2 , and hybrid CS/DS, 3 , with an iduronate residue at the non-reducing terminal [ 9 , 10 ]. This series is followed by another with two benzyl moieties in position 3 of the Uronic acid ring, 4–6 .…”

In-Depth Molecular Dynamics Study of All Possible Chondroitin Sulfate Disaccharides Reveals Key Insight into Structural Heterogeneity and Dynamism

“…Understanding their structural and energetic preferences may offer better insight into designing oligomeric CS sequences that selectively bind proteins of interest. The literature contains several reports on the atomistic characterization of CS building blocks using X-ray crystallography [ 26 ], NMR [ 27 , 28 , 29 ], molecular modeling (MM) [ 30 ] and molecular dynamics (MD) [ 31 , 32 , 33 ]. Insights from the NMR and crystallographic studies have shown that the backbone orientations of the polymeric scaffold changes as sulfate groups are introduced at various positions.…”