Further analyses of APRIL/APRIL-receptor/glycosaminoglycan interactions by biochemical assays linked to computational studies

Abstract

A proliferation-inducing ligand (APRIL) is a member of the tumor necrosis factor superfamily. APRIL is quite unique in this superfamily for at least for two reasons: i) it binds to glycosaminoglycans (GAGs) via its positively charged N-terminus; ii) one of its signaling receptor, the transmembrane activator CAML interactor (TACI) was also reported to bind GAGs. Here, as provided by biochemical evidences with the use of an APRIL deletion mutant linked to computational studies, APRIL-GAG interaction involved other regions than the APRIL N-terminus. Preferential interaction of APRIL with heparin followed by chondroitin sulfate E were confirmed by in silico analysis. Both computational and experimental approaches did not reveal heparan sulfate binding to TACI. Together, computational results corroborated experiments contributing with atomistic details to the knowledge on this biologically relevant trimolecular system. Additionally, a high-throughput rigorous analysis of the free energy calculations data was performed to critically evaluate the applied computational methodologies.

The potential role of glycosaminoglycans in serum amyloid A fibril formation by in silico approaches

“…Five representative structures, which was found to be an appropriate number to avoid undersampling of docked solutions [39] , were chosen for each cluster of the docked structures obtained by molecular docking, and they were used as starting structures for molecular dynamics (MD) simulations. Additionally, simulations of the unbound SAA dimer and monomer were performed to elucidate a potential effect of GAG binding on the protein unfolding process.…”

“…All MD simulations were performed in AMBER16 [33] with ff99SBonlysc parameters for proteins and GLYCAM06 [35] parameters for GAGs, respectively. The total length of each MD simulation was 25 ns, which is appropriate for this type of system according to our previous analysis [39] . For the SAA monomer alone and SAA monomer complexed with HP dp2, dp4, dp6 and dp8 complexes MD simulations have been further extended to 100 ns for the DSSP analysis.…”

Advanced Molecular Dynamics Approaches to Model a Tertiary Complex APRIL/TACI with Long Glycosaminoglycans

“…Depending on their arrangement and sulfation pattern, those units may display 408 [ 4 ] variants, of which 202 are found in mammals [ 5 , 6 ]. Although GAG’s certain binding specificity has been observed in several biologically relevant systems [ 7 , 8 , 9 ], protein–GAG interactions are often predominantly electrostatics-driven, and their binding energies correlate with the GAG net charge [ 10 , 11 , 12 , 13 ]. Despite the fact that computational studies of GAGs persist as a general challenge due to the required conformational sampling and their periodicity, there are numerous successful studies on proteins complexes with shorter GAG oligosaccharides (of length up to octasaccharides) [ 1 , 14 , 15 , 16 , 17 , 18 ].…”

“…In this study, a 24-mer and a 48-mer of heparin (HP) were docked to two complexes of a proliferation-inducing ligand (APRIL) protein and its receptors—the transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI) and the B cell maturation antigen (BCMA). APRIL is a member of the TNF superfamily [ 25 ] that was shown to bind GAGs (chondroitin sulfate and heparan sulfate) [ 13 , 26 , 27 , 28 ]. Such binding is thought to mediate APRIL’s oligomerization and, therefore, enable its role in cell signaling [ 29 ].…”

“…Such binding is thought to mediate APRIL’s oligomerization and, therefore, enable its role in cell signaling [ 29 ]. The GAG binding region on APRIL’s surface is located near the N-terminus of the protein alongside a stretch of positively charged lysine residues [ 13 ]. Additionally, it was reported that the C-terminus spatially close to the N-terminus, together with several arginine residues on the side of the protein, also contribute to GAG binding [ 13 ].…”