Molecular Dynamics Simulations Reveal Key Roles of the Interleukin-6 Alpha Receptor in the Assembly of the Human Interleukin-6 Receptor Complex

Abstract

Human interleukin-6 (hIL-6) is a pleiotropic cytokine with three distinct receptor epitopes, termed sites I, II, and III, which function to assemble a signaling complex. hIL-6 signals via a glycoprotein 130 (gp130) homodimer after initially forming a heterodimer with the nonsignaling α-receptor (IL-6Rα). The molecular description of the assembly of the hIL-6 signaling complex remains elusive because available structures provide descriptions of hIL-6 in its free and fully bound receptor forms, but not for intermediate steps that are crucial in the stepwise assembly of the signaling complex. In this report, molecular dynamics simulations provide atomic details describing the functional role of the initial hIL-6/IL-6Rα complex in facilitating subsequent interactions with gp130, which have not been previously shown. IL-6Rα binding to hIL-6 rigidifies the flexible N-terminus of the hIL-6 AB-loop through interactions with the D2 domain of IL-6Rα. This rigidification combined with repositioning of residues involved in gp130 receptor recognition promotes gp130 binding at site III. Binding of gp130 receptors at sites II and III is coupled with the release of the hIL-6 N-terminal AB-loop interaction and a pivoting of IL-6Rα around the hIL-6 helix bundle to the state of the hIL-6/IL-6Rα/gp130 complex.

Mutations Alter RNA-Mediated Conversion of Human Prions

“…Protein-docking studies by Schillinger et al suggest that the increased flexibility enhances the rate of assembly for the human interleukin-6 receptor complex. 26 Conversely, Kouza et al saw a decline in the rate of aggregation of amyloidogenic monomers with increased flexibility of the peptide. 27 It is likely specific to our system that the increased rigidity of this key reason is connected with enhanced unfolding and (presumed) subsequent aggregation.…”

Mechanistic and Structural Insights on the IL-15 System through Molecular Dynamics Simulations

“…In addition to structural and in vitro studies, molecular dynamics (MD) simulations are of prime interest to investigate at the atomic level the time-dependent behavior of the interleukin family members, in particular to get deeper insights within their structure and function relationships. In a recent study, MD simulations pointed out the key roles of the IL-6Rα chain in the assembly of the human IL-6 receptor complex [17], whereas a previous work, combining NMR measurements and MD calculations, had pointed out significant heterogeneity in terms of backbone fluctuations according to the IL-6 receptor epitopes [18]. Due to their structural similarity, IL-2 and IL-15 have often been simultaneously investigated combining (i) experiments to probe their structural (through X-ray crystallography) and/or affinity (with Surface Plasmon Resonance studies) features, and, (ii) molecular modeling, to reveal the major role of specific IL-2/IL-15 regions in the stabilization of particular receptor bound conformations [10,11].…”

Molecular dynamics analysis of the binding of human interleukin‐6 with interleukin‐6 α‐receptor

“…For this purpose, we computed intraprotein contact maps for hIL‐6 in the apo state and the hIL‐6/IL‐6Rα complex. If the distance between nonhydrogen atoms of any pairs of residues is <5 Å, then it is defined as a contact 28 …”

“…Glu56 did not make a salt bridge in either the apo state or the complex simulations. However, this residue has been observed to form a salt bridge with gp130‐D1 signaling complex resulting in stabilization of the bound state of the final complex 28 …”

“…Computational approaches can be very helpful here to provide a deeper understanding of protein‐receptor interactions governing the biophysics of molecular recognition. In a previous study, the structures for hIL‐6, viral IL‐6 (vIL‐6) and LIF were compared with a view to understanding how vIL‐6 and LIF can directly bind to gp130 without engaging with the α‐receptor 28 . This study revealed that the binding of hIL‐6 to IL‐6Rα rigidifies the flexible N‐terminus of the AB loop which promotes binding to gp130 while vIL‐6 and LIF are less flexible than apo hIL‐6 and are able to directly recruit gp130.…”