Aβ1-25-Derived Sphingolipid-Domain Tracer Peptide SBD Interacts with Membrane Ganglioside Clusters via a Coil-Helix-Coil Motif

Abstract

The Amyloid-β (Aβ)-derived, sphingolipid binding domain (SBD) peptide is a fluorescently tagged probe used to trace the diffusion behavior of sphingolipid-containing microdomains in cell membranes through binding to a constellation of glycosphingolipids, sphingomyelin, and cholesterol. However, the molecular details of the binding mechanism between SBD and plasma membrane domains remain unclear. Here, to investigate how the peptide recognizes the lipid surface at an atomically detailed level, SBD peptides in the environment of raft-like bilayers were examined in micro-seconds-long molecular dynamics simulations. We found that SBD adopted a coil-helix-coil structural motif, which binds to multiple GT1b gangliosides via salt bridges and CH–π interactions. Our simulation results demonstrate that the CH–π and electrostatic forces between SBD monomers and GT1b gangliosides clusters are the main driving forces in the binding process. The presence of the fluorescent dye and linker molecules do not change the binding mechanism of SBD probes with gangliosides, which involves the helix-turn-helix structural motif that was suggested to constitute a glycolipid binding domain common to some sphingolipid interacting proteins, including HIV gp120, prion, and Aβ.

Characterization of Lipid–Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

“…Cholesterol was also reported to affect the conformation of Aβ, , reducing Aβ-induced membrane disruption. , In addition, cholesterol can affect Aβ-membrane interactions through asymmetric distribution within the bilayer . Other simulations studying shorter versions of the Aβ peptide − also demonstrated drastic conformational change upon membrane binding and assessed lipid composition effects. − …”

Toxin-glycolipid interactions measured by imaging surface plasmon resonance on artificial membranes predicts diffusion behavior and lipid dependence of binding to cells

“…This linker construction was earlier shown to interfere minimally with binding of another ganglioside-interacting probe, the Sphingolipid Binding Domain of Aβ (SBD; (Hebbar et al, 2008; Lauterbach et al, 2012; Steinert et al, 2008; Wang et al, 2015)). The addition of the fluorophore allowed us to characterize the diffusion behaviour of the peptide via spectroscopic and fluorescence imaging, in parallel with the imaging-surface plasmon resonance (iSPR) binding studies described in the next section.…”

“…This linker construction was earlier shown to interfere minimally with binding of another ganglioside-interacting probe, the Sphingolipid Binding Domain of Aβ (SBD; (Hebbar et al, 2008;Lauterbach et al, 2012;Steinert et al, 2008;Wang et al, 2015)).…”

The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics Simulations

“…The fluorescent peptide bound to isolated raft fractions from human neuroblastomas and insect neuronal cells, and thus could constitute a useful raft probe. More recently, a simulation study of this peptide was carried out, in interaction with POPC/Chol/SSM bilayers (15:10:4 mole ratio), containing varying amounts (0–12%) of ganglioside GT1b [ 146 ]. Both unlabeled and different versions of the labeled peptide, with different linkers (reflective of those used in previously published experimental data) were included in the sequence for MD.…”