The pleckstrin homology domain (PH) of general receptor for phosphoionositides 1 (GRP1) binds to the phosphatidylinositol (3,4,5)-triphosphate (PIP3), which acts as a second messenger. The specific interaction of PIP3 lipids with the GRP1 protein is essential for key processes such as cellular growth, DNA synthesis, and apoptosis. This study reports all-atom molecular dynamics simulations employing the HMMM (Highly Mobile Membrane Mimetic) model of GRP1 PH domain on lipid bilayers containing PC, PS, and PIP3 lipids in varying compositions. No binding of the PH domain to pure PC membranes was observed but the incorporation of anionic lipids (PS and PIP3) resulted in the formation of membrane-bound configurations, suggesting an electrostatically driven association. Distinct PIP3 binding modes, each corresponding to a different distribution of basic residues on GRP1 PH domain, were observed. These binding modes involve PIP3 interactions either at “canonical” and/or “alternate” site. Our data suggest that the binding of the PH domain to PIP3 lipids tilts the lipid headgroup by ~ 17 ± 5 degree relative to its optimal orientation and pulls the lipid by 2.4 ± 1.3 Å out of the membrane. Furthermore, using enhanced sampling techniques we have characterized the dissociation pathway of GRP1 PH domain from the anionic membranes. The dissociation free energy profiles highlight the cooperative role of surrounding PS lipids in stabilizing “canonical” mode over “alternate” binding mode. Taken together these simulations demonstrate that multiple anionic lipid binding sites on GRP1 PH domain contributes to the high-affinity membrane interactions, enhancing our understanding on membrane recognition by GRP1 PH domain.

Microscopic characterization of membrane binding and lipid-protein interactions in pH domain using advanced simulations techniques

2019 Spring National Meeting

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