Binding of Ca²⁺-Independent C2 Domains to Lipid Membranes: a Multi-Scale Molecular Dynamics Study

Abstract

C2 domains facilitate protein-lipid interaction in cellular recognition and signalling processes. They possess a β-sandwich structure, with either type I or type II topology. C2 domains can interact with anionic lipid bilayers in either a Ca2+-dependent or a Ca2+-independent manner. The mechanism of recognition of anionic lipids by Ca2+-independent C2 domains is incompletely understood. We have used molecular dynamics (MD) simulations to explore the membrane interactions of six Ca2+-independent C2 domains, from KIBRA, PI3KC2α, RIM2, PTEN, SHIP2, and Smurf2. In coarse grained MD simulations these C2 domains bound to lipid bilayers, forming transient interactions with zwitterionic (phosphatidylcholine, PC) bilayers compared to long lived interactions with anionic bilayers also containing either phosphatidylserine (PS) or PS and phosphatidylinositol bisphosphate (PIP2). Type I C2 domains bound non-canonically via the front, back or side of the β sandwich, whereas type II C2 domains bound canonically, via the top loops (as is typically the case for Ca2+-dependent C2 domains). C2 domains interacted strongly (up to 120 kJ/mol) with membranes containing PIP2 causing the bound anionic lipids to clustered around the protein. The C2 domains bound less strongly to anionic membranes without PIP2 (<50 kJ/mol), and most weakly to neutral membranes (<33 kJ/mol). Productive binding modes were identified and further analysed in atomistic simulations. For PTEN and SHIP2, CG simulations were also performed of the intact enzymes (i.e. phosphatase domain plus C2 domain) with PIP2-contating bilayers and the roles of the two domains in membrane localization were compared. From a methodological perspective, these studies establish a multiscale simulation protocol for studying membrane binding/recognition proteins, capable of revealing binding modes alongside details of lipid binding affinity and specificity.

Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations

“…This is in line with previous studies of other PIP-binding domains, e.g. PH [ 23 ] and C2 [ 24 ], which interact with multiple PIPs and other anionic lipids.…”

Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations

“…This is in line with previous studies of other PIP-binding domains, e.g. PH [19] and C2 [20], which interact with multiple PIPs and other anionic lipids.…”

Specific interactions of peripheral membrane proteins with lipids: what can molecular simulations show us?

“…Alternative forms of interaction exist, such as insertion of hydrophobic loops (10)(11)(12)(13)(14)(15)(16) or hydrophobic helices (17) into the membrane, cation-π interactions between aromatic residues and choline headgroups (18,19), or covalent attachment to a lipid whose hydrophobic tail is inserted into the lipid bilayer (20) (Figure 2). (21). (B) Ion-promoted electrostatic binding.…”

“…The reported variation between repeats can be significant, reflecting the complicated energy landscape for a PMP with several membrane interaction sites binding a membrane with different lipid constituents, as well as the likely non-ergodic nature of single MD trajectories. Through these repeats it is often possible to see multiple minima reflecting different binding sites on the same PMP (21,98,100). Some of these may reflect genuine metastable states which act as important intermediates before the final binding pose.…”