Interaction of SNARE Mimetic Peptides with Lipid bilayers: Effects of Secondary Structure, Bilayer Composition and Lipid Anchoring

Abstract

The coiled-coil forming peptides ‘ K ’ enriched in lysine and ‘ E ’ enriched in glutamic acid have been used as a minimal SNARE mimetic system for membrane fusion. Here we describe atomistic molecular dynamics simulations to characterize the interactions of these peptides with lipid bilayers for two different compositions. For neutral phosphatidylcholine (PC)/phosphatidylethanolamine (PE) bilayers the peptides experience a strong repulsive barrier against adsorption, also observed in potential of mean force (PMF) profiles calculated with umbrella sampling. For peptide K , a minimum of −12 k B T in the PMF provides an upper bound for the binding free energy whereas no stable membrane bound state could be observed for peptide E . In contrast, the electrostatic interactions with negatively charged phosphatidylglycerol (PG) lipids lead to fast adsorption of both peptides at the head-water interface. Experimental data using fluorescently labeled peptides confirm the stronger binding to PG containing bilayers. Lipid anchors have little effect on the peptide-bilayer interactions or peptide structure, when the peptide also binds to the bilayer in the absence of a lipid anchor. For peptide E , which does not bind to the PC bilayer without a lipid anchor, the presence of such an anchor strengthens the electrostatic interactions between the charged side chains and the zwitterionic head-groups and leads to a stabilization of the peptide’s helical fold by the membrane.

Shifting Polar Residues Across Primary Sequence Frames of Transmembrane Domains Calibrates Membrane Permeation Thermodynamics

“…The presence of such hysteresis was also observed for several wellreported pore-forming RCs 34 and even for other peptides with the same choice of RC (i.e., DIST-Z) as used in this investigation. 50,51 Similarly, in the present report, the trend obtained from the backward PMFs is in reasonable agreement with the trends from the forward PMFs, yet the limitations of this report regarding the suboptimal choice of RC cannot be ruled out. However, the concern of insufficient sampling around the transition states has been carefully noted and taken care of by inclusion of a second RC that provided a decent account of the relevant energy landscapes.…”

“…It is worth mentioning that it is a fairly common concern for the suboptimal RCs; though the end-state populations can be efficiently distinguished along these RCs, the relevant transition states are often inadequately captured at an affordable computational cost due to the involvement of a slower degrees of freedom orthogonal to the chosen RC. The presence of such hysteresis was also observed for several well-reported pore-forming RCs and even for other peptides with the same choice of RC (i.e., DIST-Z) as used in this investigation. , Similarly, in the present report, the trend obtained from the backward PMFs is in reasonable agreement with the trends from the forward PMFs, yet the limitations of this report regarding the suboptimal choice of RC cannot be ruled out. However, the concern of insufficient sampling around the transition states has been carefully noted and taken care of by inclusion of a second RC that provided a decent account of the relevant energy landscapes.…”

Phospholipases in neuronal function: A role in learning and memory?

“…The pre‐synaptic plasma membrane is also characterized by ‘islands’ of high and low fluidity (i.e. lipid rafts (Sonnino et al, ; Sonnino and Prinetti, )) and lipid membrane anchors (Wagle et al, ), likely reflecting lipid involvement in the nanoscale protein organization required for neuroexocytosis (Figure b). In agreement, a recent study demonstrated that the size of the fatty acyl side chain of specific phosphatidylserine molecules controls the protein cluster organization of the outer hemi‐membrane (Raghupathy et al, ).…”

Munc13 binds and recruits SNAP25 to chaperone SNARE complex assembly

“…We had anticipated that it would be necessary to use palmitoylated SNAP25 in this experiment, but instead observed that even nonpalmitoylated SNAP25, added at low (150 n m ) concentrations in solution, bound to the bilayer. This is likely due to the amphipathic nature of two SNARE motifs of SNAP25 [7] as it is well established that amphipathic peptides associate strongly with phospholipid surfaces as their hydrophobic side chains could insert into the lipid bilayers [58,59]. On its own, freely diffusing Alexa Fluor 555‐labeled SNAP25 molecules thus bound were monomeric and uniformly distributed on the lipid bilayer surface (Fig.…”