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

Swapnil Wagle,Reinhard Lipowsky,Vasil N Georgiev,Tom Robinson,Andrea Grafmüller,Rumiana Dimova

doi:10.1038/s41598-019-43418-w

Swapnil Wagle, Reinhard Lipowsky + Show 4 more

Open Access

https://doi.org/10.1038/s41598-019-43418-w

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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 kBT 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.

Highlights

A number of studies have investigated different variations of this system, studying the effect of peptide length[19], orientation[20], linker and anchor types[21,22,23] and attachment point[24] on the peptides’ helicity, coiled-coil forming ability and efficiency at generating vesicle fusion
Peptide E adopted a random coil structure. These results are consistent with CD experiments[17,45], which indicate that peptide K remains at least partially folded, while no indication for alpha helical structure is found for peptide E
The potential of mean force (PMF) calculated for these simulations (Fig. 2C) shows a stable adsorbed state of peptide K at the head-tail interface, with a binding free energy of about −12 kBT

Summary

Introduction

A number of studies have investigated different variations of this system, studying the effect of peptide length[19], orientation[20], linker and anchor types[21,22,23] and attachment point[24] on the peptides’ helicity, coiled-coil forming ability and efficiency at generating vesicle fusion. A more recent study has shown that the use of polar water with the MARTINI force field strongly reduces the tendency of the peptides to adsorb[38] In those simulations, only peptide K is found to embed in the membrane. All atom molecular dynamics (MD) simulations have been used to assess the membrane interactions of the adsorbed peptide[25,38] and to determine the affinity of the fusion peptides to the bilayer with umbrella sampling[39]. These simulations suggest that both peptides adsorb strongly at the head-group water interface, but do not embed in the bilayer. As a proof of principle, we experimentally explore the adsorption of the peptides to giant unilamellar vesicles[42] as a model system, using the same membrane composition as in the simulations

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