Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations

Abstract

Membrane topology changes such as poration, stalk formation, and hemi-fusion rupture are essential to cellular function, but their molecular details, energetics, and kinetics are still not fully understood. Here we present a unified energetic and mechanistic picture of metastable pore defects in tensionless lipid membranes. We used an exhaustive committor analysis to test and select optimal reaction coordinates and also to determine the nucleation mechanism. These reaction coordinates were used to calculate free energy landscapes that capture the full process and end states. The identified barriers agree with the committor analysis. To enable sufficient sampling of the complete transition path for our atomistic simulations, we developed a novel "gizmo" potential biasing scheme. The simulations suggest that the essential step in the nucleation is the initial merger of lipid headgroups at the nascent pore center. To facilitate this event, an indentation pathway is energetically preferred to a hydrophobic defect. Continuous water columns that span the indentation were determined to be on-path transients that precede the nucleation barrier. This study gives a quantitative description of the nucleation mechanism and energetics of small metastable pores and illustrates a systematic approach to uncover the mechanisms of diverse cellular membrane remodeling processes. STATEMENT OF SIGNIFICANCEThe primary steps and nucleation of lipid membrane pore formation are key to membrane fusion, viral infection, and vesicular cellular transport. Despite decades experimental and theoretical studies, the underlying mechanisms are still not fully understood at the atomic level. Using a committor-based reaction coordinate and atomistic simulations, we report new structural and energetics insight into the full poration process. We find that the pore nucleates via an elastic indentation rather than by forming a hydrophobic defect. Subsequently, water pierces the thinned slab as a prerequisite for the following axial merger of the first lipid headgroups from opposite monolayers, which precedes and best characterizes the transition state. We also identify a metastable prepore basin, thereby explaining previous indirect experimental evidence.

Joint Reaction Coordinate for Computing the Free-Energy Landscape of Pore Nucleation and Pore Expansion in Lipid Membranes

“…Because pore nucleation and pore expansion occur along different directions in conformational space, it has been difficult to define a unified reaction coordinate (RC) for the overall process. Namely, during nucleation, the membrane is locally thinning, followed by the penetration of water and head groups into the hydrophobic core of the membrane. − Hence, nucleation is primarily characterized by a transition of polar atoms perpendicular to the membrane plane. In contrast, expansion of an established pore involves the increase of the pore radius, that is, a transition of the (already established) pore rim parallel to the membrane plane.…”

A joint reaction coordinate for computing the free energy landscape of pore nucleation and pore expansion in lipid membranes

“…Namely, during nucleation, the membrane is locally thinning, followed by the penetration of water and head groups into the hydrophobic core of the membrane. [12][13][14] Hence, nucleation is primarily characterized by a transition of polar atoms perpendicular to the membrane plane. In contrast, expansion of an established pore involves the increase of the pore radius, that is a transition of the (already established) pore rim parallel to the membrane plane.…”

Cardiolipin prevents pore formation in phosphatidylglycerol bacterial membrane models

“…The steps during pore formation mediated by the insertion and aggregation of peptides were described by unbiased molecular dynamics (MD) simulations [27][28][29]. The energetic cost of formation of pores has also been quantified in allatom MD simulations [30,31], for distinct lipid types [32] and also in the presence of solutes [33][34][35], as well as in coarse-grain simulations [36]. These simulations revealed the existence of metastable states during pore formation, which were tightly linked to the hydrophilic head-hydrophobic tail volume ratio [32].…”