Characterization of 3D Voronoi tessellation nearest neighbor lipid shells provides atomistic lipid disruption profile of protein containing lipid membranes

Abstract

Quantifying protein-induced lipid disruptions at the atomistic level is a challenging problem in membrane biophysics. Here we propose a novel 3D Voronoi tessellation nearest-atom-neighbor shell method to classify and characterize lipid domains into discrete concentric lipid shells surrounding membrane proteins in structurally heterogeneous lipid membranes. This method needs only the coordinates of the system and is independent of force fields and simulation conditions. As a proof-of-principle, we use this multiple lipid shell method to analyze the lipid disruption profiles of three simulated membrane systems: phosphatidylcholine, phosphatidylcholine/cholesterol, and beta-amyloid/phosphatidylcholine/cholesterol. We observed different atomic volume disruption mechanisms due to cholesterol and beta-amyloid Additionally, several lipid fractional groups and lipid-interfacial water did not converge to their control values with increasing distance or shell order from the protein. This volume divergent behavior was confirmed by bilayer thickness and chain orientational order calculations. Our method can also be used to analyze high-resolution structural experimental data.

Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface

“…This region is defined as the lipid insertion domain. However, in our recent studies on monomeric beta-amyloid peptide in various lipid bilayers, the lipid insertion domain was alpha-helix rich (Qiu et al, 2014; Cheng et al, 2015c). …”

Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models

“…Conventionally, it is calculated from the lateral dimensions of the simulation box divided by the number of lipids in a membrane leaflet (Table ), but in this case, the APL distribution remains unknown. Besides the conventional APL calculation, the average APL can also be obtained via a Voronoi tessellation (VT)-based technique for simple and multicomponent lipid bilayers , as well as complex protein–membrane , systems. The great advantage of VT technique is that it provides not only APL distribution beyond the average but also local structural information of the bilayer surface .…”

“…Besides the conventional APL calculation, the average APL can also be obtained via a Voronoi tessellation (VT)-based technique for simple and multicomponent lipid bilayers , as well as complex protein–membrane , systems. The great advantage of VT technique is that it provides not only APL distribution beyond the average but also local structural information of the bilayer surface . For instance, local disturbances caused by the direct permeation of small molecules can be identified by VT-based APL distribution. ,, To find such local disturbances, the NpT trajectories had been analyzed by a VT-based in-house Python script (powered by Python 2.7 and MDAnalysis 0.18.1), in which the phosphorous atom was projected to the macroscopic XY surface of the membrane, while the periodic boundary conditions were also taken into account.…”