Dataset on interactions of membrane active agents with lipid bilayers

Abstract

We address drug interactions with lipids using in silico simulations and in vitro experiments. The data article provides extended explanations on molecular mechanisms behind membrane action of membrane-active agents (MAAs): antimicrobial peptides and chemotherapy drugs. Complete interpretation of the data is found in the associated original article 'charge-based interactions of antimicrobial peptides and general drugs with lipid bilayers' [1]. Data on molecular dynamic simulations of the drug lipid complexes are provided. Additional data and information are provided here to explain the connectivity among various information and techniques used for understanding of the membrane action and/or binding of MAAs including aptamers. Brief explanation has been provided on the possibility of achieving a converted triangle from newly discovered quadrangle, sides of which explain four different phenomena: 'membrane effects', 'detection and quantification', 'origin of energetics' and 'structure stability' while drug effects occur. Triangle or quadrangle corners represent various techniques that were applied.

Keywords: Direct detection method; Drugs; Electrostatic interactions; Ion channel; Lipid membrane.

Fig. 1

(a) Root mean square deviation of the backbone of Alm in 10 ns simulation (red curve in Figure 1(a)) with initial conformation of Alm-PS shown in the left lower inset. The right inset shows the conformation of Alm-PS at the end of the simulation. (b) Molecular dynamics simulation data representing the change in the AMP–lipid center of mass distance d_AMP–lipid with time [2]. Five curves with different colors represent five independent initial AMP–lipid complexes. The inset shows the cartoon representations of initial structures of five AMP-lipid complexes with AMP following the color of the corresponding curve.

Fig. 2

Solvent-accessible (SA) areas for four complexes are plotted against the AMP–lipid center of mass separation distance d_AMP–lipid [2]. It shows SA areas are fluctuating around 2300 and 1800 square angstrom for gA-lipid and Ala-lipid, respectively, which are independent of d_AMP–lipid for the four complexes.

Fig. 3

In all four histogram plots (upper panel) of time versus d_AMP–lipid, the time durations when AMP/lipid stay together (height) within a distance (width) during 10 ns simulations are presented [2]. Lower panels show the histograms of non-bonded van der Waals (vdW) energy (E_vdW) and electrostatic (ES) interactions energy (E_ES). To avoid color conflict, E_vdW and E_ES are shown to occupy half-half widths, although each half represents the whole width of the corresponding histogram.

Fig. 4

A (virtual) universal triangle connecting various information on MAA-lipid interactions using various techniques. Other techniques may also fit in this triangle to produce similar information.