Computer modelling studies of the bilayer/water interface

Abstract

This review summarises high resolution studies on the interface of lamellar lipid bilayers composed of the most typical lipid molecules which constitute the lipid matrix of biomembranes. The presented results were obtained predominantly by computer modelling methods. Whenever possible, the results were compared with experimental results obtained for similar systems. The first and main section of the review is concerned with the bilayer-water interface and is divided into four subsections. The first describes the simplest case, where the interface consists only of lipid head groups and water molecules and focuses on interactions between the lipid heads and water molecules; the second describes the interface containing also mono- and divalent ions and concentrates on lipid-ion interactions; the third describes direct inter-lipid interactions. These three subsections are followed by a discussion on the network of direct and indirect inter-lipid interactions at the bilayer interface. The second section summarises recent computer simulation studies on the interactions of antibacterial membrane active compounds with various models of the bacterial outer membrane. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Is the tilt of the lipid head group correlated with the number of intermolecular interactions at the bilayer interface?

“…However, 16:0 MGDG makes only 6.46 H-bonds with water compared to 9.10 AE 0.20 for 18:3 MGDG and its both chains are saturated thus A L for the 16:0 MGDG bilayer is smaller. Based on this result, one can conclude that dependencies observed for PC bilayers [4] hold also for the MGDG bilayer.…”

“…Its value is determined by the balance of interactions taking place at the bilayer interface, particularly the balance between lipid-lipid and lipid-water interactions, and also by the balance of interactions at the interface and those in the bilayer core [2,3]. In phosphatidylcholine (PC) bilayers, a strong correlation between an average A L and an average number of water molecules in the first hydration shell of the head group (head group hydration) [4,5], and also between an average A L and an average number of intermolecular interactions at the bilayer interface [4] were demonstratedwith increasing head group hydration, A L increases, with increasing number of interlipid interactions, A L decreases. Such correlations were shown to hold also between A L of an individual PC molecule and the number of intermolecular interactions this molecule makes at the interface [4].The aim of the analyses presented in this paper is elucidation of whether and how intermolecular interactions at the lipid bilayer interface are possibly related to the orientation of the lipid head groups, and whether the same relation holds for a galactolipid bilayer as for a PC bilayer.…”

“…In phosphatidylcholine (PC) bilayers, a strong correlation between an average A L and an average number of water molecules in the first hydration shell of the head group (head group hydration) [4,5], and also between an average A L and an average number of intermolecular interactions at the bilayer interface [4] were demonstratedwith increasing head group hydration, A L increases, with increasing number of interlipid interactions, A L decreases. Such correlations were shown to hold also between A L of an individual PC molecule and the number of intermolecular interactions this molecule makes at the interface [4].The aim of the analyses presented in this paper is elucidation of whether and how intermolecular interactions at the lipid bilayer interface are possibly related to the orientation of the lipid head groups, and whether the same relation holds for a galactolipid bilayer as for a PC bilayer. The analyses were carried out for 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) and 1,2-di-O-acyl-3-O-b-D-galactopyranosylsn-glycerol (monogalactolipid, MGDG) with both alinolenoyl (di-18:3, cis) acyl chains, lipid bilayers.…”

Defining the Subcellular Distribution and Metabolic Channeling of Phosphatidylinositol

“…Outside of these in vitro biochemical studies, imaging breakthroughs using endogenous membrane-binding protein domains have allowed for the visualization of embedded lipid species with high spatial and temporal resolution in live cells (Varnai et al, 2017; Wills et al, 2018). The refinement and rational design of lipid biosensors has been aided by detailed structural and biophysical studies that have established sequence features that directly contribute to the specificity and affinity of peripheral membrane-binding protein domains based on the recognition of general membrane features as well as individual lipid components (Lee, 2003; Cho and Stahelin, 2005; Pogozheva et al, 2013; Whited and Johs, 2015; Pasenkiewicz-Gierula et al, 2016). Despite these progresses, imaging applications are currently limited to only a few classes of lipids and have been predominantly focused on lipids involved in cellular signaling.…”

Lipid membranes: Theory and simulations bridged to experiments

“…In the article by Pasenkiewicz-Gierula et al [5], the key interactions between lipid head groups, water, and ions as well as their networks are discussed in full. Pasenkiewicz-Gierula et al also provide a concrete example of polymyxin B that is one of antimicrobial compounds interacting with lipid headgroups.…”