Abstract
Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol.
Highlights
In order to assess equilibrium properties of the used molecular DPPC model, we performed first simulations of single DPPC molecules. This allows us to determine the evolution of structural correlations during Monte Carlo (MC) sampling and thereby to assess the effect of the molecular constraints used in the description of DPPC
We describe the challenges and advantages of MC compared to other simulation methods and provide a concrete implementation of local move MC for efficient equilibration of lipid bilayer structures
While previous atomistic MC simulations of membranes use configurational biased MC (CBMC) [65], cavity-biased moves [66], or local moves in the torsion angle space [67,79], our study shows the first implementation of an efficient move set in the torsion and bond angle space for lipid assemblies
Summary
Analysis of the molecular mechanisms underlying membrane lipid organization is of crucial importance for understanding the function of membranes in living cells. There is the subcortical actin playing an important role in membrane organization and dynamics [12,13,14,15,16,17], the extracellular oriented glycocalyx [18] and the well-established transbilayer phospholipid asymmetry [19]. This compositional complexity together with the dynamically varying solute and ion composition on both sides of the plasma membrane naturally call for many different modeling approaches being suitable for each level of description [20,21,22,23]
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