A criterion to identify the equilibration time in lipid bilayer simulations

Rodolfo D Porasso,José J López Cascales

doi:10.4279/pip.040005

Abstract

With the aim of establishing a criterion for identifying when a lipid bilayer has reached steady state using the molecular dynamics simulation technique, lipid bilayers of different composition in their liquid crystalline phase were simulated in aqueous solution in presence of CaCl$_2$ as electrolyte, at different concentration levels. In this regard, we used two different lipid bilayer systems: one composed by 288 DPPC (DiPalmitoylPhosphatidylCholine) and another constituted by 288 DPPS (DiPalmitoylPhosphatidylSerine). In this sense, for both type of lipid bilayers, we have studied the temporal evolution of some lipids properties, such as the surface area per lipid, the deuterium order parameter, the lipid hydration and the lipid-calcium coordination. From their analysis, it became evident how each property has a different time to achieve equilibrium. The following order was found, from faster property to slower property: coordination of ions $\approx$ deuterium order parameter $>$ area per lipid $\approx$ hydration. Consequently, when the hydration of lipids or the mean area per lipid are stable we can ensure that the lipid membrane has reached the steady state.Received: 3 September 2012, Accepted: 24 October 2012; Edited by: M. C. Barbosa; DOI:http://dx.doi.org/10.4279/PIP.040005Cite as: R. D. Porasso, J. J. López Cascales, Papers in Physics 4, 040005 (2012)

Highlights

Over the last few decades, different computational techniques have emerged in different fields of science, some of them being extensively implemented and used by a great number of scientists around the globe
For both type of lipid bilayers, we have studied the temporal evolution of some lipids properties, such as the surface area per lipid, the deuterium order parameter, the lipid hydration and the lipid-calcium coordination
Different molecular Dynamics (MD) simulations of lipid bilayer formed by 288 DPPC were carried out in aqueous solutions for different concentrations of CaCl2, from 0, up to 0.50 N

Summary

Introduction

Over the last few decades, different computational techniques have emerged in different fields of science, some of them being extensively implemented and used by a great number of scientists around the globe. The Molecular Dynamics (MD) simulation is a very popular computational technique, which is widely used to obtain insight with atomic detail of steady and dynamic properties in the fields of biology, physics and chemistry In this regard, a critical aspect that must be identified in all the MD simulations is related to the required equilibration time to achieve a steady state. Considering the literature, a vast dispersion of equilibration times associated to the binding of ions to the membrane has been reported, where values ranging from 5 to 100 ns have been suggested for monovalent and divalent cations [25, 27,28,29, 32, 37, 38] In this regard, we carried out four independent simulations of a lipid bilayer formed by 288 DPPC in aqueous solutions, for different concentrations of CaCl2 to provide an overview of their equilibration times. In order to generalize our results, a bilayer formed by 288 DPPS in its liquid crystalline phase, in presence of CaCl2 at 0.25N, was simulated as well

Methodology

Molecular n weight

Hydration Number

Conclusions