Molecular dynamics simulations of ionic concentration gradients across model bilayers

Atomistic Insights into Cryptochrome Interprotein Interactions

It is striking that the mechanism by which birds sense geomagnetic fields during the biannual migration seasons is not entirely understood. A protein believed to be responsible for avian magnetoreception is the flavoprotein cryptochrome (CRY), which fulfills many of the criteria for a magnetic field sensor. Some experiments, however, indicate that magnetoreception in birds may be disturbed by extremely weak radio frequency fields, an effect that likely cannot be described by an isolated CRY protein. An explanation can possibly be delivered if CRY binds to another protein inside a cell that would possess certain biochemical properties, and it is, therefore, important to identify possible intracellular CRY interaction partners. The goal of this study is to investigate a possible interaction between CRY4 and the iron-sulfur-containing assembly protein (ISCA1) from Erithacus rubecula (European robin), which has recently been proposed to be relevant for magnetic field sensing. The interaction between the proteins is established through classical molecular dynamics simulations for several possible protein-docking modes. The analysis of these simulations concludes that the ISCA1 complex and CRY4 are capable of binding; however, the peculiarities of this binding argue strongly against ISCA1 as relevant for magnetoreception.

Molecular-dynamics simulation of a ceramide bilayer

Ceramide is the simplest lipid in the biologically important class of glycosphingolipids. Ceramide is an important signaling molecule and a major component of the strateum corneum layer in the skin. In order to begin to understand the biophysical properties of ceramide, we have carried out a molecular-dynamics simulation of a hydrated 16:0 ceramide lipid bilayer at 368 K (5 degrees above the main phase transition). In this paper we describe the simulation and present the resulting properties of the bilayer. We compare the properties of the simulated ceramide bilayer to an earlier simulation of 18:0 sphingomyelin, and we discuss the results as they relate to experimental data for ceramide and other sphingolipids. The most significant differences arise at the lipid/water interface, where the lack of a large ceramide polar group leads to a different electron density and a different electrostatic potential but, surprisingly, not a different overall "dipole potential," when ceramide is compared to sphingomyelin.

Changes in phosphatidylcholine headgroup tilt and water order induced by monovalent salts: molecular dynamics simulations

The association between monovalent salts and neutral lipid bilayers is known to influence global bilayer structural properties such as headgroup conformational fluctuations and the dipole potential. The local influence of the ions, however, has been unknown due to limited structural resolution of experimental methods. Molecular dynamics simulations are used here to elucidate local structural rearrangements upon association of a series of monovalent Na(+) salts to a palmitoyl-oleoyl-phosphatidylcholine bilayer. We observe association of all ion types in the interfacial region. Larger anions, which are meant to rationalize data regarding a Hofmeister series of anions, bind more deeply within the bilayer than either Cl(-) or Na(+). Although the simulations are able to reproduce experimentally measured quantities, the analysis is focused on local properties currently invisible to experiments, which may be critical to biological systems. As such, for all ion types, including Cl(-), we show local ion-induced perturbations to headgroup tilt, the extent and direction of which is sensitive to ion charge and size. Additionally, we report salt-induced ordering of the water well beyond the interfacial region, which may be significant in terms of hydration repulsion between stacked bilayers.

Dependence of ion hydration on the sign of the ion’s charge

The solvation of simple ions in water is studied using molecular dynamics simulations with a polarizable force field. Previous simulations using this potential demonstrated that anions are more favorably solvated in water than cations. The present work is an attempt to explain this result by examining the effects of ions on the surrounding water structure, with particular focus on the first solvation shell and its interactions with the surrounding water. We conclude that while the first solvation shell surrounding cations is frustrated by competition between ion-water and water-water interactions, solvation of anions is compatible with good water-water interactions.

Atomistic simulations of biologically realistic transmembrane potential gradients

We present all-atom molecular dynamics simulations of biologically realistic transmembrane potential gradients across a DMPC bilayer. These simulations are the first to model this gradient in all-atom detail, with the field generated solely by explicit ion dynamics. Unlike traditional bilayer simulations that have one bilayer per unit cell, we simulate a 170 mV potential gradient by using a unit cell consisting of three salt-water baths separated by two bilayers, with full three-dimensional periodicity. The study shows that current computational resources are powerful enough to generate a truly electrified interface, as we show the predicted effect of the field on the overall charge distribution. Additionally, starting from Poisson's equation, we show a new derivation of the double integral equation for calculating the potential profile in systems with this type of periodicity.

Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: molecular dynamics simulations

A set of all-atom molecular dynamics simulations have been performed to better understand critical phenomena regarding a Hofmeister series of anions and lipid bilayers. The simulations isolate the effect of anion size and show clear differences in the interactions with the dipolar phoshpatidylcholine headgroup. Cl- anions penetrate into the headgroup region of the bilayer, but the simulations confirm theories which predict that larger anions penetrate more deeply, into a more heterogeneous and hydrophobic molecular region. That anion size leads to such differences in partitioning in the bilayer provides atomic-level support to hypotheses inspired by several experimental studies. The ability of larger anions to bury deep within the bilayer is correlated with a less well-structured hydration shell, shedding of which upon penetration incurs a smaller penalty for the larger anions than for Cl-.