Structure and dynamics of phospholipid bilayer films under electrochemical control (original) (raw)
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Journal of Chemical Theory and Computation, 2010
Molecular dynamics simulations of fully hydrated pure bilayers of four widely studied phospholipids, 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 2-oleoyl-1palmitoyl-sn-glycero-3-phosphocholine (POPC) using a recent revision of the GROMOS96 force field are reported. It is shown that the force field reproduces the structure and the hydration of bilayers formed by each of the four lipids with high accuracy. Specifically, the solvation and the orientation of the dipole of the phosphocholine headgroup and of the ester carbonyls show that the structure of the primary hydration shell in the simulations closely matches experimental findings. This work highlights the need to reproduce a broad range of properties beyond the area per lipid, which is poorly defined experimentally, and to consider the effect of system size and sampling times well beyond those commonly used.
Molecular dynamics simulation of the fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer
2003
The structural properties of lipid bilayers in biological membranes are of great interest in biochemistry, biophysics, and medicine. The main goal of the present study was to use molecular dynamic (MD) techniques to investigate physical properties of the hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer. -- The bilayer model consists of 25 DPPC molecules per each monolayer and 44.8% water by total weight. A modified version of AMBER MD suit of programs with CHARMM22 force field for phospholipids was used in simulation. The isothermal-isobaric or NPT ensemble with a fully flexible simulation box in ROAR program was used in this study. Simulations were performed under different pressure and temperature conditions. -- According to experimental results, a liquid crystal phase (Lα) is expected with the DPPC bilayer simulated under 1 atm pressure and 323 K temperature conditions. However, area per lipid, bilayer thickness, chain tilt, and the order parameters resulting from the prese...
Biophysical Journal, 2007
Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of ;48 Å 2. To obtain fluid (L a) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 6 0.1 Å 2. Compared to the 48 Å 2 , the new value of 60.4 Å 2 is in fair agreement with the experimental value of 64 Å 2. In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field.
Molecular dynamics simulations of ether- and ester-linked phospholipids
Biochimica et Biophysica Acta (BBA) - Biomembranes, 2017
Dissimilarities in the bulk structure of bilayers composed of ether-vs esterlinked lipids are well-established; however, the atomistic interactions responsible for these differences are not well known. These differences are important in understanding of why archaea have a different bilayer composition than the other domains of life and why humans have larger concentrations of plasmalogens in specialized membranes? In this paper we simulate two lipid bilayers, the ester linked dipalmitoylphosphatidylcholine (DPPC) and the ether lined dihexadecylphosphatidylcholine (DHPC), to study these variations. The structural analysis of the bilayers reveals that DPPC is more compressible than DHPC. A closer examination of dipole potential shows DHPC, despite having a smaller dipole potential of the bilayer, has a higher potential barrier than DPPC at the surface. Analysis of water order and dynamics suggests DHPC has a more ordered, less mobile layer of water in the headgroup. These results seem to resolve the issue as to whether the decrease in permeability of DHPC is due to of differences in minimum area per lipid (A 0) or diffusion coefficient of water in the headgroup region (D head) [1] since we have shown significant changes to the order and mobility of water in that region.
Molecular Dynamics Simulations of Phospholipid Bilayers
Journal of Biomolecular Structure and Dynamics, 1994
To investigate the microscopic interactions between cholesterol and lipids in biological membranes, we have performed a series of molecular dynamics simulations of large membranes with different levels of cholesterol content. The simulations extend to 10 ns, and were performed with hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers. The bilayers contain 1024 lipids of which 0-40% were cholesterol and the rest DPPC. The effects of cholesterol on the structure and mesoscopic dynamics of the bilayer were monitored as a function of cholesterol concentration. The main effects observed are a significant ordering of the DPPC chains (as monitored by NMR type order parameters), a reduced fraction of gauche bonds, a reduced surface area per lipid, less undulations-corresponding to an increased bending modulus for the membrane, smaller area fluctuations, and a reduced lateral diffusion of DPPC-lipids as well as cholesterols.
The dynamics of water at the phospholipid bilayer surface: a molecular dynamics simulation study
Chemical Physics Letters, 2002
Molecular dynamics (MD) simulations of a fully hydrated 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) bilayer in the liquid-crystalline state were carried out to investigate the effect of the membrane on the dynamics of water. Translational and rotational motions of water near the membrane surface were restricted. The effect was the strongest for water molecules that were hydrogen (H) bonded to the phosphate (Op) and carbonyl (Oc) oxygen atoms as well as those clathrating choline group of POPC. The translational motion of Oc H bonded water was slower than that of the Op H bonded water, while the rotational motion was faster. Water clatrathing the POPC choline group was less affected than Op and Oc H bonded water. Translational diffusion of all membrane water was faster along the membrane plane than along the membrane normal. Ó
Structural effects of small molecules on phospholipid bilayers investigated by molecular simulations
Fluid Phase Equilibria, 2005
We summarize and compare recent molecular dynamics simulations on the interactions of dipalmitoylphosphatidylcholine (DPPC) bilayers in the liquid crystalline phase with a number of small molecules including trehalose, a disaccharide of glucose, alcohols, and dimethylsulfoxide (DMSO). The sugar molecules tend to stabilize the structure of the bilayer as they bridge adjacent lipid headgroups. They do not strongly change the structure of the bilayer. Alcohols and DMSO destabilize the bilayer as they increase its area per molecule in the bilayer plane and decrease the order parameter. Alcohols have a stronger detrimental effect than DMSO. The observables which we compare are the area per molecule in the plane of the bilayer, the membrane thickness, and the nuclear magnetic resonance (NMR) order parameter of DPPC hydrocarbon tails. The area per molecule and the order parameter are very well correlated whereas the bilayer thickness is not necessarily correlated with them.
Biomolecular simulations of membranes: Physical properties from different force fields
The Journal of Chemical Physics, 2008
Phospholipid force fields are of ample importance for the simulation of artificial bilayers, membranes, and also for the simulation of integral membrane proteins. Here, we compare the two most applied atomic force fields for phospholipids, the all-atom CHARMM27 and the united atom Berger force field, with a newly developed all-atom generalized AMBER force field ͑GAFF͒ for dioleoylphosphatidylcholine molecules. Only the latter displays the experimentally observed difference in the order of the C2 atom between the two acyl chains. The interfacial water dynamics is smoothly increased between the lipid carbonyl region and the bulk water phase for all force fields; however, the water order and with it the electrostatic potential across the bilayer showed distinct differences between the force fields. Both Berger and GAFF underestimate the lipid self-diffusion. GAFF offers a consistent force field for the atomic scale simulation of biomembranes.
Physical Review E, 2003
A molecular-level self-consistent-field ͑SCF͒ theory is applied to model the lipid bilayer structures composed of 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine ͑18:0/18:19cis PC͒ and 1-stearoyl-2docosahexaenoyl-sn-glycero-3-phosphatidylcholine ͑18:0/22:63cis PC͒. As compared to earlier attempts to model ͑saturated͒ PC membranes several additional features are implemented: ͑i͒ A water model is used which correctly leads to low water concentration in the bilayers. ͑ii͒ Free volume is allowed for, which is important to obtain bilayers in the fluid state. ͑iii͒ A polarization term is included in the segment potentials; this new feature corrects for a minor thermodynamic inconsistency present in ͑all͒ earlier results for charged bilayers. ͑iv͒ The CH 3 groups in the lipid molecules are assumed to have twice the volume of a CH 2 group; this leads to stable noninterdigitated bilayers. ͑v͒ A cis double bond is simulated by forcing gauche conformations along the sn-2 acyl chain. Results of an all-atom molecular dynamics ͑MD͒ simulation, using the collision dynamics method, on the same system are presented. Both SCF and MD prove, in accordance with experimental facts, that acyl unsaturation effectively reduces the length of the chain which counteracts interdigitation. It is also found that the phosphatidylcholine head group is lying almost flat on the membrane surface and the water penetrates into the bilayer upto the glycerol backbone units. From the SCF results it further followed that the free volume is not exactly evenly distributed over the bilayer. There is a small increase in free volume in the center of the bilayer as well as in the glycerol backbone region.