Molecular Dynamics Simulation of a Polyunsaturated Lipid Bilayer Susceptible to Lipid Peroxidation

Bachar, Michal; Brunelle, Patrick; Tieleman, D. Peter; Rauk, Arvi

doi:10.1021/jp036981u

Cited by 121 publications

(130 citation statements)

References 45 publications

Supporting

Mentioning

121

Contrasting

Order By: Relevance

“…In agreement with previously published results, the implementation of the Bachar et al dihedrals, 92 originally designed for polyunsaturated lipid tails, improves the agreement with the experimental S CH for the Berger force field at the double bond. 93 For the CHARMM36-UA force field there is also good agreement with the previously reported S CH .…”

Section: Journal Of Chemical Theory and Computationsupporting

confidence: 77%

“…We note that while a dispersion correction was used in the parametrization of the lipid tails, this was not reported as being applied in the membrane simulations of Ulmschneider et al 85 Finally, in addition to these new simulations, we also analyzed a Berger POPC simulation that used force field parameters for the dihedrals around the double bond of the oleoyl tail that were not studied in our previous work. 92,93 As per the additional OPLS-AA simulation, this simulation was also obtained from open-access data provided by the NMRlipids project. 94 …”

Section: 67mentioning

confidence: 99%

See 1 more Smart Citation

On the Calculation of Acyl Chain Order Parameters from Lipid Simulations

Piggot

Allison

Sessions

et al. 2017

J. Chem. Theory Comput.

108

111

View full text Add to dashboard Cite

For molecular dynamics simulations of biological membrane systems to live up to the potential of providing accurate atomic level detail into membrane properties and functions, it is essential that the force fields used to model such systems are as accurate as possible. One membrane property that is often used to assess force field accuracy is the carbon−hydrogen (or carbon−deuterium) order parameters of the lipid tails, which can be accurately measured using experimental NMR techniques. There are a variety of analysis tools available to calculate these order parameters from simulations and it is essential that these computational tools work correctly to ensure the accurate assessment of the simulation force fields. In this work we compare many of these computational tools for calculating the order parameters of POPC membranes. While tools that work on all-atom systems and tools that work on saturated lipid tails in general work extremely well, we demonstrate that the majority of the tested tools that calculate the order parameters for unsaturated united-atom lipid tails do so incorrectly. We identify tools that do perform accurate calculations and include one such program with this work, enabling rapid and accurate calculation of unitedatom lipid order parameters. Furthermore, we discuss cases in which it is nontrivial to appropriately predict the unsaturated carbon order parameters in united-atom systems. Finally, we examine order parameter splitting for carbon 2 in sn-2 lipid chains, demonstrating substantial deviations from experimental values in several all-atom and united-atom lipid force fields.

show abstract

Section: Journal Of Chemical Theory and Computationsupporting

confidence: 77%

Section: 67mentioning

confidence: 99%

On the Calculation of Acyl Chain Order Parameters from Lipid Simulations

Piggot

Allison

Sessions

et al. 2017

J. Chem. Theory Comput.

108

111

View full text Add to dashboard Cite

show abstract

“…35,36 The simple point charge water model was used. 37 The topology of the POPC molecule consisted of a united-atom description for CH, CH 2 , and CH 3 groups, based on the parameters presented by Berger et al 38 for 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC), and by Bachar et al 39 for the oleoyl chain cis-double bond. The starting structure was a fully hydrated POPC bilayer (128 POPC:5412 H 2 O).…”

Section: Simulation Detailsmentioning

confidence: 99%

Behaviour of NBD-head group labelled phosphatidylethanolamines in POPC bilayers: a molecular dynamics study

Filipe

Santos

Ramalho

et al. 2015

Phys. Chem. Chem. Phys.

View full text Add to dashboard Cite

A complete homologous series of fluorescent phosphatidylethanolamines (diC n PE), labelled at the head group with a 7-nitrobenz-2-oxa-1,3-diazo-4-yl(NBD) fluorophore and inserted in 1-palmitoyl, 2-oleoyl-snglycero-3-phosphocholine (POPC) bilayers, was studied using atomistic molecular dynamics simulations. The longer-chained derivatives of NBD-diC n PE, with n = 14, 16, and 18, are commercially available, and widely used as fluorescent membrane probes. Properties such as location of atomic groups and acyl chain order parameters of both POPC and NBD-diC n PE, fluorophore orientation and hydrogen bonding, membrane electrostatic potential and lateral diffusion were calculated for all derivatives in the series. Most of these probes induce local disordering of POPC acyl chains, which is on the whole counterbalanced by ordering resulting from binding of sodium ions to lipid carbonyl/glycerol oxygen atoms. An exception is found for NBD-diC 16 PE, which displays optimal matching with POPC acyl chain length and induces a slight local ordering of phospholipid acyl chains. Compared to previously studied fatty amines, acyl chain-labelled phosphatidylcholines, and sterols bearing the same fluorescent tag, the chromophore in NBD-diC n PE locates in a similar region of the membrane (near the glycerol backbone/carbonyl region) but adopts a different orientation (with the NO 2 group facing the interior of the bilayer). This modification leads to an inverted orientation of the P-N axis in the labelled lipid, which affects the interface properties, such as the membrane electrostatic potential and hydrogen bonding to lipid head group atoms. The implications of this study for the interpretation of the photophysical properties of NBD-diC n PE (complex fluorescence emission kinetics, differences with other NBD lipid probes) are discussed.

show abstract

“…39 The topology of POPC was then adapted to take into account the changed parameters for the double bond in the sn-2 acyl chain, as described elsewhere. 40,41 The UA structure and topology of cholesterol were adapted from that of Höltje et al 42 (available for download at the GROMACS webpage 43 ) by changing the molecule types from CH2/CH3 to LP2/LP3 to avoid overcondensation of the bilayer, as previously suggested, 44,45 and successfully tested by us. 46 Parameterizations of the other sterols were adapted from that of cholesterol by removing/adding the appropriate number of methylene groups from/to each chain, for androstenol and i-C5, or the other sterols, respectively.…”

Section: Simulation Detailsmentioning

confidence: 99%

Influence of the sterol aliphatic side chain on membrane properties: a molecular dynamics study

Robalo

Ramalho

Huster

et al. 2015

Phys. Chem. Chem. Phys.

View full text Add to dashboard Cite

Following a recent experimental investigation of the effect of the length of the alkyl side chain in a series of cholesterol analogues (Angew. Chem., Int. Ed., 2013, 52, 12848-12851), we report here an atomistic molecular dynamics characterization of the behaviour of methyl-branched side chain sterols (iso series) in POPC bilayers. The studied sterols included androstenol (i-C0-sterol) and cholesterol (i-C8-sterol), as well as four other derivatives (i-C5, i-C10, i-C12 and i-C14-sterol). For each sterol, both subtle local effects and more substantial differential alterations of membrane properties along the iso series were investigated. The location and orientation of the tetracyclic ring system is almost identical in all compounds. Among all the studied sterols, cholesterol is the sterol that presents the best matching with the hydrophobic length of POPC acyl chains, whereas longer-chained sterols interdigitate into the opposing membrane leaflet. In accordance with the experimental observations, a maximal ordering effect is observed for intermediate sterol chain length (i-C5, cholesterol, i-C10). Only for these sterols a preferential interaction with the saturated sn-1 chain of POPC (compared to the unsaturated sn-2 chain) was observed, but not for either shorter or longer-chained derivatives. This work highlights the importance of the sterol alkyl chain in the modulation of membrane properties and lateral organization in biological membranes.

show abstract

Molecular Dynamics Simulation of a Polyunsaturated Lipid Bilayer Susceptible to Lipid Peroxidation

Cited by 121 publications

References 45 publications

On the Calculation of Acyl Chain Order Parameters from Lipid Simulations

On the Calculation of Acyl Chain Order Parameters from Lipid Simulations

Behaviour of NBD-head group labelled phosphatidylethanolamines in POPC bilayers: a molecular dynamics study

Influence of the sterol aliphatic side chain on membrane properties: a molecular dynamics study

Contact Info

Product

Resources

About