Experimental Validation of Molecular Dynamics Simulations of Lipid Bilayers: A New Approach

Benz, Ryan W.; Castro-Roman, Francisco; Tobias, Douglas J.; White, Stephen H.

doi:10.1529/biophysj.104.046821

Cited by 165 publications

(179 citation statements)

References 40 publications

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“…Error bars (2s) were calculated using the method of block transformations, which provides an estimate of the statistical error in timecorrelated data. 120,121 The predicted percentages of NO 3 À in the interfacial region show similar trends to the experimentally measured rates of NO 2 production ( Fig. 2a and b).…”

Section: Resultssupporting

confidence: 76%

Production of gas phase NO2 and halogens from the photolysis of thin water films containing nitrate, chloride and bromide ions at room temperature

Richards-Henderson

Callahan

Nissenson

et al. 2013

Phys. Chem. Chem. Phys.

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aNitrate and halide ions coexist in particles generated in marine regions, around alkaline dry lakes, and in the Arctic snowpack. Although the photochemistry of nitrate ions in bulk aqueous solution is well known, there is recent evidence that it may be more efficient at liquid-gas interfaces, and that the presence of other ions in solution may enhance interfacial reactivity. This study examines the 311 nm photolysis of thin aqueous films of ternary halide-nitrate salt mixtures (NaCl-NaBr-NaNO 3 ) deposited on the walls of a Teflon chamber at 298 K. The films were generated by nebulizing aqueous 0.25 M NaNO 3 solutions which had NaCl and NaBr added to vary the mole fraction of halide ions. Molar ratios of chloride to bromide ions were chosen to be 0.25, 1.0, or 4.0. The subsequent generation of gas phase NO 2 and reactive halogen gases (Br 2 , BrCl and Cl 2 ) were monitored with time. The rate of gas phase NO 2 formation was shown to be enhanced by the addition of the halide ions to thin films containing only aqueous NaNO 3 .] r 1.0, the NO 2 enhancement was similar to that observed for binary NaBr-NaNO 3 mixtures, while with excess chloride NO 2 enhancement was similar to that observed for binary NaCl-NaNO 3 mixtures. Molecular dynamics simulations predict that the halide ions draw nitrate ions closer to the interface where a less complete solvent shell allows more efficient escape of NO 2 to the gas phase, and that bromide ions are more effective in bringing nitrate ions closer to the surface. The combination of theory and experiments suggests that under atmospheric conditions where nitrate ion photochemistry plays a role, the impact of other species such as halide ions should be taken into account in predicting the impacts of nitrate ion photochemistry.

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Section: Resultssupporting

confidence: 76%

Production of gas phase NO2 and halogens from the photolysis of thin water films containing nitrate, chloride and bromide ions at room temperature

Richards-Henderson

Callahan

Nissenson

et al. 2013

Phys. Chem. Chem. Phys.

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“…This force field has been show to replicate both equilibrium and dynamical experimental properties well (25,26) and provides higher performance than explicit-hydrogen lipids. Amino acids where modeled with the all-atom force field OPLS-AA/L (27), and standard OPLS LorenzBertheholtz combination rules applied to nonbonded interactions between lipids and amino acid analogs.…”

Section: Methodsmentioning

confidence: 97%

Protein contents in biological membranes can explain abnormal solvation of charged and polar residues

Johansson

Lindahl

2009

Proc. Natl. Acad. Sci. U.S.A.

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Transmembrane helices are generally believed to insert into membranes based on their hydrophobicity. Nevertheless, there are important exceptions where polar residues have great functional importance, for instance the S4 helix of voltage-gated ion channels. It has been shown experimentally that insertion can be accomplished by hydrophobic counterbalance, predicting an arginine insertion cost of only 2.5 kcal/mol, compared with 14.9 kcal/mol in cyclohexane. Previous simulations of pure bilayers have produced values close to the pure hydrocarbon, which has lead to spirited discussion about the experimental conditions. Here, we have performed computer simulations of models better mimicking biological membranes by explicitly including protein helices at mass fractions from 15% to 55%, as well as an actual translocon. This has a striking effect on the solvation free energy of arginine. With some polar residues present, the solvation cost comes close to experimental observation at approximately 30% mass fraction, and negligible at 40%. In the presence of a translocon in the membrane, the cost of inserting arginine next to the lateral gate can be as low as 3-5 kcal/mol. The effect is mainly due to the extra helices making it easier to retain hydration water. These results offer a possible explanation for the discrepancy between the in vivo hydrophobicity scale and computer simulations and highlight the importance of the high protein contents in membranes. Although many membrane proteins are stable in pure bilayers, such simplified models might not be sufficiently accurate for insertion of polar or charged residues in biological membranes.free energy of insertion ͉ impurities ͉ lipid bilayer ͉ membrane protein ͉ molecular dynamics simulations

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“…For DMPC lipids, the united atom model based on the GROMOS [30] force field was used with modifications by Berger [31]. The force field was validated previously in works [32,33,34]. Also, the united atom approach was used to describe articaine drug molecules (except for the polar H atoms bound to the nitrogen atoms).…”

Section: Molecular Structuresmentioning

confidence: 99%

Molecular dynamics simulations of local anesthetic articaine in a lipid bilayer

Mojumdar

Lyubartsev

2010

Biophysical Chemistry

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In order to investigate structural and dynamical properties of local anesthetic articaine in a model lipid bilayer, a series of molecular dynamics simulations have been performed. Simulations were carried out for neutral and charged (protonated) forms of articaine inserted in fully hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayer. For comparison purpose, a fully hydrated DMPC bilayer without articaine was also simulated. The length of each simulation was 200 ns. Various properties of the lipid bilayer systems in the presence of both charged and uncharged forms of articaine taken at two different concentrations have been examined: membrane area per lipid, mass density distributions, order parameters, radial distribution functions, head group tilt, diffusion coefficients, electrostatic potential, etc, and compared with results of previous simulations of DMPC bilayer in presence of lidocaine. It was shown that addition of both charged and neutral forms of articaine causes increase of the dipole electrostatic potential in the membrane interior.

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Experimental Validation of Molecular Dynamics Simulations of Lipid Bilayers: A New Approach

Cited by 165 publications

References 40 publications

Production of gas phase NO2 and halogens from the photolysis of thin water films containing nitrate, chloride and bromide ions at room temperature

Production of gas phase NO2 and halogens from the photolysis of thin water films containing nitrate, chloride and bromide ions at room temperature

Protein contents in biological membranes can explain abnormal solvation of charged and polar residues

Molecular dynamics simulations of local anesthetic articaine in a lipid bilayer

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