Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions

Luo, Yun; Roux, Benoı̂t

doi:10.1021/jz900079w

Cited by 300 publications

(464 citation statements)

References 52 publications

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“…CHARMM-36 parameters were used for DMPC lipid bilayer and bound cholesterol molecule (41)(42)(43). The TIP3P water model and recently developed ion parameters were used for all molecular dynamics simulations (44). Three K ϩ ions were added into the selectivity filter of the TM domain of the Kir channel to occupy sites S0:S2:S4, and the cavity was hydrated by running grand-canonical Monte-Carlo simulations (45).…”

Section: Methodsmentioning

confidence: 99%

Identification of Novel Cholesterol-binding Regions in Kir2 Channels

Rosenhouse‐Dantsker

Noskov

Durdağı

et al. 2013

Journal of Biological Chemistry

123

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Background: Cholesterol modulates inwardly rectifying potassium (Kir) channels. Results: Using a combined computational-experimental approach, we identified two putative cholesterol-binding regions in Kir2.1 that suggest the existence of a novel cholesterol binding motif. Conclusion: Cholesterol binds to nonannular surfaces in the transmembrane domain of Kir2.1. Significance: These findings provide new insights into the mechanisms underlying lipid regulation of ion channels.

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Section: Methodsmentioning

confidence: 99%

Identification of Novel Cholesterol-binding Regions in Kir2 Channels

Rosenhouse‐Dantsker

Noskov

Durdağı

et al. 2013

Journal of Biological Chemistry

123

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“…The nonbonded interaction FIX (NBFIX) term in the CHARMM force field parameter set can be employed to use different van der Waals interactions between specific atom pairs instead of atom type-based generic Lennard-Jones parameters (48,49). When the original Ca 2þ parameters were used, a few systems including the AB-B model showed acute angles between the O6-C2 (in GlcN) vector and the O6-C4 0 (in GlcN 0 ) vector because of too tight binding between Ca 2þ and phosphate oxygen atoms in Lipid A (Fig.…”

Section: Nonbonded Interaction Fix Parameters and Their Effects On Mementioning

confidence: 99%

Bilayer Properties of Lipid A from Various Gram-Negative Bacteria

Kim

Patel

Park

et al. 2016

Biophysical Journal

132

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Lipid A is the lipid anchor of a lipopolysaccharide in the outer leaflet of the outer membrane of Gram-negative bacteria. In general, lipid A consists of two phosphorylated N-acetyl glucosamine and several acyl chains that are directly linked to the two sugars. Depending on the bacterial species and environments, the acyl chain number and length vary, and lipid A can be chemically modified with phosphoethanolamine, aminoarabinose, or glycine residues, which are key to bacterial pathogenesis. In this work, homogeneous lipid bilayers of 21 distinct lipid A types from 12 bacterial species are modeled and simulated to investigate the differences and similarities of their membrane properties. In addition, different neutralizing ion types (Ca 2þ , K þ , and Na þ ) are considered to examine the ion's influence on the membrane properties. The trajectory analysis shows that (1) the area per lipid is mostly correlated to the acyl chain number, and the area per lipid increases as a function of the acyl chain number; (2) the hydrophobic thickness is mainly determined by the average acyl chain length with slight dependence on the acyl chain number, and the hydrophobic thickness generally increases with the average acyl chain length; (3) a good correlation is observed among the area per lipid, hydrophobic thickness, and acyl chain order; and (4) although the influence of neutralizing ion types on the area per lipid and hydrophobic thickness is minimal, Ca 2þ stays longer on the membrane surface than K þ or Na þ , consequently leading to lower lateral diffusion and a higher compressibility modulus, which agrees well with available experiments.

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“…For the explicit-solvent simulations we utilized the modified CHARMM TIP3P water model, 39 an updated van der Waals radius for the sodium ion, 40 and a modified sodium-chloride van der Waals interaction distance to reduce sodium chloride contact-ion pair formation. 41 In all simulations, the SHAKE algorithm was applied to the bonds and angles involving hydrogen atoms to allow a 2 fs time step. The titration degrees of freedom were propagated using the Langevin algorithm with a collision frequency of 5 ps −1 .…”

Section: Computational Details a Simulation Protocolmentioning

confidence: 99%

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

Wallace

Shen²

2012

The Journal of Chemical Physics

100

178

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Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK a values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

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Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions

Cited by 300 publications

References 52 publications

Identification of Novel Cholesterol-binding Regions in Kir2 Channels

Identification of Novel Cholesterol-binding Regions in Kir2 Channels

Bilayer Properties of Lipid A from Various Gram-Negative Bacteria

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

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