Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation

Laner, Monika; Horta, Bruno A. C.; Hünenberger, Philippe H.

doi:10.1016/j.jmgm.2014.10.016

Cited by 6 publications

(11 citation statements)

References 108 publications

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“…Mat. A, Table A.10), alkali and halide ions 90 , and 2016H66-compatible biomolecular building blocks for peptides, nucleic acids, carbohydrates (including cyclodextrins 124 ), lipids (including mono-and diglycerides 97,101,[107][108][109][110]125 ) and cofactors (see details in the Appendix of Suppl. Mat.…”

Section: Introductionmentioning

confidence: 99%

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Horta

Merz

Fuchs

et al. 2016

J. Chem. Theory Comput.

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287

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This article reports on the calibration and validation of a new GROMOS-compatible parameter set 2016H66 for small organic molecules in the condensed phase. The calibration is based on 62 organic molecules spanning the chemical functions alcohol, ether, aldehyde, ketone, carboxylic acid, ester, amine, amide, thiol, sulfide, and disulfide, as well as aromatic compounds and nucleic-acid bases. For 57 organic compounds, the calibration targets are the experimental pure-liquid density ρliq and the vaporization enthalpy ΔHvap, as well as the hydration free energy ΔGwat and the solvation free energy ΔGche in cyclohexane, at atmospheric pressure and at (or close to) room temperature. The final root-mean-square deviations (RMSD) for these four quantities over the set of compounds are 32.4 kg m(-3), 3.5 kJ mol(-1), 4.1 kJ mol(-1), and 2.1 kJ mol(-1), respectively, and the corresponding average deviations (AVED) are 1.0 kg m(-3), 0.2 kJ mol(-1), 2.6 kJ mol(-1), and 1.0 kJ mol(-1), respectively. For the five nucleic-acid bases, the parametrization is performed by transferring the final 2016H66 parameters from analogous organic compounds followed by a slight readjustment of the charges to reproduce the experimental water-to-chloroform transfer free energies ΔGtrn. The final RMSD for this quantity over the five bases is 1.7 kJ mol(-1), and the corresponding AVED is 0.8 kJ mol(-1). As an initial validation of the 2016H66 set, seven additional thermodynamic, transport, and dielectric properties are calculated for the 57 organic compounds in the liquid phase. The agreement with experiment in terms of these additional properties is found to be reasonable, with significant deviations typically affecting either a specific chemical function or a specific molecule. This suggests that in most cases, a classical force-field description along with a careful parametrization against ρliq, ΔHvap, ΔGwat, and ΔGche results in a model that appropriately describes the liquid in terms of a wide spectrum of its physical properties.

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Section: Introductionmentioning

confidence: 99%

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Horta

Merz

Fuchs

et al. 2016

J. Chem. Theory Comput.

Self Cite

144

287

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“…In general, the environmentally modulated effective headgroup cross-section will be larger than the (fixed) tail cross-section, making a vertical packing of all-trans chains extremely unfavorable. In the context of monoglycerides, there are three possible mechanisms to relieve the effect of this mismatch between headgroup and tail cross-sections (Laner et al 2014): (1) single-lipid tilting or kinking; (2) collective tilting; (3) interdigitation. These three mechanisms are active in the LC, GL and ID phases, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…In summary, θ is positively correlated with a xy , whereas is only weakly sensitive to the environmental conditions for a given phase. The correlation between area per lipid and tilting behavior is further explored in a companion article (Laner et al 2014).…”

Section: Simulationmentioning

confidence: 99%

“…Consequently, the order parameter increase from GL to ID results in principle from both the tighter chain packing and the suppression of the tilting. The relative influence of these two components is further discussed in a companion article (Laner et al 2014).…”

Section: Interdigitated Phasementioning

confidence: 99%

“…However, the biologically most relevant phospholipids such as DPPC remain relatively challenging to simulate, owing to difficulties in the force field design (Anézo et al 2003;Klauda et al 2008) and treatment of electrostatic interactions (Tieleman et al 2002;Anézo et al 2003;Patra et al 2003Patra et al , 2004Kastenholz and Hünenberger 2004;Cordomí et al 2007;Reif et al 2009) (charged or zwitterionic headgroup), and to the slow convergence of system properties with respect to both system size (Takaoka et al 2000;Anézo et al 2003;de Vries et al 2005b;Herce and Garcia 2006;Baştug et al 2006;Klauda et al 2008;Laner et al 2013) (long-range correlations) and simulation timescale (Tieleman et al 1997;Takaoka et al 2000;de Vries et al 2005b;Klauda et al 2006;Nagarajan et al 2012) (slow conformational relaxation). For this reason, it is also interesting to consider less complex bilayer systems such as monoglyceride lipid systems (Horta et al 2010b;Laner et al 2013Laner et al , 2014Laner and Hünenberger 2014a, b).…”

Section: Introductionmentioning

confidence: 99%

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Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations

2014

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The influence of the cosolutes trehalose and methanol on the structural, dynamic and thermodynamic properties of a glycerol-1-monopalmitate (GMP) bilayer and on its main transition temperature [Formula: see text] is investigated using atomistic molecular dynamics simulations (600 ns) of a GMP bilayer patch (2 × 8 × 8 lipids) at different temperatures in the range of 302 to 338 K and considering three different cosolute concentrations. Depending on the environment and temperature, these simulations present no or a single GL[Formula: see text]LC, LC[Formula: see text]GL or LC[Formula: see text]ID transition, where LC, GL and ID are the liquid crystal, gel and interdigitated phases, respectively. The trehalose molecules form a coating layer at the bilayer surface, promote the hydrogen-bonded bridging of the lipid headgroups, preserve the interaction of the headgroups with trapped water and induce a slight lateral expansion of the bilayer in the LC phase, observations that may have implications for the phenomenon of anhydrobiosis. However, this cosolute does not affect [Formula: see text] and its dependence on hydration in the concentration range considered. On the other hand, methanol molecules intercalate between the lipid headgroups, promote a lateral expansion of the bilayer in the LC phase and induce a concentration dependent decrease of [Formula: see text], observations that may have implications for the phenomenon of anesthesia. The occurrence of an ID phase in the presence of this cosolute may be viewed as an extreme consequence of lateral expansion. The analysis of the simulations also suggests the existence of two basic conservation principles: (1) the hydrogen-bond saturation principle rests on the observation that for all species present in the different systems, the total numbers of hydrogen-bonds per molecule is essentially constant, the only factor of variability being their distribution among different partners; (2) the densest packing principle rests on the observation that the effective volume per methylene group in the interior of the bilayer is only weakly sensitive to the environment, with values comparable to those for liquid (LC) and solid (ID) alkanes, or intermediate (GL).

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Effect of methanol on the phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations: In quest of the biphasic effect

Laner

Hünenberger

2015

Journal of Molecular Graphics and Modelling

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Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation

Cited by 6 publications

References 108 publications

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Effect of the cosolutes trehalose and methanol on the equilibrium and phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations

Effect of methanol on the phase-transition properties of glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulations: In quest of the biphasic effect

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