Methodological Issues in Lipid Bilayer Simulations

Anézo, Céline; Vries, de Alex; Hd, Höltje; Tieleman, D. Peter; Marrink, Siewert J.

doi:10.1021/jp0348981

Cited by 340 publications

(352 citation statements)

References 51 publications

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“…This was followed by equilibration in conditions of constant number of atoms, pressure and temperature for 15 ns with the pressure set at 1 bar. Such long equilibration is necessary for proper equilibration of the lipids after embedding a protein in the membrane (54). We monitored the size of the system in the x, y, and z axes to confirm the stabilization on the dioleoylphosphatidylcholine bilayer.…”

Section: Methodsmentioning

confidence: 99%

Critical Hydrogen Bond Formation for Activation of the Angiotensin II Type 1 Receptor

Cabana

Holleran

Beaulieu

et al. 2013

Journal of Biological Chemistry

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Background:The N111G and N111W mutations make the AT 1 receptor constitutively active and inactivable, respectively. Results: The orientation and interactions of D74 2.50 are influenced by the residue at position 111 3.35 . Conclusion: H-bond formation between D742.50 and N46 1.50 is critical for AT 1 receptor activation. Significance: This novel molecular switch could be involved in the GPCR activation mechanism as it involves highly conserved residues D 2.50 and N 1.50 .

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Section: Methodsmentioning

confidence: 99%

Critical Hydrogen Bond Formation for Activation of the Angiotensin II Type 1 Receptor

Cabana

Holleran

Beaulieu

et al. 2013

Journal of Biological Chemistry

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“…The importance of accurately accounting for long-range interactions in molecular dynamics simulations has been an area of active research for a long time as it is a crucial issue in computational modeling [59,60,[62][63][64][65][66][67][68][69][70]. It is essential there-fore, to develop reliable and efficient methods to deal with these interactions as well as to use them with care and insight.…”

Section: Molecular Dynamic Simulations Of Ion Channelsmentioning

confidence: 99%

Molecular dynamics simulations of potassium channels

Domene

2007

Open Chemistry

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Despite the complexity of ion-channels, MD simulations based on realistic all-atom models have become a powerful technique for providing accurate descriptions of the structure and dynamics of these systems, complementing and reinforcing experimental work. Successful multidisciplinary collaborations, progress in the experimental determination of three-dimensional structures of membrane proteins together with new algorithms for molecular simulations and the increasing speed and availability of supercomputers, have made possible a considerable progress in this area of biophysics. This review aims at highlighting some of the work in the area of potassium channels and molecular dynamics simulations where numerous fundamental questions about the structure, function, folding and dynamics of these systems remain as yet unresolved challenges.

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“…35 The Lennard-Jones interactions were cut off at 1 nm without shift or switch functions. Since truncation of electrostatic interactions is known to lead to pronounced artifacts in simulations of lipid bilayers, [36][37][38] the long-range interactions were handled using the particle-mesh Ewald (PME) method. 39,40 All simulations were performed in the NpT ensemble at 323 K and 1 bar.…”

Section: Model and Simulation Detailsmentioning

confidence: 99%

Effect of Monovalent Salt on Cationic Lipid Membranes As Revealed by Molecular Dynamics Simulations

Gurtovenko

Miettinen²,

Karttunen³

et al. 2005

J. Phys. Chem. B

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An atomic-scale understanding of cationic lipid membranes is required for development of gene delivery agents based on cationic liposomes. To address this problem, we recently performed molecular dynamics (MD) simulations of mixed lipid membranes comprised of cationic dimyristoyltrimethylammonium propane (DMTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC) (Biophys. J. 2004, 86, 3461-3472). Given that salt ions are always present under physiological conditions, here we focus on the effects of monovalent salt (NaCl) on cationic (DMPC/DMTAP) membranes. Using atomistic MD simulations, we found that saltinduced changes in membranes depend strongly on their composition. When the DMTAP mole fraction is small (around 6%), the addition of monovalent salt leads to a considerable compression of the membrane and to a concurrent enhancement of the ordering of lipid acyl chains. That is accompanied by reorientation of phosphatidylcholine headgroups in the outward normal direction and slight changes in electrostatic properties. We attribute these changes to complexation of DMPC lipids with Na + ions which penetrate deep into the membrane and bind to the carbonyl region of the DMPC lipids. In contrast, at medium and high molar fractions of cationic DMTAP (50 and 75%) a substantial positive surface charge density of the membranes prevents the binding of Na + ions, making such membranes almost insensitive to monovalent salt. Finally, we compare our results to the Poisson-Boltzmann theory. With the exception of the immediate vicinity of the bilayer plane, we found excellent agreement with the theory. This is as expected since unlike in the theoretical description the surface is now structured due to its atomic scale nature.

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Methodological Issues in Lipid Bilayer Simulations

Cited by 340 publications

References 51 publications

Critical Hydrogen Bond Formation for Activation of the Angiotensin II Type 1 Receptor

Critical Hydrogen Bond Formation for Activation of the Angiotensin II Type 1 Receptor

Molecular dynamics simulations of potassium channels

Effect of Monovalent Salt on Cationic Lipid Membranes As Revealed by Molecular Dynamics Simulations

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