All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields

Skjevik, Åge A.; Madej, Benjamin D.; Dickson, Callum J.; Teigen, Knut; Walker, Ross C.; Gould, Ian R.

doi:10.1039/c4cc09584g

Cited by 55 publications

(57 citation statements)

References 32 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The same initial random configuration of lipids, ions and water was used in all three repeats, but different random seeds were generated in each case. The following strategy was applied: 14 (I) 10000 steps of minimization; (II) 10 ns simulation at production temperature with isotropic pressure scaling ( NPT ) and a time step of 0.5 fs; (III) 10 ns simulation at production temperature with isotropic pressure scaling ( NPT ) and a time step of 1.0 fs; (IV) simulation at production temperature with anisotropic pressure scaling ( NPT ) and 2.0 fs time step. The production temperature (Table 1) was kept above the phase transition temperature of the relevant phospholipid across all three simulation steps.…”

Section: Methodsmentioning

confidence: 99%

“…10 In a recently published communication, 14 we showed for the first time bilayer self-assembly in unbiased MD simulations where all atoms are explicitly treated. Four types of zwitterionic phospholipids assembled from random configurations into stable bilayers characterized by structural properties in good agreement with experiment.…”

Section: Introductionmentioning

confidence: 91%

“…In the present work we significantly expand upon the subject introduced in the communication 14 through the inclusion of a broader range of lipids, a more comprehensive structural analysis of assembled bilayers (on the level of lipid force field validation papers) and the addition of a third all-atom lipid force field, Slipids. 17–19 The selection of lipids has been extended to include four types of negatively charged phospholipids – palmitoyl-oleoyl-phosphatidylserine (POPS), palmitoyl-oleoyl-phosphatidylglycerol (POPG), dioleoyl-phosphatidylserine (DOPS) and dioleoyl-phosphatidylglycerol (DOPG) – which together with the original set (dipalmitoyl-phosphatidylcholine (DPPC), palmitoyl-oleoyl-phosphatidylcholine (POPC), dioleoyl-phosphatidylcholine (DOPC) and palmitoyl-oleoyl-phosphatidylethanolamine (POPE)) ensures that head groups of varying charge (zwitterionic/anionic) and size are represented, as well as hydrophobic tail portions with varying degrees of unsaturation.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Simulation of lipid bilayer self-assembly using all-atom lipid force fields

Skjevik

Madej

Dickson

et al. 2016

Phys. Chem. Chem. Phys.

Self Cite

View full text Add to dashboard Cite

In this manuscript we expand significantly on our earlier communication by investigating the bilayer self-assembly of eight different types of phospholipids in unbiased molecular dynamics (MD) simulations using three widely used all-atom lipid force fields. Irrespective of the underlying force field, the lipids are shown to spontaneously form stable lamellar bilayer structures within 1 microsecond, the majority of which display properties in satisfactory agreement with the experimental data. The lipids self-assemble via the same general mechanism, though at formation rates that differ both between lipid types, force fields and even repeats on the same lipid/force field combination. In addition to zwitterionic phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipids, anionic phosphatidylserine (PS) and phosphatidylglycerol (PG) lipids are represented. To our knowledge this is the first time bilayer self-assembly of phospholipids with negatively charged head groups is demonstrated in all-atom MD simulations.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 91%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Simulation of lipid bilayer self-assembly using all-atom lipid force fields

Skjevik

Madej

Dickson

et al. 2016

Phys. Chem. Chem. Phys.

Self Cite

View full text Add to dashboard Cite

show abstract

“…For instance, a variety of atomistic force fields, including CHARMM, [1][2][3] AMBER, [4] and GROMOS, [5] have been extensively used to simulate the structural and dynamic properties of lipid membranes. between cell interior and exterior.…”

Section: Introductionmentioning

confidence: 99%

Extension of CAVS coarse‐grained model to phospholipid membranes: The importance of electrostatics

2017

View full text Add to dashboard Cite

It is evident from experiment that electrostatic potential (or dipole potential) is positive inside PC or PE lipid bilayers in the absence of ions. MARTINI coarse-grained (CG) model, which has been widely used in simulating physical properties of lipid bilayers, fails to reproduce the positive value for the dipole potential in the membrane interior. Although the total dipole potential can be correctly described by the BMW/MARTINI model, the contribution from the ester dipoles, playing a nontrivial role in the electrostatic potential across lipid membranes, is neglected by this hybrid approach. In the ELBA CG model, the role of the ester dipoles is considered, but it is overweighed because various atomistic models have consistently shown that water is actually the leading contributor of dipole potential. Here, we present a CG approach by combining the BMW-like water model (namely CAVS model) with the ELBA-like lipid model proposed in this work. Our CG model was designed not only to correctly reproduce the positive values for the dipole potential inside PC and PE lipid bilayers but also to properly balance the individual contributions from the ester dipoles and water, surmounting the limitations of current CG models in the calculations of dipole potential. © 2017 Wiley Periodicals, Inc.

show abstract

“…The MM potential represents a phenomenological parametrization of the potential energy of a system and is widely used to describe structure and properties of macromolecular systems, such as polypeptides [43][44][45][46][47], proteins [47][48][49][50][51], DNA [32,[52][53][54], lipids [51,[55][56][57], and many others. All physically important interactions in a system, i.e.…”

Section: Molecular Mechanics Potentialmentioning

confidence: 99%

Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

et al. 2016

View full text Add to dashboard Cite

Abstract. The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, we provide several illustrative case studies where dynamical topology is necessary. In particular, it is shown that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation-or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems.

show abstract

All-atom lipid bilayer self-assembly with the AMBER and CHARMM lipid force fields

Cited by 55 publications

References 32 publications

Simulation of lipid bilayer self-assembly using all-atom lipid force fields

Simulation of lipid bilayer self-assembly using all-atom lipid force fields

Extension of CAVS coarse‐grained model to phospholipid membranes: The importance of electrostatics

Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

Contact Info

Product

Resources

About