Molecular Dynamics Simulation of a Phospholipid Micelle

Wendoloski, John J.; Kimatian, Stephen J.; Schutt, Clarence E.; Salemme, F. R.

doi:10.1126/science.2916118

Cited by 103 publications

(66 citation statements)

References 19 publications

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“…Micelles are aggregates of amphiphilic molecules whose hydrophilic head groups are exposed to solvent and whose aliphatic chains pack compactly in the hydrophobic micelle interior [77]. Even though the palette of such amphiphilic molecules is broad, for biological or biochemical applications single-tailed species are most commonly used to mimic a lipid bilayer environment.…”

Section: Micelle Simulationsmentioning

confidence: 99%

Computer Simulation of Antimicrobial Peptides

Mátyus

Kandt²,

Tieleman³

2007

CMC

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Naturally occurring and synthetic peptides may be a novel class of clinically useful antibiotics. A large body of experimental data on structure function relationships for such peptides is available, but the molecular mechanism of their action remains elusive in most cases. Computer simulations can give detailed insights into the interactions between peptides and lipid bilayers, at least one crucial step in the antimicrobial mechanism. Here we review recent simulations of antimicrobial peptides and discuss potential future contributions of computer simulations in understanding and ultimately designing antimicrobial peptides.

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Section: Micelle Simulationsmentioning

confidence: 99%

Computer Simulation of Antimicrobial Peptides

Mátyus

Kandt²,

Tieleman³

2007

CMC

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“…Other aqueous micellar systems have also been studied by Molecular Dynamics simulations, such as octyl glucoside [21], dodecylphosphocholine [22][23][24], lysophosphatidylethanolamine [25], sodium pentadecafluorooctanoate [26], sodium dodecyl sulfate [27][28][29] and 2,3,6,7,10,11-hexakis(1,4,7-trioxaoctyl)triphenylene [30]. Except for sodium dodecyl sulfate [27][28][29] all micellar systems studied are non-ionic, what makes computer simulations comparatively less time consuming, since long range interactions may be safely ignored when ionic species are absent.…”

Section: Introductionmentioning

confidence: 99%

Molecular dynamics simulation of the sodium octanoate micelle in aqueous solution

Moura

Freitas

2005

Chemical Physics Letters

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We have performed a series of 10 ns Molecular Dynamics simulations of the sodium octanoate micelle in aqueous solution in the constant NpT ensemble, at p = 1 bar and T = 300 K. Two molecular topologies were studied, one with all internal degrees of freedom and the other constraining bond stretching and angle bending degrees of freedom. Two Lennard-Jones parameters for sodium ions, namely the OPLS andÅqvist parameters, were used. The results show an artificial enhancement of stable sodium bridges between octanoate anions when the OPLS parameters for sodium are used. TheÅqvist parameters give a micellar structure in good agreement with experimental and thermodynamical evidences. It is also observed that the aggregation of monomers is strongly dependent on the molecular topology. When theÅqvist parameters were employed, the model system without constraining geometry had one dissociated monomer after 10 ns, while the model system with bond length and bond angle constraining had five dissociated monomers after a 10 ns trajectory.

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“…Brownian dynamics (30) and mean field stochastic boundary molecular dynamics ( ( 49), and Xiang (50). In addition, MD simulations have also been reported on quasi-spherical micelles in the presence of water (51)(52)(53)(54)(55)(56).…”

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confidence: 96%

Interaction of an Amphiphilic Peptide with a Phospholipid Bilayer Surface by Molecular Dynamics Simulation Study

Huang¹,

Loew²

1995

Journal of Biomolecular Structure and Dynamics

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Corticotropin-releasing factor (CRF) is the principal neuroregulator of adrenocorticotropic hormone (ACTH) secretion. Previous experiments have demonstrated that CRF binds avidly to the surface of single egg phosphatidylcholine vesicles and its amphiphilic secondary structure might play an important role in the function. In this study, the interaction of the residues 13-41 in human CRF with the surface of a DOPC bilayer was investigated by molecular dynamics (MD) simulation in order to understand the role of the membrane surface in the formation of the amphiphilic alpha helix as well as to determine the effects of the peptide on the lipid bilayer. The model used included 60 DOPC molecules, 1 helical peptide (CRF13-41) on the bilayer surface, and explicit waters of solvation in the lipid polar head group regions, together with constant-volume periodic boundary conditions in three dimensions. The MD simulation was carried out for 510 ps. In addition, CRF13-41, initially in a helical form, was simulated in vacuo as a control. The results indicate that while it was completely unstable in vacuo, the peptide helical form was generally maintained on the bilayer surface, but with distortions near the terminal ends. The peptide was confined to the bilayer headgroup/water region, similar to that reported from neutron diffraction measurement of tripeptides bound to the phosphatidylcholine bilayer surface (Ref 1). The amphiphilicity of the peptide matched that of the bilayer headgroup environment, with the hydrophilic side oriented toward water and the hydrophobic side making contact with the bilayer hydrocarbon core. These results support the hypothesis that the amphiphilic environment of a membrane surface is important in the induction of peptide amphiphilic alpha-helical secondary structure. Two major effects of the peptide on the lipids were found: the first CH2 segment in the lipid chains was significantly disordered and the lipid headgroup distribution was broadened towards the water region.

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Molecular Dynamics Simulation of a Phospholipid Micelle

Cited by 103 publications

References 19 publications

Computer Simulation of Antimicrobial Peptides

Computer Simulation of Antimicrobial Peptides

Molecular dynamics simulation of the sodium octanoate micelle in aqueous solution

Interaction of an Amphiphilic Peptide with a Phospholipid Bilayer Surface by Molecular Dynamics Simulation Study

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