Computer simulation study of fullerene translocation through lipid membranes

Wong-ekkabut, Jirasak; Baoukina, Svetlana; Triampo, Wannapong; Tang, I‐Ming; Tieleman, D. Peter; Monticelli, Luca

doi:10.1038/nnano.2008.130

Cited by 472 publications

(522 citation statements)

References 42 publications

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“…However, the smaller κ seen in our simulations for DOPE suggests that PE headgroup dehydration at the upper (negative intrinsic curvature) leaflet is more favorable than for DOPC, consistent with the smaller hydration shells of the PE headgroups, which imply smaller hydration repulsion. At low curvature, our κ results also agree with previous simulation results [7,21,[44][45][46][47][48][49][50][51][52] (a table is presented in the Supplemental Material [29]). …”

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confidence: 90%

Exploiting Lipid Permutation Symmetry to Compute Membrane Remodeling Free Energies

2016

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A complete physical description of membrane remodeling processes, such as fusion or fission, requires knowledge of the underlying free energy landscapes, particularly in barrier regions involving collective shape changes, topological transitions, and high curvature, where Canham-Helfrich (CH) continuum descriptions may fail. To calculate these free energies using atomistic simulations, one must address not only the sampling problem due to high free energy barriers, but also an orthogonal sampling problem of combinatorial complexity stemming from the permutation symmetry of identical lipids. Here, we solve the combinatorial problem with a permutation reduction scheme to map a structural ensemble into a compact, nondegenerate subregion of configuration space, thereby permitting straightforward free energy calculations via umbrella sampling. We applied this approach, using a coarse-grained lipid model, to test the CH description of bending and found sharp increases in the bending modulus for curvature radii below 10 nm. These deviations suggest that an anharmonic bending term may be required for CH models to give quantitative energetics of highly curved states. DOI: 10.1103/PhysRevLett.117.188102 Membrane remodeling is essential for many cellular transport functions, notably fusion [1] and fission [2]. However, despite continued interest, the underlying lipidic mechanisms and energetics are not fully understood. Atomistic and near-atomistic molecular dynamics (MD) simulations provide sufficient temporal and spatial resolution to probe lipidic mechanisms. However, standard MD fails to reach the high energy barriers (≫k B T) which often dictate mechanisms and kinetics. Biasing methods are thus required to address the sampling problem for high energy barriers.An additional and ubiquitous obstacle, in both describing and biasing lipidic transitions, is the N! degeneracy of lipid configuration space arising from the permutation symmetry of N identical lipids. The same combinatorial symmetry lies at the heart of the Gibbs paradox [3][4][5], which is resolved by a 1=N! scaling of the partition function, to account for physically indistinguishable (degenerate) states.In contrast to this straightforward analytical correction, this permutation symmetry poses a severe challenge to atomistic simulations and free energy calculations involving lipids: sampling the space of degenerate states (via self-diffusion) shrouds the collective structural changes of interest and precludes the use of lipidic collective coordinate biasing schemes. Accordingly, special purpose methods (that circumvent this hindrance) have been developed to direct lipidic transitions using boundary conditions [6,7], external guiding potentials [8,9], probe particles [10], density biasing [11,12], and single-lipid restraints [13,14].Here, we describe and apply a rigorous method to directly address this N! degeneracy, using permutation reduction (PR) [15,16]. The method exploits permutation symmetry by remapping structures from the full N! degenerate configur...

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confidence: 90%

Exploiting Lipid Permutation Symmetry to Compute Membrane Remodeling Free Energies

2016

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“…So far, experimental methods can provide for these systems only limited information at the molecular scale level. For this reason, several simulation studies involving CNT and lipid bilayers have been reported [17,18,[21][22][23][24][25][26][27]. On the contrary, molecular dynamics simulations based on atomistic or coarse-grained models can provide detailed information on these processes.…”

Section: Introductionmentioning

confidence: 99%

“…In particular, hydrophobic 4 nanopores [23], fullerenes [24,25], SWCNT [18], and the piercing mechanism of a single CNT into a model membrane [26] have been studies using CG models. The mechanism of spontaneous insertion of short pristine CNTs has been recently studied by Sansom et.…”

Section: Introductionmentioning

confidence: 99%

Spontaneous insertion of carbon nanotube bundles inside biomembranes: A hybrid particle-field coarse-grained molecular dynamics study

Sarukhanyan¹,

Roccatano²,

Kawakatsu³

et al. 2014

Chemical Physics Letters

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The processes of CNTs bundle formation and insertion/rearrangement inside lipid bilayers, as models of cellular membranes, is described and analyzed in details using simulations on the microsecond scale. Molecular Dynamics simulations employing hybrid particle-field models (MD-SCF) show that during the insertion process lipid molecules coat bundles surfaces The distortions of bilayers are more pronounced for systems undergoing to insertion of bundles made of longer CNTs. Interestingly, in this case, for the insertion of bundles in perpendicular orientation, it has been possible to observe, for the first time, a transient poration of the bilayer and a subsequent water percolation through it.

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“…16,23,29,30 These models were shown to be successful in predicting bulk material properties 31 as well as in describing molecular level phenomena. [32][33][34] In this paper we explore the effect of hydrophobic mismatch on the cross-angle distribution of simulated TM helices. We simulate a CG model of a TM a-helix that contains no specic residue information and explore its interactions under various hydrophobic mismatch conditions.…”

Section: Introductionmentioning

confidence: 99%

Lipid mediated packing of transmembrane helices – a dissipative particle dynamics study

Benjamini

Smit

2013

Soft Matter

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Interactions of transmembrane (TM) helices play a key role in many cell processes. The configuration and cross angle these helices adopt are traditionally attributed to specific residue interactions. We present a different approach, in which specific residues are disregarded, and the role of the membrane in TM helix packing is investigated. We introduce a coarse-grained model of TM helices and obtain their characteristic configurations in the membrane both as a single helix and as paired helices. Our analysis shows that hydrophobic mismatch has a substantial effect in determining not only the tilt angles of TM helices but also the cross angles between helix pairs, for a large range of hydrophobic mismatches. We discuss the origin of this effect as well as the deviations from the common trend. Additionally, we explore the effect of hydrophobic mismatch on the Potential of Mean Force (PMF) between TM helices and discuss the importance of helical geometry in forming crossed configurations. Our observations suggest that hydrophobic mismatch must be taken into account when analyzing configurations of TM helix pairs. Hydrophobic mismatch through its effect on helix tilt can explain many cross-angle distribution features, making the role of specific interactions in determining helix pair configurations less significant.

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Computer simulation study of fullerene translocation through lipid membranes

Cited by 472 publications

References 42 publications

Exploiting Lipid Permutation Symmetry to Compute Membrane Remodeling Free Energies

Exploiting Lipid Permutation Symmetry to Compute Membrane Remodeling Free Energies

Spontaneous insertion of carbon nanotube bundles inside biomembranes: A hybrid particle-field coarse-grained molecular dynamics study

Lipid mediated packing of transmembrane helices – a dissipative particle dynamics study

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