Four-Scale Description of Membrane Sculpting by BAR Domains

Arkhipov, Anton; Yin, Ying; Schulten, Klaus

doi:10.1529/biophysj.108.132563

Cited by 250 publications

(335 citation statements)

References 78 publications

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“…The same idea (in a slightly different implementation) has recently been applied by Arkhipov et al to a different solvent free CG lipid model. 212 These authors also find that within the obtained accuracy the measured bending modulus does not depend on tether radius.…”

Section: Example Applicationsmentioning

confidence: 57%

Multiscale modeling of emergent materials: biological and soft matter

Murtola

Bunker

Vattulainen

et al. 2009

Phys. Chem. Chem. Phys.

260

234

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On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models Moritz Winger, Daniel Trzesniak, Riccardo Baron and Wilfred F. In this review, we focus on four current related issues in multiscale modeling of soft and biological matter. First, we discuss how to use structural information from detailed models (or experiments) to construct coarse-grained ones in a hierarchical and systematic way. This is discussed in the context of the so-called Henderson theorem and the inverse Monte Carlo method of Lyubartsev and Laaksonen. In the second part, we take a different look at coarse graining by analyzing conformations of molecules. This is done by the application of self-organizing maps, i.e., a neural network type approach. Such an approach can be used to guide the selection of the relevant degrees of freedom. Then, we discuss technical issues related to the popular dissipative particle dynamics (DPD) method. Importantly, the potentials derived using the inverse Monte Carlo method can be used together with the DPD thermostat. In the final part we focus on solvent-free modeling which offers a different route to coarse graining by integrating out the degrees of freedom associated with solvent.

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Section: Example Applicationsmentioning

confidence: 57%

Multiscale modeling of emergent materials: biological and soft matter

Murtola

Bunker

Vattulainen

et al. 2009

Phys. Chem. Chem. Phys.

260

234

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“…These theories showed that two undeformable parallel rods undergo an attractive interaction, but the interaction is repulsive for a perpendicular orientation. The adsorption and assembly of BAR domains have been investigated using atomic and coarse-grained molecular simulations [48][49][50]. Further, tubular formation via membrane protrusion was simulated using a dynamically triangulated membrane model [51,52] and meshless membrane models [53,54].…”

Section: Introductionmentioning

confidence: 99%

Acceleration and suppression of banana-shaped-protein-induced tubulation by addition of small membrane inclusions of isotropic spontaneous curvatures

Noguchi

2017

Soft Matter

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The membrane tubulation induced by banana-shaped protein rods is investigated by using coarsegrained meshless membrane simulations. It is found that the tubulation is promoted by laterally isotropic membrane inclusions that generate the same sign of spontaneous curvature as the adsorbed protein rods. The inclusions are concentrated in the tubules and reduce the bending energy of the tip of the tubules. On the other hand, the inclusions with an opposite curvature suppress the tubulation by percolated-network formation at a high protein-rod density while they induce a spherical membrane bud at a low rod density. When equal amounts of the two types of inclusions (with positive and negative curvatures) are added, their effects cancel each other for the first short period but later the tubulation is slowly accelerated. A positive surface tension suppresses the tubulation. Out results suggest that the cooperation of scaffolding of BAR (Bin/Amphiphysin/Rvs) domains and isotropic membrane inclusions is important for the tubulation.

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“…Atomic and coarse-grained molecular simulations [40][41][42][43][44][45] have been employed to investigate molecular-scale interactions between BAR proteins and lipids. The scaffold formation [43] and linear assembly [44] of BAR domains have been demonstrated.…”

Section: Introductionmentioning

confidence: 99%

Shape deformation of lipid membranes by banana-shaped protein rods: Comparison with isotropic inclusions and membrane rupture

Noguchi

2016

Phys. Rev. E

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The assembly of curved protein rods on fluid membranes is studied using implicit-solvent meshless membrane simulations. As the rod curvature increases, the rods on a membrane tube assemble along the azimuthal direction first and subsequently along the longitudinal direction. Here, we show that both transition curvatures decrease with increasing rod stiffness. For comparison, curvature-inducing isotropic inclusions are also simulated. When the isotropic inclusions have the same bending rigidity as the other membrane regions, the inclusions are uniformly distributed on the membrane tubes and vesicles even for large spontaneous curvature of the inclusions. However, the isotropic inclusions with much larger bending rigidity induce shape deformation and are concentrated on the region of a preferred curvature. For high rod density, high rod stiffness, and/or low line tension of the membrane edge, the rod assembly induces vesicle rupture, resulting in the formation of a high-genus vesicle. A gradual change in the curvature suppresses this rupture. Hence, large stress, compared to the edge tension, induced by the rod assembly is the key factor determining rupture. For rod curvature with the opposite sign to the vesicle curvature, membrane rupture induces inversion of the membrane, leading to division into multiple vesicles as well as formation of a high-genus vesicle.

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Four-Scale Description of Membrane Sculpting by BAR Domains

Cited by 250 publications

References 78 publications

Multiscale modeling of emergent materials: biological and soft matter

Multiscale modeling of emergent materials: biological and soft matter

Acceleration and suppression of banana-shaped-protein-induced tubulation by addition of small membrane inclusions of isotropic spontaneous curvatures

Shape deformation of lipid membranes by banana-shaped protein rods: Comparison with isotropic inclusions and membrane rupture

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