Towards an understanding of membrane-mediated protein–protein interactions

Yiannourakou, Marianna; Marsella, Luca; Meyer, Frédérick de; Smit, Berend

doi:10.1039/b902190f

Cited by 17 publications

(23 citation statements)

References 41 publications

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“…In addition, there have been a number of computational investigations on the interactions of cylindrical inclusions and preassembled lipid membranes [32][33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48]. Our earlier investigations on the self-assembly of lipids and nanotubes with hairs at both ends demonstrated their selforganization into a hybrid vesicle or a bicelle, depending upon the relative fraction of NTs to lipids in the solution [49].…”

Section: Introductionmentioning

confidence: 95%

Interactions of End-functionalized Nanotubes with Lipid Vesicles: Spontaneous Insertion and Nanotube Self-Organization

Dutt¹,

Nayhouse²,

Kuksenok³

et al. 2011

CNANO

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Via Dissipative Particle Dynamics (DPD) approach, we study the spontaneous insertion of amphiphilic nanotubes into a lipid vesicle, which is immersed in a hydrophilic solvent. Individual lipids are composed of a hydrophilic head group and two hydrophobic tails. Each nanotube encompasses an ABA architecture, with a hydrophobic shaft (B) and two hydrophilic ends (A). To facilitate the selective transport of species through the nanotubes, we introduce hydrophilic tethers at one end of the tube. We show that nanotubes initially located in the host solvent spontaneously penetrate the vesicle's membrane and assume a transmembrane position, with the hydrophilic tethers extending from the surface of the vesicle. Adding nanotubes one at a time after the previous nanotube has been inserted, we characterize the interactions among the nanotubes that have self-assembled into the vesicle's membrane and focus on their clustering within the membrane. We also show that the nanotube insertion and clustering within the vesicle strongly affects the vesicle shape in cases of a sufficiently large number of tubes. Ultimately, these nanotube-lipid systems can be used for creating hybrid controlled release vesicles.

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Section: Introductionmentioning

confidence: 95%

Interactions of End-functionalized Nanotubes with Lipid Vesicles: Spontaneous Insertion and Nanotube Self-Organization

Dutt¹,

Nayhouse²,

Kuksenok³

et al. 2011

CNANO

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“…Information obtained from PMFs, such as the orientational dependence of the free energy of association, are necessary for parameterizing yet coarser (i.e. more approximate) models (for example those of Yiannourakou et al [33]), in order to enable simulation studies of the emergent properties of large, crowded and complex membrane models [47].…”

Section: Discussionmentioning

confidence: 99%

“…The umbrella sampling was performed using simulation windows in which one protein was restrained at relative positions with the desired inter-protein separation. We chose this measure as our reaction coordinate because it is a natural choice for characterizing the separation of two proteins and it would also enable the PMFs to be used to parameterize larger scale models, as done by Yiannourakou et al [33].…”

Section: Methodsmentioning

confidence: 99%

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The Free Energy Landscape of Dimerization of a Membrane Protein, NanC

et al. 2014

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Membrane proteins are frequently present in crowded environments, which favour lateral association and, on occasions, two-dimensional crystallization. To better understand the non-specific lateral association of a membrane protein we have characterized the free energy landscape for the dimerization of a bacterial outer membrane protein, NanC, in a phospholipid bilayer membrane. NanC is a member of the KdgM-family of bacterial outer membrane proteins and is responsible for sialic acid transport in E. coli. Umbrella sampling and coarse-grained molecular dynamics were employed to calculate the potentials of mean force (PMF) for a variety of restrained relative orientations of two NanC proteins as the separation of their centres of mass was varied. We found the free energy of dimerization for NanC to be in the range of to . Differences in the depths of the PMFs for the various orientations are related to the shape of the proteins. This was quantified by calculating the lipid-inaccessible buried surface area of the proteins in the region around the minimum of each PMF. The depth of the potential well of the PMF was shown to depend approximately linearly on the buried surface area. We were able to resolve local minima in the restrained PMFs that would not be revealed using conventional umbrella sampling. In particular, these features reflected the local organization of the intervening lipids between the two interacting proteins. Through a comparison with the distribution of lipids around a single freely-diffusing NanC, we were able to predict the location of these restrained local minima for the orientational configuration in which they were most pronounced. Our ability to make this prediction highlights the important role that lipid organization plays in the association of two NanCs in a bilayer.

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“…The interaction between the peptides was shown to be strongly oscillatory, due to packing of lipids in between them at short distances, and these oscillations persisted to larger separations in the lower-temperature gel phases. In principle, the resulting PMF can then be used to obtain a better understanding of membrane-mediated interactions [34], and this could be the subject of a future study.…”

Section: Discussionmentioning

confidence: 99%

Coarse-grained simulation of transmembrane peptides in the gel phase

Al-Lehyani

Grime

Bano

et al. 2013

Journal of Computational Physics

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We use Dissipative Particle Dynamics simulations, combined with parallel tempering and umbrella sampling, to investigate the potential of mean force between model transmembrane peptides in the various phases of a lipid bilayer, including the low-temperature gel phase. The observed oscillations in the effective interaction between peptides are consistent with the different structures of the surrounding lipid phases.

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Towards an understanding of membrane-mediated protein–protein interactions

Cited by 17 publications

References 41 publications

Interactions of End-functionalized Nanotubes with Lipid Vesicles: Spontaneous Insertion and Nanotube Self-Organization

Interactions of End-functionalized Nanotubes with Lipid Vesicles: Spontaneous Insertion and Nanotube Self-Organization

The Free Energy Landscape of Dimerization of a Membrane Protein, NanC

Coarse-grained simulation of transmembrane peptides in the gel phase

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