Suppressing membrane height fluctuations leads to a membrane-mediated interaction among proteins

Sapp, Kayla; Maibaum, Lutz

doi:10.1103/physreve.94.052414

Cited by 8 publications

(9 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Equilibrium techniques cannot describe active vesicle fluctuations due to the presence of non-conservative contact forces, so we turn to a dynamical membrane description. The Langevin equation governing membrane shape changes is given by [12,16,41] ∂h(x, t)…”

mentioning

confidence: 99%

Active Contact Forces Drive Nonequilibrium Fluctuations in Membrane Vesicles

Takatori

Sahu

2020

Phys. Rev. Lett.

View full text Add to dashboard Cite

We analyze the non-equilibrium shape fluctuations of giant unilamellar vesicles encapsulating motile bacteria. Owing to bacteria-membrane collisions, we experimentally observe a significant increase in the magnitude of membrane fluctuations at low wave numbers, compared to the wellknown thermal fluctuation spectrum. We interrogate these results by numerically simulating membrane height fluctuations via a modified Langevin equation, which includes bacteria-membrane contact forces. Taking advantage of the length and time scale separation of these contact forces and thermal noise, we further corroborate our results with an approximate theoretical solution to the dynamical membrane equations. Our theory and simulations demonstrate excellent agreement with non-equilibrium fluctuations observed in experiments. Moreover, our theory reveals that the fluctuation-dissipation theorem is not broken by the bacteria; rather, membrane fluctuations can be decomposed into thermal and active components.arXiv:1911.01337v1 [cond-mat.soft]

show abstract

mentioning

confidence: 99%

Active Contact Forces Drive Nonequilibrium Fluctuations in Membrane Vesicles

Takatori

Sahu

2020

Phys. Rev. Lett.

View full text Add to dashboard Cite

show abstract

“…Our implicit lipid model can be combined with complex networks of protein-protein interactions to efficiently simulate a range of systems involving reversible localization to the membrane, such as models of clathrin-cage assembly [7,35,61,62] and cell polarization [37], or experiments involving binding and oligomerization on membranes [63]. Integration with continuum models of surfaces, as we have done here, is especially critical for developing quantitative and dynamical models of membrane dynamics as they are driven by proteins [64][65][66][67].…”

Section: ⅴ Discussion/conclusionmentioning

confidence: 99%

An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology

Yogurtcu

Kothari

et al. 2019

Preprint

View full text Add to dashboard Cite

Localization of proteins to a membrane is an essential step in a broad range of biological processes such as signaling, virion formation, and clathrin-mediated endocytosis. The strength and specificity of proteins binding to a membrane depend on the lipid composition. Single-particle reaction-diffusion methods offer a powerful tool for capturing lipid-specific binding to membrane surfaces by treating lipids explicitly as individual diffusible binding sites. However, modeling lipid particle populations is expensive. Here we present an algorithm for reversible binding of proteins to continuum surfaces with implicit lipids, providing dramatic speed-ups to many body simulations. Our algorithm can be readily integrated into most reaction-diffusion software packages. We characterize changes to kinetics that emerge from explicit versus implicit lipids as well as surface adsorption models, showing excellent agreement between our method and the full explicit lipid model. Compared to models of surface adsorption, which couple together binding affinity and lipid concentration, our implicit lipid model decouples them to provide more flexibility for controlling surface binding properties and lipid inhomogeneity, and thus reproducing binding kinetics and equilibria. Crucially, we demonstrate our method's application to membranes of arbitrary curvature and topology, modeled via a subdivision limit surface, again showing excellent agreement with explicit lipid simulations. Unlike adsorption models, our method retains the ability to bind lipids after proteins are localized to the surface (through e.g. a protein-protein interaction), which can greatly increase stability of multi-protein complexes on the surface. Our method will enable efficient cell-scale simulations involving proteins localizing to realistic membrane models, which is a critical step for predictive modeling and quantification of in vitro and in vivo dynamics. Ⅰ. Introduction:Proteins localize to membranes via multiple different binding modes, including recognition and binding to highly specific lipid head-groups (e.g. PI(4,5)P 2 ) [1], electrostatically driven adherence to negatively charged membranes [2] (as performed by many BAR-domain proteins) [3,4], and binding to membrane-inserted proteins (e.g. Ras) [5,6]. Once proteins have localized to the surface, they can be further stabilized by interactions with additional lipids or transmembrane proteins, and these subsequent binding events are effectively two dimensional (2D) in their search [6,7]. Capturing these various forms of membrane binding is critical for effective kinetic and spatial modeling of cell-scale systems with quantitative comparison to experiment, both in equilibrium and non-equilibrium systems. Because molecular modeling approaches that could capture the fundamental electrostatic or hydrophobic nature of these interactions are too expensive at this scale [8,9], rate-based approaches such as reaction-diffusion provide a powerful alternative [10][11][12][13][14]. These modeling approaches can be us...

show abstract

“…We conclude our theoretical developments for single-component lipid membranes by discussing the coupling of the membrane equations of motion with the surrounding fluid. While the bulk fluid provides an additional dissipative mechanism via the bulk viscosity and dominates dissipation for long wavelength undulations [79][80][81][82], the bulk fluid can contribute negligibly in systems with membrane deformations on the order of five microns or less [39,52,53]. Consequently, the surrounding fluid can sometimes be excluded when studying small length scale phenomena.…”

Section: Coupling To Bulk Fluidmentioning

confidence: 99%

“…A computational implementation of the aforementioned conditions at a fluid-structure interface is provided in [83] in the context of liquid menisci and elastic membranes. For small deformations of the membrane, one can use the Oseen tensor to couple the bulk fluid and the membrane, as done in [80,81].…”

Section: Coupling To Bulk Fluidmentioning

confidence: 99%

Irreversible thermodynamics of curved lipid membranes

2017

View full text Add to dashboard Cite

The theory of irreversible thermodynamics for arbitrarily curved lipid membranes is presented here. The coupling between elastic bending and irreversible processes such as intramembrane lipid flow, intramembrane phase transitions, and protein binding and diffusion is studied. The forms of the entropy production for the irreversible processes are obtained, and the corresponding thermodynamic forces and fluxes are identified. Employing the linear irreversible thermodynamic framework, the governing equations of motion along with appropriate boundary conditions are provided.

show abstract

Suppressing membrane height fluctuations leads to a membrane-mediated interaction among proteins

Cited by 8 publications

References 52 publications

Active Contact Forces Drive Nonequilibrium Fluctuations in Membrane Vesicles

Active Contact Forces Drive Nonequilibrium Fluctuations in Membrane Vesicles

An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology

Irreversible thermodynamics of curved lipid membranes

Contact Info

Product

Resources

About