Simulating realistic membrane shapes

Pezeshkian, Weria; Marrink, Siewert J.

doi:10.1016/j.ceb.2021.02.009

Cited by 58 publications

(60 citation statements)

References 71 publications

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“…In the past few decades, many powerful computational methods have been developed for the description of biological structures and functions. A large number of biological phenomena are now accessible for computational analysis, ranging from biomolecular dynamics, enzymatic processes, and virus assembly to the structure of small organelles [ 12 , 13 , 14 ], making computer simulation techniques an indispensable tool. Additionally, they are used for biomolecular engineering and drug design [ 15 , 16 , 17 , 18 ], Nevertheless, all computational methods have their strength in specific ranges of time and length scales, while they are inapplicable outside these ranges.…”

Section: Methodsmentioning

confidence: 99%

“…( C ) Mesoscopic simulations of hundreds of toxin particles remodeling the membrane shape (picture is obtained from ref. [ 13 ]). ( D ) Back mapping structure from “C” to CG model for investigations with molecular detail (picture is obtained from ref.…”

Section: Figurementioning

confidence: 99%

“…( D ) Back mapping structure from “C” to CG model for investigations with molecular detail (picture is obtained from ref. [ 13 ]).…”

Section: Figurementioning

confidence: 99%

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Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell

Pezeshkian

Shillcock

Ipsen

2021

Toxins

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Many bacteria secrete toxic protein complexes that modify and disrupt essential processes in the infected cell that can lead to cell death. To conduct their action, these toxins often need to cross the cell membrane and reach a specific substrate inside the cell. The investigation of these protein complexes is essential not only for understanding their biological functions but also for the rational design of targeted drug delivery vehicles that must navigate across the cell membrane to deliver their therapeutic payload. Despite the immense advances in experimental techniques, the investigations of the toxin entry mechanism have remained challenging. Computer simulations are robust complementary tools that allow for the exploration of biological processes in exceptional detail. In this review, we first highlight the strength of computational methods, with a special focus on all-atom molecular dynamics, coarse-grained, and mesoscopic models, for exploring different stages of the toxin protein entry mechanism. We then summarize recent developments that are significantly advancing our understanding, notably of the glycolipid–lectin (GL-Lect) endocytosis of bacterial Shiga and cholera toxins. The methods discussed here are also applicable to the design of membrane-penetrating nanoparticles and the study of the phenomenon of protein phase separation at the surface of the membrane. Finally, we discuss other likely routes for future development.

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Section: Methodsmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

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Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell

Pezeshkian

Shillcock

Ipsen

2021

Toxins

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“…MD can be used to simulate the dynamics of both symmetric and asymmetric lipid bilayers under different conditions. The molecular models used by MD can either be fully atomistic or more coarse-grained, thus offering different levels of detail and the opportunity to examine various modes of membrane dynamics by simulating bilayers of different sizes and shapes [5,[81][82][83].…”

Section: Molecular Dynamics (Md) Simulations Used To Model Asymmetric Membranesmentioning

confidence: 99%

Model Membrane Systems Used to Study Plasma Membrane Lipid Asymmetry

et al. 2021

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It is well known that the lipid distribution in the bilayer leaflets of mammalian plasma membranes (PMs) is not symmetric. Despite this, model membrane studies have largely relied on chemically symmetric model membranes for the study of lipid–lipid and lipid–protein interactions. This is primarily due to the difficulty in preparing stable, asymmetric model membranes that are amenable to biophysical studies. However, in the last 20 years, efforts have been made in producing more biologically faithful model membranes. Here, we review several recently developed experimental and computational techniques for the robust generation of asymmetric model membranes and highlight a new and particularly promising technique to study membrane asymmetry.

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“…However, the deep understanding of the factors governing the formation of such complex amphiphilic arrangements is still unknown, partially due to the scattered nature and incorrect annotations of reported data. On the other hand, considerable advancement in recognition of intrinsic and extrinsic factors playing a role in elementary membrane bending and curvature sensing has been made, forming a solid foundation for further studies in understanding how the complex architecture of cubic membranes controls cellular traffic (Assoian et al, 2019;Callens et al, 2020;Campelo et al, 2014;Jarsch et al, 2016;Kozlov et al, 2014;Lou et al, 2018;Pezeshkian and Marrink, 2021;Raven, 2021;Simunovic et al, 2019;van Zanten and Mayor, 2015;Zimmerberg and Kozlov, 2006) Recently there is a growing interest in the possibility of obtaining nature-inspired and, therefore, stable, large length-scaled cubic systems (>50 nm) to develop concepts to tackle different multidisciplinary issues and healthcare problems (reviewed in Mezzenga et al, 2019). Naturally occurring cubic systems are an important inspiration for designing biomimetic nanostructures used in, e.g., drug delivery systems (Mulet et al, 2013;Porras-Gomez and Leal, 2019), controlled release of solubilized molecules (Clulow et al, 2020), material science (Han and Che, 2018;Kresge et al, 1992), and in the determination of protein structure (Speziale et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

SPIRE, Surface Projection Image Recognition Environment for bicontinuous phases: application for plastid cubic membranes

Hain

Bykowski

Saba

et al. 2021

Preprint

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Bicontinuous membranes in cell organelles epitomise nature's ability to create complex functional nanostructures. Like their synthetic counterparts, these membranes are characterised by continuous membrane sheets draped onto topologically complex saddle-shaped surfaces with a periodic network-like structure. In cell organelles, their structure sizes around 50-500 nm and fluid nature make Transmission Electron Microscopy (TEM) the analysis method of choice to decipher nanostructural features. Here we present a tool to identify bicontinuous structures from TEM sections by comparison to mathematical nodal surface models, including the hexagonal lonsdaleite geometry. Our approach, following pioneering work by Deng and Mieczkowski (1998), creates synthetic TEM images of known bicontinuous geometries for interactive structure identification. We apply the method to the inner membrane network in plant cell chloroplast precursors and achieve a robust identification of the bicontinuous diamond surface as the dominant geometry in several plant species. This represents an important step in understanding their as yet elusive structure-function relationship.

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Simulating realistic membrane shapes

Cited by 58 publications

References 71 publications

Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell

Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell

Model Membrane Systems Used to Study Plasma Membrane Lipid Asymmetry

SPIRE, Surface Projection Image Recognition Environment for bicontinuous phases: application for plastid cubic membranes

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