Numerical insights into the phase diagram of p-atic membranes with spherical topology

Hansen, Allan Grønhøj; Ramakrishnan, N.; Kumar, P. B. Sunil; Ipsen, John Hjort

doi:10.1140/epje/i2017-11515-7

Cited by 4 publications

(4 citation statements)

References 41 publications

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“…These features are well verified in ref. 82 where the simulation results agrees well with theory in analytically tractable limits.…”

Section: Methodssupporting

confidence: 74%

Mesoscale simulation of biomembranes with FreeDTS

Pezeshkian,

Ipsen

2024

Nat Commun

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We present FreeDTS software for performing computational research on biomembranes at the mesoscale. In this software, a membrane is represented by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins. Several algorithms are included in the software to simulate complex membranes at different conditions such as framed membranes with constant tension, vesicles and high-genus membranes with various fixed volumes or constant pressure differences and applying external forces to membrane regions. Furthermore, the software allows the user to turn off the shape evolution of the membrane and focus solely on the organization of proteins. As a result, we can take realistic membrane shapes obtained from, for example, cryo-electron tomography and backmap them into a finer simulation model. In addition to many biomembrane applications, this software brings us a step closer to simulating realistic biomembranes with molecular resolution. Here we provide several interesting showcases of the power of the software but leave a wide range of potential applications for interested users.

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“…These features are well verified in ref. 82 where the simulation results agrees well with theory in analytically tractable limits.…”

Section: Methodssupporting

confidence: 74%

Mesoscale simulation of biomembranes with FreeDTS

Pezeshkian,

Ipsen

2024

Nat Commun

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“…Q ij is the least common multiple of the degree of the i,j proteins symmetry in the plane of the membrane ( N ). Note that the interaction energy in Equation (5) can also be used to model lipid domain formations in multicomponent membranes (Ramakrishnan et al, 2010; Hansen et al, 2017).…”

Section: Methodsmentioning

confidence: 99%

A Multi-Scale Approach to Membrane Remodeling Processes

Pezeshkian

König

Marrink

et al. 2019

Front. Mol. Biosci.

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We present a multi-scale simulation procedure to describe membrane-related biological processes that span over a wide range of length scales. At macroscopic length-scale, a membrane is described as a flexible thin film modeled by a dynamic triangulated surface with its spatial conformations governed by an elastic energy containing only a few model parameters. An implicit protein model allows us to include complex effects of membrane-protein interactions in the macroscopic description. The gist of this multi-scale approach is a scheme to calibrate the implicit protein model using finer scale simulation techniques e.g., all atom and coarse grain molecular dynamics. We previously used this approach and properly described the formation of membrane tubular invaginations upon binding of B-subunit of Shiga toxin. Here, we provide a perspective of our multi-scale approach, summarizing its main features and sketching possible routes for future development.

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“…These studies cover a large number of protein domains that include the BAR family, ENTH, and Shiga toxins. Ramakrishnan et al [164–168] have explored the anisotropic elasticity based nematic membrane model to study protein-induced shape changes in vesicular membranes. In the anisotropic elasticity model, the protein is represented as an in-plane nematic field whose local orientation is denoted n̂ .…”

Section: Membrane Remodeling At the Cellular Scalementioning

confidence: 99%

“…Ramakrishnan et al [164][165][166][167][168] have explored the anisotropic elasticity based nematic membrane model to study proteininduced shape changes in vesicular membranes. In the anisotropic elasticity model, the protein is represented as an in-plane nematic field whose local orientation is denoted n. The presence of such in-plane fields have been previously considered in the study of orientational order in lipid membranes that arise due to the presence of anisotropic phospholipids [169][170][171], and lipid tilt and chirality [172][173][174].…”

Section: Membrane Remodeling At the Cellular Scalementioning

confidence: 99%

Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales

Ramakrishnan

Bradley

Tourdot

et al. 2018

J. Phys.: Condens. Matter

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At the micron scale, where cell organelles display an amazing complexity in their shape and organization, the physical properties of a biological membrane can be better-understood using continuum models subject to thermal (stochastic) undulations. Yet, the chief orchestrators of these complex and intriguing shapes are a specialized class of membrane associating often peripheral proteins called curvature remodeling proteins (CRPs) that operate at the molecular level through specific protein-lipid interactions. We review multiscale methodologies to model these systems at the molecular as well as at the mesoscopic and cellular scales, and also present a free energy perspective of membrane remodeling through the organization and assembly of CRPs. We discuss the morphological space of nearly planar to highly curved membranes, methods to include thermal fluctuations, and review studies that model such proteins as curvature fields to describe the emergent curved morphologies. We also discuss several mesoscale models applied to a variety of cellular processes, where the phenomenological parameters (such as curvature field strength) are often mapped to models of real systems based on molecular simulations. Much insight can be gained from the calculation of free energies of membranes states with protein fields, which enable accurate mapping of the state and parameter values at which the membrane undergoes morphological transformations such as vesiculation or tubulation. By tuning the strength, anisotropy, and spatial organization of the curvature-field, one can generate a rich array of membrane morphologies that are highly relevant to shapes of several cellular organelles. We review applications of these models to budding of vesicles commonly seen in cellular signaling and trafficking processes such as clathrin mediated endocytosis, sorting by the ESCRT protein complexes, and cellular exocytosis regulated by the exocyst complex. We discuss future prospects where such models can be combined with other models for cytoskeletal assembly, and discuss their role in understanding the effects of cell membrane tension and the mechanics of the extracellular microenvironment on cellular processes.

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Numerical insights into the phase diagram of p-atic membranes with spherical topology

Cited by 4 publications

References 41 publications

Mesoscale simulation of biomembranes with FreeDTS

Mesoscale simulation of biomembranes with FreeDTS

A Multi-Scale Approach to Membrane Remodeling Processes

Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales

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