A Multi-Scale Approach to Membrane Remodeling Processes

Weria Pezeshkian, Melanie König, Siewert J. Marrink, John H. Ipsen*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

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.

Original languageEnglish
Article number59
JournalFrontiers in Molecular Biosciences
Volume6
Number of pages7
ISSN2296-889X
DOIs
Publication statusPublished - 23. Jul 2019

Fingerprint

Membranes
Shiga Toxin
Molecular Dynamics Simulation
Conformations
Molecular dynamics
Membrane Proteins
Proteins
Thin films
Atoms

Keywords

  • dynamic triangulated surfaces
  • implicit protein model
  • Martini coarse-grain simulation
  • membrane remodeling
  • Shiga toxin
  • simulation of continuum model

Cite this

Pezeshkian, Weria ; König, Melanie ; Marrink, Siewert J. ; Ipsen, John H. / A Multi-Scale Approach to Membrane Remodeling Processes. In: Frontiers in Molecular Biosciences. 2019 ; Vol. 6.
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A Multi-Scale Approach to Membrane Remodeling Processes. / Pezeshkian, Weria; König, Melanie; Marrink, Siewert J.; Ipsen, John H.

In: Frontiers in Molecular Biosciences, Vol. 6, 59, 23.07.2019.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - A Multi-Scale Approach to Membrane Remodeling Processes

AU - Pezeshkian, Weria

AU - König, Melanie

AU - Marrink, Siewert J.

AU - Ipsen, John H.

PY - 2019/7/23

Y1 - 2019/7/23

N2 - 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.

AB - 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.

KW - dynamic triangulated surfaces

KW - implicit protein model

KW - Martini coarse-grain simulation

KW - membrane remodeling

KW - Shiga toxin

KW - simulation of continuum model

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DO - 10.3389/fmolb.2019.00059

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JO - Frontiers in Molecular Biosciences

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SN - 2296-889X

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