Modeling membranes in situ DOI Creative Commons
Chelsea M. Brown, ‪Siewert J. Marrink

Current Opinion in Structural Biology, Journal Year: 2024, Volume and Issue: 87, P. 102837 - 102837

Published: May 13, 2024

Molecular dynamics simulations of cellular membranes have come a long way-from simple model lipid bilayers to multicomponent systems capturing the crowded and complex nature real cell membranes. In this opinionated minireview, we discuss current challenge simulate in their native environment, situ, with prospect reaching level whole cells organelles using an integrative modeling framework.

Language: Английский

Molecular sorting on a fluctuating membrane DOI Creative Commons

Damiano Andreghetti,

Luca Dall’Asta, A. Gamba

et al.

SciPost Physics, Journal Year: 2025, Volume and Issue: 18(3)

Published: March 18, 2025

Molecular sorting in biological membranes is essential for proper cellular function. It also plays a crucial role the budding of enveloped viruses from host cells. We recently proposed that this process driven by phase separation, where formation and growth domains depend primarily on direct intermolecular interactions. In addition to these, Casimir-like forces—arising entropic effects fluctuating —may play significant molecular distillation process. Here, using combination theoretical analysis numerical simulations, we explore how forces between rigid membrane inclusions contribute sorting, particularly biologically relevant regime interactions are weak. Our results show these enhance reducing critical radius new facilitating capture molecules within domains. identify relative rigidity supermolecular as key parameter controlling efficiency, offering insights into physical principles underlying systems.

Language: Английский

Citations

1
Non-ideal mixing of lipids: A molecular dynamics perspective DOI
Yelyzaveta Berezovska, Raisa Kociurzynski, Fabrice Thalmann

et al.

The Journal of Chemical Physics, Journal Year: 2025, Volume and Issue: 162(6)

Published: Feb. 12, 2025

Lipid membranes have complex compositions, and modeling the thermodynamic properties of multi-component lipid systems remains a remote goal. In this work, we attempt to describe thermodynamics binary mixtures by mapping coarse-grained molecular dynamics two-dimensional simple fluid mixtures. By computing analyzing density fluctuations model bilayer, determine numerical value quadratic coupling term appearing in regular solutions for dipalmitoylphosphatidylcholine–dilinoleoylphosphatidylcholine pair lipids at three different compositions. Our methodology is general discussed detail.

Language: Английский

Citations

0
TS2CG as a membrane builder DOI Creative Commons
Fabian Schuhmann, Jan A. Stevens,

Neda Rahmani

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 17, 2025

Abstract Molecular dynamics (MD) simulations excel at capturing biological processes the molecular scale but rely on a well-defined initial structure. As MD now extend to whole-cell-level modeling, new tools are needed efficiently build structures. Here, we introduce TS2CG version 2, designed construct coarse-grained membrane structures with any desired shape and lateral organization. This enables precise placement of lipids proteins based curvature preference, facilitating creation large, near-equilibrium membranes. Additional features include controlled pore generation specific edges for stabilization. Moreover, Python interface allows users functionality while maintaining high performance C++ core. To demonstrate its capabilities, showcase challenging simulations, including Möbius strip membrane, vesicle lipid domain as continental plates (Martini globe), entire mitochondrial membranes exhibiting heterogeneity due curvature, along comprehensive set tutorials.

Language: Английский

Citations

0
Modeling membranes in situ DOI Creative Commons
Chelsea M. Brown, ‪Siewert J. Marrink

Current Opinion in Structural Biology, Journal Year: 2024, Volume and Issue: 87, P. 102837 - 102837

Published: May 13, 2024

Molecular dynamics simulations of cellular membranes have come a long way-from simple model lipid bilayers to multicomponent systems capturing the crowded and complex nature real cell membranes. In this opinionated minireview, we discuss current challenge simulate in their native environment, situ, with prospect reaching level whole cells organelles using an integrative modeling framework.

Language: Английский

Citations

3