Building complex membranes with Martini 3

Tugba Nur Ozturk; Melanie König; Timothy S Carpenter; Kasper B Pedersen; Tsjerk A Wassenaar; Helgi I Ingólfsson; Siewert J Marrink

doi:10.1016/bs.mie.2024.03.010

Building complex membranes with Martini 3

Methods Enzymol. 2024:701:237-285. doi: 10.1016/bs.mie.2024.03.010. Epub 2024 Apr 9.

Authors

Tugba Nur Ozturk¹, Melanie König², Timothy S Carpenter¹, Kasper B Pedersen³, Tsjerk A Wassenaar⁴, Helgi I Ingólfsson⁵, Siewert J Marrink⁶

Affiliations

¹ Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States.
² Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
³ Department of Chemistry, Aarhus University, Aarhus C, Denmark.
⁴ Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands; Institute for Life Science and Technology, Hanze University of Applied Sciences, Groningen, The Netherlands.
⁵ Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States. Electronic address: [email protected].
⁶ Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands. Electronic address: [email protected].

PMID: 39025573
DOI: 10.1016/bs.mie.2024.03.010

Abstract

The Martini model is a popular force field for coarse-grained simulations. Membranes have always been at the center of its development, with the latest version, Martini 3, showing great promise in capturing more and more realistic behavior. In this chapter we provide a step-by-step tutorial on how to construct starting configurations, run initial simulations and perform dedicated analysis for membrane-based systems of increasing complexity, including leaflet asymmetry, curvature gradients and embedding of membrane proteins.

Keywords: Asymmetrical membranes; Complex membranes; Curved membranes; Embedding proteins in membranes; Leaflet asymmetry; Martini 3; Membrane set up.

MeSH terms

Cell Membrane / chemistry
Cell Membrane / metabolism
Lipid Bilayers* / chemistry
Membrane Proteins* / chemistry
Molecular Dynamics Simulation*

Substances

Lipid Bilayers
Membrane Proteins