Molecular dynamics simulation of an entire cell

Jan A Stevens; Fabian Grünewald; P A Marco van Tilburg; Melanie König; Benjamin R Gilbert; Troy A Brier; Zane R Thornburg; Zaida Luthey-Schulten; Siewert J Marrink

doi:10.3389/fchem.2023.1106495

Molecular dynamics simulation of an entire cell

Front Chem. 2023 Jan 18:11:1106495. doi: 10.3389/fchem.2023.1106495. eCollection 2023.

Authors

Jan A Stevens¹, Fabian Grünewald¹, P A Marco van Tilburg¹, Melanie König¹, Benjamin R Gilbert², Troy A Brier², Zane R Thornburg², Zaida Luthey-Schulten², Siewert J Marrink¹

Affiliations

¹ Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.
² Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Champaign, IL, United States.

Abstract

The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell's components with atomic resolution. In contrast to their real-world counterparts, computational microscopes are currently on the brink of meeting this challenge. In this perspective, we show how an integrative approach can be employed to model an entire cell, the minimal cell, JCVI-syn3A, at full complexity. This step opens the way to interrogate the cell's spatio-temporal evolution with molecular dynamics simulations, an approach that can be extended to other cell types in the near future.

Keywords: JCVI-syn3A; Martini force field; coarse grain; integrative modeling; minimal cell; polyply.

Grants and funding

SM acknowledges funding from the ERC with the Advanced grant 101053661 (“COMP-O-CELL”), and funding from NWO through the NWA grant “The limits to growth: The challenge to dissipate energy” and BaSyc (“Building a Synthetic Cell”) consortium. ZL-S acknowledges funding from NSF (MCB: 2221237 “Simulating a growing minimal cell: Integrating experiment and theory”; PHY: 1430124 “Center for the Physics of Living Cells”; PHY: 1505008 and 2014027 “Collaborative Research Network from Physics of Living Systems”).