‘Assembly and analysis of cell-scale membrane envelopes’
Open accessAbstract
The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms─a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.
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Previous works on large-scale membrane-enveloped systems have shown that finding the balance of interior solvent and lipid leaflets is a non-trivial task.
“Previous works on large-scale membrane-enveloped systems (Pezeshkian et al., 2021; Vermaas et al., 2022) have shown that finding this balance is a non-trivial task.”
From Molecular dynamics simulation of an entire cell (2023) · cites this paper as Vermaas et al., 2022
Unbalanced systems might experience strong osmotic pressures and membrane (curvature) stress, causing unwanted shape deformations all the way to membrane rupture.
“Unbalanced systems might experience strong osmotic pressures and membrane (curvature) stress, causing unwanted shape deformations all the way to membrane rupture.”
From Molecular dynamics simulation of an entire cell (2023) · cites this paper as Vermaas et al., 2022
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Flagged first, then by citations
Cited by
Sorted by citations
Two decades of Martini: Better beads, broader scope
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Molecular dynamics simulation of an entire cell
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“Previous works on large-scale membrane-enveloped systems (Pezeshkian et al., 2021; Vermaas et al., 2022) have shown that fi nding this balance is a non-trivial task.”
Background
- Authors
- Vermaas, J. V., Mayne, C. G., Shinn, E., & Tajkhorshid, E.
- Affiliations
- National Laboratory of the Rockies (US)
- University of Illinois Urbana-Champaign (US)
- Corresponding author
- Vermaas, Josh V.
- Tajkhorshid, Emad
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2021-12-15
- Volume
- 62
- Issue
- 3
- Pages
- 602-617
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- PMC
- PMC8903035
- OpenAlex
- W4200276510
- Cited by
- 30
- References
- 117
- Citations by year
- 2026: 2 · 2025: 7 · 2024: 4 · 2023: 10 · 2022: 7
- FWCI
- 1.65
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Journal of Chemical Information and Modeling (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- Laboratory Directed Research and Development
- National Institute of General Medical Sciences (P41-GM104601)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Keywords
- protocells, Martini coarse-grained model, bacterial membranes, water flux, molecular dynamics simulation, simulation workflow
- MeSH terms
- Cell Membrane, Membrane Proteins, Software, Water, Molecular Dynamics Simulation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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