Building structural models of a whole mycoplasma cell
Open accessAbstract
Building structural models of entire cells has been a long-standing cross-discipline challenge for the research community, as it requires an unprecedented level of integration between multiple sources of biological data and enhanced methods for computational modeling and visualization. Here, we present the first 3D structural models of an entire Mycoplasma genitalium (MG) cell, built using the CellPACK suite of computational modeling tools. Our model recapitulates the data described in recent whole-cell system biology simulations and provides a structural representation for all MG proteins, DNA and RNA molecules, obtained by combining experimental and homology-modeled structures and lattice-based models of the genome. We establish a framework for gathering, curating and evaluating these structures, exposing current weaknesses of modeling methods and the boundaries of MG structural knowledge, and visualization methods to explore functional characteristics of the genome and proteome. We compare two approaches for data gathering, a manually-curated workflow and an automated workflow that uses homologous structures, both of which are appropriate for the analysis of mesoscale properties such as crowding and volume occupancy. Analysis of model quality provides estimates of the regularization that will be required when these models are used as starting points for atomic molecular dynamics simulations.
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Genome-wide models have been developed to represent other bacterial organisms, including Escherichia coli.
“Since this pioneering work, genome-wide models have been developed to represent other bacterial organisms, including Escherichia coli.8,20–22”
From How to build the virtual cell with artificial intelligence: Priorities and opportunities (2024) · cites this paper as [21]
The Introduction describes models of bacterial components, including Escherichia coli cytoplasm, but explicitly calls them models of portions of organisms. It does not establish that genome-wide models of E. coli had been developed. (LLM, conf=0.86)
Experimental — accuracy not yet measuredStructural models of Mycoplasma genitalium and JCVI-syn3A have also been created.
“Structural models of Mycoplasma genitalium and JCVI-syn3A have also been created.”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [8]
The Abstract states that the authors created 3D structural models of an entire Mycoplasma genitalium cell. The passages from our copy do not establish that a structural model of JCVI-syn3A was created, so that part of the sentence is unsupported by this source. (LLM, conf=0.87)
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“The current state-of-the-art uses static representations of heterogeneous cell-scale structures such as cellPACK (Johnson et al., 2015; Maritan et al., 2022), genome-scale well-stirred reaction models for metabolism (Karr et al., 2012; Macklin et al., 2014; Karr et al., 2015; Breuer et al., 2019;…”
Method‘Assembly and analysis of cell-scale membrane envelopes’
Vermaas, J. V., Mayne, C. G., Shinn, E., & Tajkhorshid, E. (2022) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c01050 · Cited by 30 · see citing works
Bringing the genetically minimal cell to life on a computer in 4D
Thornburg, Z. R., Maytin, A., Kwon, J., Brier, T. A., Gilbert, B. R., Fu, E., Gao, Y.-L., Quenneville, J., Wu, T., Li, H., et al. (2026) · Cell · doi:10.1016/j.cell.2026.02.009 · Cited by 44 · see citing works
Dynamics of chromosome organization in a minimal bacterial cell
Gilbert, B. R., Thornburg, Z. R., Brier, T. A., Stevens, J. A., Grünewald, F., Stone, J. E., Marrink, S. J., & Luthey-Schulten, Z. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1214962 · Cited by 19 · see citing works
- Authors
- Maritan, M., Autin, L., Karr, J., Covert, M. W., Olson, A. J., & Goodsell, D. S.
- Affiliations
- Scripps Research Institute (US)
- Icahn School of Medicine at Mount Sinai (US)
- Stanford University (US)
- Rutgers, The State University of New Jersey (US)
- Corresponding author
- Goodsell, David S.
- ORCID
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2022-01
- Volume
- 434
- Issue
- 2
- Pages
- 167351
- ISSN
- 0022-2836 (ISSN-L)
- PMC
- PMC8752489
- OpenAlex
- W3214093190
- Cited by
- 75
- References
- 85
- Citations by year
- 2026: 14 · 2025: 10 · 2024: 12 · 2023: 22 · 2022: 14 · 2021: 3
- FWCI
- 4.00
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (am, 325 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Journal of Molecular Biology (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Scripps Research Institute
- National Institutes of Health (R01 GM120604, R35 GM119771, 30120)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- Mycoplasma genitalium, homology modeling, three-dimensional cell structure, intracellular crowding, model quality assessment, molecular dynamics simulation
- MeSH terms
- Bacteria, Models, Structural, Mycoplasma, Genome, Bacterial, Computational Biology, Proteome, Mycoplasma genitalium, Molecular Dynamics Simulation, Transcriptome
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