Fundamental behaviors emerge from simulations of a living minimal cell

Thornburg, Zane R.; Bianchi, David M.; Brier, Troy A.; Gilbert, Benjamin R.; Earnest, Tyler M.; Melo, Marcelo C.R.; Safronova, Nataliya; Sáenz, James; Cook, András T.; Wise, Kim S.; Hutchison, Clyde A.; Smith, Hamilton O.; Glass, John I.; Luthey‐Schulten, Zaida

doi:10.1016/j.cell.2021.12.025

Cited by 80 publications

(111 citation statements)

References 115 publications

(256 reference statements)

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“…Proteins appear in the ribosome with certain rates that depend on their types. Within the framework of stochastic dynamics this process can be modeled as particle addition to the system 14,62,63 …”

Section: Basic Principles Of Stochastic Dynamicsmentioning

confidence: 99%

“…The theoretical explanation of the Brownian motion phenomenon was suggested by Albert Einstein 7 . It was followed by the experimental work by Jean Baptiste Perrin 10,11 resulting in the proof of Einstein's theory and also by the further advances in the theory of the Brownian motion leading to the formulation of the theory of random walks and stochastic dynamics being applicable in many areas of natural science research and beyond, see, for example, References 12–14.…”

Section: Introductionmentioning

confidence: 99%

“…Another important area of applications of the developed methodology concerns biological systems and processes therein. Many biological processes are driven by diffusion and have a probabilistic nature 14,42,43 . Computational modeling of such systems is an important area of modern research, and the developed methodology opens many new possibilities for the research advances in this area.…”

Section: Introductionmentioning

confidence: 99%

“…Many biological processes are driven by diffusion and have a probabilistic nature. 14,42,43 Computational modeling of such systems is an important area of modern research, and the developed methodology opens many new possibilities for the research advances in this area. Similar statements can be made for research in computational physics, chemistry, and material science.…”

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confidence: 99%

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Multiscale modeling of stochastic dynamics processes with MBN Explorer

et al. 2022

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Stochastic dynamics describes processes in complex systems having the probabilistic nature. They can involve very different dynamical systems and occur on very different temporal and spatial scale. This paper discusses the concept of stochastic dynamics and its implementation in the popular program MBN EXPLORER. Stochastic dynamics in MBN EXPLORER relies on the Monte Carlo approach and permits simulations of physical, chemical, and biological processes. The paper presents the basic theoretical concepts underlying stochastic dynamics implementation and provides several examples highlighting its applicability to different systems, such as diffusing proteins seeking an anchor point on a cell membrane, deposition of nanoparticles on a surface leading to structures with fractal morphologies, and oscillations of compounds in an autocatalytic reaction. The chosen examples illustrate the diversity of applications that can be modeled by means of stochastic dynamics with MBN EXPLORER.

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Section: Basic Principles Of Stochastic Dynamicsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

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Multiscale modeling of stochastic dynamics processes with MBN Explorer

et al. 2022

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“…Mycoplasmas have been at the center of landmark studies such as the production of the first cell governed by a chemically synthesized genome, and later of the first minimal synthetic bacterial cell (12,13). Mycoplasmas are also the first cells for which complete and accurate predictive mathematical models have been developed (14)(15)(16).…”

Section: Introductionmentioning

confidence: 99%

Imaging minimal bacteria at the nanoscale: a reliable and versatile process to perform Single Molecule Localization Microscopy in mycoplasmas

Rideau

Villa

Belzanne

et al. 2022

Preprint

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Mycoplasmas are the smallest free-living organisms. These bacteria are important models for both fundamental and Synthetic Biology, owing to their highly reduced genomes. They are also relevant in the medical and veterinary fields, as they are pathogenic of both humans and most livestock species. Mycoplasma cells have minute sizes, often in the 300-800 nanometers range. As these dimensions are close to the diffraction limit of visible light, fluorescence imaging in mycoplasmas is often poorly informative. Recently developed Super-Resolution Imaging techniques can break this diffraction limit, improving the imaging resolution by an order of magnitude and offering a new nanoscale vision of the organization of these bacteria. These techniques have however not been applied to mycoplasmas before. Here, we describe an efficient and reliable protocol to perform Single-Molecule Localization Microscopy (SMLM) imaging in mycoplasmas. We provide a polyvalent transposon-based system to express the photo-convertible fluorescent protein mEos3.2, enabling Photo-Activated Localization Microscopy (PALM) in most Mycoplasma species. We also describe the application of direct STochastic Optical Reconstruction Microscopy (dSTORM). We showcase the potential of these techniques by studying the subcellular localization of two proteins of interest. Our work highlights the benefits of state-of-the-art microscopy techniques for mycoplasmology and provides an incentive to further the development SMLM strategies to study these organisms in the future.

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Single‐molecule approaches reveal outer membrane protein biogenesis dynamics

2022

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Outer membrane proteins (OMPs) maintain the viability of Gram-negative bacteria by functioning as receptors, transporters, ion channels, lipases, and porins. Folding and assembly of OMPs involves synchronized action of chaperones and multi-protein machineries which escort the highly hydrophobic polypeptides to their target outer membrane in a folding competent state. Previous studies have identified proteins and their involvement along the OMP biogenesis pathway. Yet, the mechanisms of action and the intriguing ability of all these molecular machines to work without the typical cellular energy source of ATP, but solely based on thermodynamic principles, are still not well understood. Here, we highlight how different single-molecule studies can shed additional light on the mechanisms and kinetics of OMP biogenesis.

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Fundamental behaviors emerge from simulations of a living minimal cell

Cited by 80 publications

References 115 publications

Multiscale modeling of stochastic dynamics processes with MBN Explorer

Multiscale modeling of stochastic dynamics processes with MBN Explorer

Imaging minimal bacteria at the nanoscale: a reliable and versatile process to perform Single Molecule Localization Microscopy in mycoplasmas

Single‐molecule approaches reveal outer membrane protein biogenesis dynamics

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