Integrative visualization of the molecular structure of a cellular microdomain

Goodsell, David S.; Lasker, Keren

doi:10.1002/pro.4577

Cited by 4 publications

(4 citation statements)

References 103 publications

(122 reference statements)

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“…Importantly, CAHS condensation is dynamic, inducible, and reversible, making it distinct from the current models for intermediate filament assembly. It is of note that other, non‐cytoskeletal, proteins such as the bacterial polar organizing protein Z (PopZ), form assemblages through similar mechanisms, thus these mechanisms of assembly are not exclusive to structural functionality (Bowman et al, 2010 ; Goodsell & Lasker, 2023 ).…”

Section: Discussionmentioning

confidence: 99%

Labile assembly of a tardigrade protein induces biostasis

Sanchez‐Martinez,

Nguyen,

Biswas

et al. 2024

Protein Science

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Tardigrades are microscopic animals that survive desiccation by inducing biostasis. To survive drying tardigrades rely on intrinsically disordered CAHS proteins, which also function to prevent perturbations induced by drying in vitro and in heterologous systems. CAHS proteins have been shown to form gels both in vitro and in vivo, which has been speculated to be linked to their protective capacity. However, the sequence features and mechanisms underlying gel formation and the necessity of gelation for protection have not been demonstrated. Here we report a mechanism of fibrillization and gelation for CAHS D similar to that of intermediate filament assembly. We show that in vitro, gelation restricts molecular motion, immobilizing and protecting labile material from the harmful effects of drying. In vivo, we observe that CAHS D forms fibrillar networks during osmotic stress. Fibrillar networking of CAHS D improves survival of osmotically shocked cells. We observe two emergent properties associated with fibrillization; (i) prevention of cell volume change and (ii) reduction of metabolic activity during osmotic shock. We find that there is no significant correlation between maintenance of cell volume and survival, while there is a significant correlation between reduced metabolism and survival. Importantly, CAHS D's fibrillar network formation is reversible and metabolic rates return to control levels after CAHS fibers are resolved. This work provides insights into how tardigrades induce reversible biostasis through the self‐assembly of labile CAHS gels.

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Section: Discussionmentioning

confidence: 99%

Labile assembly of a tardigrade protein induces biostasis

Sanchez‐Martinez,

Nguyen,

Biswas

et al. 2024

Protein Science

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“…, (Miao et al, 2017, described DNA nanostructure visualization across multiple abstractions with smooth transitions between levels of abstraction to provide continuous visualisation across scales. Goodsell worked on integrative illustrations for the coronavirus, the minimal cell JCVI-syn3.0 and the microdomain of Caulobacter crescentus (Goodsell et al, 2020;Goodsell, 2022;Goodsell and Lasker, 2023). The main idea is to simplify visual complexity by employing streamlined representations, utilizing orthographic projection to preserve scaling relationships, and employing a color scheme that emphasizes the functional compartments of the molecular system.…”

Section: Visual Abstraction Formalismmentioning

confidence: 99%

From complex data to clear insights: visualizing molecular dynamics trajectories

Belghit,

Spivak,

Dauchez

et al. 2024

Front. Bioinform.

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Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories. This massive increase in raw simulation data creates additional processing and visualization challenges. Effective visualization techniques play a vital role in facilitating the analysis and interpretation of molecular dynamics simulations. In this paper, we focus mainly on the techniques and tools that can be used for visualization of molecular dynamics simulations, among which we highlight the few approaches used specifically for this purpose, discussing their advantages and limitations, and addressing the future challenges of molecular dynamics visualization.

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“…We chose a mid-range value of 3.4 x 106 nm 3 for our standard cell models, which corresponds to approximately 0.56% of the total cytoplasmic volume. Information from global measurements of mRNA translation rates 24 and fluorescence intensity measurements of FP-tagged proteins have been combined to provide the following estimates of protein abundance in C. crescentus stalked cells: PopZ 8,200; CtrA 25,402; CpdR 6,044; RcdA 2,583 46 . Using these numbers as a guide, we set the total number of A and B proteins in our model at 2,500 each.…”

Section: Computational Simulationmentioning

confidence: 99%

Phospho-signaling couples polar asymmetry and proteolysis within a membraneless microdomain inC. crescentus

Ahmed,

Bowman

2023

Preprint

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Asymmetric cell division in bacteria is achieved through cell polarization, where regulatory proteins are directed to specific cell poles. Curiously, both poles contain a membraneless microdomain, established by the polar assembly hub PopZ, through most of the cell cycle, yet many PopZ clients are unipolar and transiently localized. We find that PopZ’s interaction with the response regulator CpdR is controlled by phosphorylation, via the histidine kinase CckA. Phosphorylated CpdR does not interact with PopZ and is not localized to cell poles. At poles where CckA acts as a phosphatase, de-phosphorylated CpdR binds directly with PopZ and subsequently recruits ClpX, substrates, and other members of a protease complex to the cell pole. We also find that co-recruitment of protease components and substrates to polar microdomains enhances their coordinated activity. This study connects phosphosignaling with polar assembly and the activity of a protease that triggers cell cycle progression and cell differentiation.

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Integrative visualization of the molecular structure of a cellular microdomain

Cited by 4 publications

References 103 publications

Labile assembly of a tardigrade protein induces biostasis

Labile assembly of a tardigrade protein induces biostasis

From complex data to clear insights: visualizing molecular dynamics trajectories

Phospho-signaling couples polar asymmetry and proteolysis within a membraneless microdomain inC. crescentus

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