Martini 3 Coarse-Grained Force Field for Carbohydrates

Grünewald, Fabian; Punt, Mats H; Jefferys, Elizabeth; Vainikka, Petteri; König, Melanie; Virtanen, Valtteri; Meyer, Travis A.; Pezeshkian, Weria; Gormley, Adam J.; Karonen, Maarit; Sansom, Mark S.P.; Souza, Paulo C. T.; Marrink, Siewert J.

doi:10.1021/acs.jctc.2c00757

Cited by 51 publications

(49 citation statements)

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“…In particular, A complementary outcome of the present investigation is a library of trajectories for systems of variable cellulose and callose concentration in water (at fixed water content) covering a few hundred ns. This data base is suitable for tuning a coarse grained model (for instance of the Martini family) 60 that is needed to extend significantly the size and time scales of the simulation. The computations described in this paper have been running on CPUs and GPUs of different supercomputers, with a (relatively modest) effort corresponding to a few million (equivalent) core-hours.…”

Section: Discussionmentioning

confidence: 99%

Cellulose-Callose Hydrogels: a Computational Exploration of their Structure and Mechanical Properties

Kumari

Benitez‐Alfonso

Ballone

2023

Preprint

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The accumulation of callose ($\beta$-1,3 glucans) greatly affects plant cell wall physico-mechanical properties and intercellular communication. In this paper, the structural, bonding and mechanical properties of cellulose - callose hydrogel mixtures, consisting of $90$ wt\% water and $10$ wt\% polysaccharide, have been investigated by atomistic molecular dynamics simulations. Systems of this kind have recently been investigated experimentally aiming at gaining insight into the properties underlying callose roles in plant cell walls. The simulation results show that samples of $N=1.5\times 10^6$ atoms and volume $V=(25)^3$ nm$^3$ simulated for $300$ ns provide a qualitatively consistent view of the hydrogel properties, although a quantitative comparison with experiments might require to extend significantly the linear size of the samples and the time scale of the simulation. A complementary set of simulations have been carried out for model samples representing dense cellulose-callose structures, contaminated by or immersed in water. The results provide a valuable microscopic picture for the interpretation of experimental data on cellulose-callose hydrogels, and, in perspective, might help understanding the role of mixing callose and cellulose in critical cell wall structures. All the simulation data provide a tuning and testing ground for the development of coarse-grained models that are required for the systematic investigation of mechanical properties of cellulose, callose and water mixtures.

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Section: Discussionmentioning

confidence: 99%

Cellulose-Callose Hydrogels: a Computational Exploration of their Structure and Mechanical Properties

Kumari

Benitez‐Alfonso

Ballone

2023

Preprint

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“…In this regard, the Martini force field is an excellent candidate, as demonstrated by the wide range of application studies using Martini over the past 2 decades ( Marrink et al, 2022 ). Additionally, parameters for a large variety of biomolecules are already available, including proteins ( de Jong et al, 2013 ), lipids ( Wassenaar et al, 2015 ), polynucleotides ( Uusitalo et al, 2015 ; Uusitalo et al, 2017 ), carbohydrates ( López et al, 2009 ; Grünewald and Punt, 2022 ) and metabolites ( Sousa et al, 2021 ; Alessandri et al, 2022 ). A curated collection of all parameters is available from the Martini Database ( Hilpert et al, 2022 ).…”

Section: Building Cells With the Martini Ecosystemmentioning

confidence: 99%

Molecular dynamics simulation of an entire cell

et al. 2023

Self Cite

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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.

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“…To accurately represent these complex systems, compatible models for other molecules (nucleic acids, PEG, salt, sugars) with well-parametrized intermolecular interactions are needed. Coarse-grained models of DNA have been developed and used with coarse-grained protein models, 125 and the Martini model was extended to model carbohydrates carbohydrates, 143 but further development for these and other molecules is needed. To complicate matters further, cells are not at equilibrium like most simulated systems�although characterizing the equilibrium behavior is still a useful starting point for systems close to equilibrium.…”

Section: Future Directions For Simulation Developmentmentioning

confidence: 99%

Theoretical and Data-Driven Approaches for Biomolecular Condensates

Saar

Qian

et al. 2023

Chem. Rev.

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Biomolecular condensation processes are increasingly recognized as a fundamental mechanism that living cells use to organize biomolecules in time and space. These processes can lead to the formation of membraneless organelles that enable cells to perform distinct biochemical processes in controlled local environments, thereby supplying them with an additional degree of spatial control relative to that achieved by membranebound organelles. This fundamental importance of biomolecular condensation has motivated a quest to discover and understand the molecular mechanisms and determinants that drive and control this process. Within this molecular viewpoint, computational methods can provide a unique angle to studying biomolecular condensation processes by contributing the resolution and scale that are challenging to reach with experimental techniques alone. In this Review, we focus on three types of dry-lab approaches: theoretical methods, physicsdriven simulations and data-driven machine learning methods. We review recent progress in using these tools for probing biomolecular condensation across all three fields and outline the key advantages and limitations of each of the approaches. We further discuss some of the key outstanding challenges that we foresee the community addressing next in order to develop a more complete picture of the molecular driving forces behind biomolecular condensation processes and their biological roles in health and disease.

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Martini 3 Coarse-Grained Force Field for Carbohydrates

Cited by 51 publications

References 100 publications

Cellulose-Callose Hydrogels: a Computational Exploration of their Structure and Mechanical Properties

Cellulose-Callose Hydrogels: a Computational Exploration of their Structure and Mechanical Properties

Molecular dynamics simulation of an entire cell

Theoretical and Data-Driven Approaches for Biomolecular Condensates

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