Integrative modeling of JCVI-Syn3A nucleoids with a modular approach

Goodsell, David S.; Autin, Ludovic

doi:10.1016/j.crstbi.2023.100121

Current Research in Structural Biology

2024

DOI: 10.1016/j.crstbi.2023.100121

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Integrative modeling of JCVI-Syn3A nucleoids with a modular approach

David S. Goodsell,

Ludovic Autin

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Cited by 1 publication

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Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells

Mathur,

Ghosh,

Nunes-Alves

2024

J. Chem. Inf. Model.

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Macromolecular crowding in the cellular cytoplasm can potentially impact diffusion rates of proteins, their intrinsic structural stability, binding of proteins to their corresponding partners as well as biomolecular organization and phase separation. While such intracellular crowding can have a large impact on biomolecular structure and function, the molecular mechanisms and driving forces that determine the effect of crowding on dynamics and conformations of macromolecules are so far not well understood. At a molecular level, computational methods can provide a unique lens to investigate the effect of macromolecular crowding on biomolecular behavior, providing us with a resolution that is challenging to reach with experimental techniques alone. In this review, we focus on the various physics-based and data-driven computational methods developed in the past few years to investigate macromolecular crowding and intracellular protein condensation. We review recent progress in modeling and simulation of biomolecular systems of varying sizes, ranging from single protein molecules to the entire cellular cytoplasm. We further discuss the effects of macromolecular crowding on different phenomena, such as diffusion, protein−ligand binding, and mechanical and viscoelastic properties, such as surface tension of condensates. Finally, we discuss some of the outstanding challenges that we anticipate the community addressing in the next few years in order to investigate biological phenomena in model cellular environments by reproducing in vivo conditions as accurately as possible.

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Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells

Mathur,

Ghosh,

Nunes-Alves

2024

J. Chem. Inf. Model.

View full text Add to dashboard Cite

show abstract

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Integrative modeling of JCVI-Syn3A nucleoids with a modular approach

Cited by 1 publication

References 26 publications

Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells

Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells

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