Multiscale Modeling of Protein-RNA Condensation in and Out of Equilibrium

Laghmach, Rabia; Malhotra, Isha; Potoyan, Davit A.

doi:10.1007/978-1-0716-2663-4_5

Cited by 1 publication

(2 citation statements)

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“…For more information on this topic, please refer to the review titled Computational approaches to predict protein-protein interactions in crowded cellular environments by G. Grassmann, published in this issue and other works . These approaches will shed light on critical molecular interactions, transitional states, and dynamic behaviors, which might be challenging to directly observe using traditional wet lab techniques …”

Section: Discussionmentioning

confidence: 99%

“…432 These approaches will shed light on critical molecular interactions, transitional states, and dynamic behaviors, which might be challenging to directly observe using traditional wet lab techniques. 433 The combination of theoretical frameworks and computational methodologies paves the way for the strategic design of biomolecular condensates with tailored properties or functionalities. 7 By modifying molecular parameters within simulations, it is possible to predict the impacts of mutations, binding affinities, or other alterations on the behavior of biomolecular condensates.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

RNA: The Unsuspected Conductor in the Orchestra of Macromolecular Crowding

Zacco,

Broglia,

Kurihara

et al. 2024

Chem. Rev.

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This comprehensive Review delves into the chemical principles governing RNA-mediated crowding events, commonly referred to as granules or biological condensates. We explore the pivotal role played by RNA sequence, structure, and chemical modifications in these processes, uncovering their correlation with crowding phenomena under physiological conditions. Additionally, we investigate instances where crowding deviates from its intended function, leading to pathological consequences. By deepening our understanding of the delicate balance that governs molecular crowding driven by RNA and its implications for cellular homeostasis, we aim to shed light on this intriguing area of research. Our exploration extends to the methodologies employed to decipher the composition and structural intricacies of RNA granules, offering a comprehensive overview of the techniques used to characterize them, including relevant computational approaches. Through two detailed examples highlighting the significance of noncoding RNAs, NEAT1 and XIST, in the formation of phase-separated assemblies and their influence on the cellular landscape, we emphasize their crucial role in cellular organization and function. By elucidating the chemical underpinnings of RNAmediated molecular crowding, investigating the role of modifications, structures, and composition of RNA granules, and exploring both physiological and aberrant phase separation phenomena, this Review provides a multifaceted understanding of the intriguing world of RNA-mediated biological condensates.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%