Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry

Abstract

Motions in biomolecules are critical for biochemical reactions. In cells, many biochemical reactions are executed inside of biomolecular condensates formed by ultradynamic intrinsically disordered proteins. A deep understanding of the conformational dynamics of intrinsically disordered proteins in biomolecular condensates is therefore of utmost importance but is complicated by diverse obstacles. Here we review emerging data on the motions of intrinsically disordered proteins inside of liquidlike condensates. We discuss how liquid–liquid phase separation modulates internal motions across a wide range of time and length scales. We further highlight the importance of intermolecular interactions that not only drive liquid–liquid phase separation but appear as key determinants for changes in biomolecular motions and the aging of condensates in human diseases. The review provides a framework for future studies to reveal the conformational dynamics of intrinsically disordered proteins in the regulation of biomolecular condensate chemistry.

Model biomolecular condensates have heterogeneous structure quantitatively dependent on the interaction profile of their constituent macromolecules

“…(74, 75) Thirdly, the dense phase evolves on multiple timescales, indicating a complex internal dynamics of the IDPs. (23) Finally, our model predicts that the location of attractive domains on IDPs is critical for their phase separation. When the binding sites at the polymer endcaps are disabled, the dense phase dissolves.…”

“…(21) These processes depend on the ease with which enzymes and reactants can diffuse, fluctuate, and interact within. (22,23) A better understanding of how the molecular architecture of scaffold IDPs influences the material properties of BCs would help elucidate the physical mechanisms underlying their functions and guide the identification of targets for drugs, (24) opening up new approaches to attack cancer and other diseases. (25)(26)(27)(28) Although many biomolecular condensates are fluid, (29) they do not behave as simple liquids.…”

“…Computational modelling has been extensively used to connect molecular details such as multivalency and hydrophobicity to IDP phase behaviour in model systems. (44)(45)(46)(47) Exquisite detail on residue-residue interactions (48) and the conformational dynamics of IDPs within condensates is revealed by Atomistic Molecular dynamics (aaMD) simulations, (23,49) but these are limited to nearmolecular system sizes and short times. Coarse-grained simulation techniques simplify the atomic details of proteins in order to simulate thousands of molecules.…”

“…(35, 36) Such experiments show that recapitulating the dynamics of condensates does not require the complex environment of a living cell. (23) It has been conjectured that reversible phase separation is indicative of cellular health while irreversible rigidification of BCs marks a cell’s transition into disease states. (29) Empirically classifying biomolecular condensates on a spectrum from fluid (healthy) to rigid (disease) motivates us to learn how their material properties arise from their constituent IDPs.…”

Contributions of the N-terminal intrinsically disordered region of the SARS-CoV-2 nucleocapsid protein to RNA-induced phase separation

“…In parallel to the changes in sample turbidity, many cross-peaks disappeared from the 1 H- 15 N HSQC of N SARS-CoV-2 (Figure S3), but partially reappeared at high RNA concentration (Figure 5A). The disappearance of the NMR signals at conditions of LLPS likely arise from increased relaxation rates in the protein when it is concentrated into the viscous phase of N SARS-CoV-2 /RNA droplets 30 . Additional 1 H- 13 C XL-ALSOFAST HSQC experiments further showed that even for the more flexible methyl groups, RNA-induced LLPS of N SARS-CoV-2 causes severe line broadening (Figure S4).…”