Biomolecular condensates can form through the liquid-liquid phase separation (LLPS) of proteins and RNAs in cells. However, other states of organization, including mesostructured network microstructures and physical gels, have been observed, the physical mechanism of which are not well understood. We use the Polymer Reference Interaction Site Model liquid state integral equation theory to study the equilibrium behavior of (generally aperiodic in sequence) biomolecular condensates based on a minimal sticker-spacer associating polymer model. The role of polymer packing fraction, sequence, and the strength and range of intermolecular interactions on macromolecular scale spatial organization and phase behavior is studied for typical sticker-spacer sequences. In addition to the prediction of conventional LLPS, a sequence-dependent strongly fluctuating polymeric microemulsion homogeneous state is predicted at high enough concentrations beyond the so-called Lifshitz-like point, which we suggest can be relevant to the dense phase of microstructured biomolecular condensates. New connections between local clustering and the formation of mesoscopic microdomains, the influence of attraction range, compressibility, and the role of spatial correlations across scales, are established. Our results are also germane to understanding the polymer physics of dense solutions of nonperiodic and unique sequence synthetic copolymers and provide a foundation to create new theories for how polymer diffusion and viscosity are modified in globally isotropic and homogeneous dense polymeric microemulsions.
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http://dx.doi.org/10.1063/5.0153938 | DOI Listing |
J Biol Chem
December 2024
European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. Electronic address:
The formation of biomolecular condensates contributes to intracellular compartmentalization, and plays an important role in many cellular processes. The characterization of condensates is however challenging, requiring advanced biophysical or biochemical methods that are often less suitable for in vivo studies. A particular need for easily accessible yet thorough methods that enable the characterization of condensates across different experimental systems thus remains.
View Article and Find Full Text PDFJ Cell Biol
January 2025
Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA.
Controlling biomolecular condensate formation within the nucleus is critical for genome function. In this issue, Xu et al. (https://doi.
View Article and Find Full Text PDFCurr Protoc
December 2024
Department of Biomedical Sciences, University of Padova, Padova, Italy.
Intrinsically disordered proteins (IDPs) make up around 30% of eukaryotic proteomes and play a crucial role in cellular processes and in pathological conditions such as neurodegenerative disorders and cancers. However, IDPs exhibit dynamic conformational ensembles and are often involved in the formation of biomolecular condensates. Understanding the function of IDPs is critical to research in many areas of science.
View Article and Find Full Text PDFMol Plant Pathol
December 2024
Plant Molecular and Cell Biology Program, University of Florida, Gainesville, Florida, USA.
Viroids are single-stranded circular noncoding RNAs that mainly infect crops. Upon infection, nuclear-replicating viroids engage host DNA-dependent RNA polymerase II for RNA-templated transcription, which is facilitated by a host protein TFIIIA-7ZF. The sense-strand and minus-strand RNA intermediates are differentially localised to the nucleolus and nucleoplasm regions, respectively.
View Article and Find Full Text PDFMost amino acids are encoded by multiple codons, making the genetic code degenerate. Synonymous mutations affect protein translation and folding, but their impact on RNA itself is often neglected. We developed a genetic algorithm that introduces synonymous mutations to control the diversity of structures sampled by an mRNA.
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