Liquid–liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.

In a recent paper, we have developed an efficient implementation of the ring polymer molecular dynamics (RPMD) method for calculating bimolecular chemical reaction rates in the gas phase, and illustrated it with applications to some benchmark atom-diatom reactions. In this paper, we show that the same methodology can readily be used to treat more complex polyatomic reactions in their full dimensionality, such as the hydrogen abstraction reaction from methane, H + CH(4) → H(2) + CH(3). The present calculations were carried out using a modified and recalibrated version of the Jordan-Gilbert potential energy surface. The thermal rate coefficients obtained between 200 and 2000 K are presented and compared with previous results for the same potential energy surface. Throughout the temperature range that is available for comparison, the RPMD approximation gives better agreement with accurate quantum mechanical (multiconfigurational time-dependent Hartree) calculations than do either the centroid density version of quantum transition state theory (QTST) or the quantum instanton (QI) model. The RPMD rate coefficients are within a factor of 2 of the exact quantum mechanical rate coefficients at temperatures in the deep tunneling regime. These results indicate that our previous assessment of the accuracy of the RPMD approximation for atom-diatom reactions remains valid for more complex polyatomic reactions. They also suggest that the sensitivity of the QTST and QI rate coefficients to the choice of the transition state dividing surface becomes more of an issue as the dimensionality of the reaction increases.

One of the key mechanisms used by cells to control the spatiotemporal organization of their many components is the formation and dissolution of biomolecular condensates through liquid–liquid phase separation (LLPS). Using a minimal coarse-grained model that allows us to simulate thousands of interacting multivalent proteins, we investigate the physical parameters dictating the stability and composition of multicomponent biomolecular condensates. We demonstrate that the molecular connectivity of the condensed-liquid network—i.e., the number of weak attractive protein–protein interactions per unit of volume—determines the stability (e.g., in temperature, pH, salt concentration) of multicomponent condensates, where stability is positively correlated with connectivity. While the connectivity of scaffolds (biomolecules essential for LLPS) dominates the phase landscape, introduction of clients (species recruited via scaffold–client interactions) fine-tunes it by transforming the scaffold–scaffold bond network. Whereas low-valency clients that compete for scaffold–scaffold binding sites decrease connectivity and stability, those that bind to alternate scaffold sites not required for LLPS or that have higher-than-scaffold valencies form additional scaffold–client–scaffold bridges increasing stability. Proteins that establish more connections (via increased valencies, promiscuous binding, and topologies that enable multivalent interactions) support the stability of and are enriched within multicomponent condensates. Importantly, proteins that increase the connectivity of multicomponent condensates have higher critical points as pure systems or, if pure LLPS is unfeasible, as binary scaffold–client mixtures. Hence, critical points of accessible systems (i.e., with just a few components) might serve as a unified thermodynamic parameter to predict the composition of multicomponent condensates.

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Deciphering the factors that control chromatin fiber structure is key to understanding fundamental chromosomal processes. Although details remain unknown, it is becoming clear that chromatin is polymorphic depending on internal and external factors. In particular, different lengths of the linker DNAs joining successive nucleosomes (measured in nucleosome-repeat lengths or NRLs) that characterize different cell types and cell cycle stages produce different structures. NRL is also nonuniform within single fibers, but how this diversity affects chromatin fiber structure is not clear. Here we perform Monte Carlo simulations of a coarse-grained oligonucleosome model to help interpret fiber structure subject to intrafiber NRL variations, as relevant to proliferating cells of interphase chromatin, fibers subject to remodeling factors, and regulatory DNA sequences. We find that intrafiber NRL variations have a profound impact on chromatin structure, with a wide range of different architectures emerging (highly bent narrow forms, canonical and irregular zigzag fibers, and polymorphic conformations), depending on the NRLs mixed. This stabilization of a wide range of fiber forms might allow NRL variations to regulate both fiber compaction and selective DNA exposure. The polymorphic forms spanning canonical to sharply bent structures, like hairpins and loops, arise from large NRL variations and are surprisingly more compact than uniform NRL structures. They are distinguished by tail-mediated far-nucleosome interactions, in addition to the near-nucleosome interactions of canonical 30-nm fibers. Polymorphism is consistent with chromatin's diverse biological functions and heterogeneous constituents. Intrafiber NRL variations, in particular, may contribute to fiber bending and looping and thus to distant communication in associated regulatory processes.coarse-grained modeling | chromatin polymorphism | nonuniform NRL | chromatin bending and looping T he DNA inside eukaryotic nuclei is not found free, but tightly packed along with histone and nonhistone proteins in the form of chromatin structures. Chromatin organization and structural transitions directly impact fundamental cellular processes such as DNA transcription, replication, repair, and recombination. However, our understanding of chromatin structure, how it is regulated by internal and external factors, and the relationship between structure and biological functions remain elusive. The challenge in solving these questions arises from the complex cellular milieu, chromatin's diverse and varying composition, and the limited resolution of experimental methods for large systems.Chromatin consists of a repeating sequence of nucleoprotein blocks (or nucleosomes) joined by DNA linker segments. The nucleosome structure is well understood at atomic resolution (1, 2). Its histone protein octamer (two copies each of H2A, H2B, H3, and H4) has ∼147 bp of DNA wrapped around it (1) and 10 highly positively charged and flexible tails (two N-terminal domains from each histone dimer and ...