Expansion of Intrinsically Disordered Proteins Increases the Range of Stability of Liquid-Liquid Phase Separation.

Proteins containing intrinsically disordered regions (IDRs) are ubiquitous within biomolecular condensates, which are liquid-like compartments within cells formed through liquid-liquid phase separation (LLPS). The sequence of amino acids of a protein encodes its phase behaviour, not only by establishing the patterning and chemical nature (e.g., hydrophobic, polar, charged) of the various binding sites that facilitate multivalent interactions, but also by dictating the protein conformational dynamics. Besides behaving as random coils, IDRs can exhibit a wide-range of structural behaviours, including conformational switching, where they transition between alternate conformational ensembles. Using Molecular Dynamics simulations of a minimal coarse-grained model for IDRs, we show that the role of protein conformation has a non-trivial effect in the liquid-liquid phase behaviour of IDRs. When an IDR transitions to a conformational ensemble enriched in disordered extended states, LLPS is enhanced. In contrast, IDRs that switch to ensembles that preferentially sample more compact and structured states show inhibited LLPS. This occurs because extended and disordered protein conformations facilitate LLPS-stabilising multivalent protein-protein interactions by reducing steric hindrance; thereby, such conformations maximize the molecular connectivity of the condensed liquid network. Extended protein configurations promote phase separation regardless of whether LLPS is driven by homotypic and/or heterotypic protein-protein interactions. This study sheds light on the link between the dynamic conformational plasticity of IDRs and their liquid-liquid phase behaviour

Valency and Binding Affinity Variations Can Regulate the Multilayered Organization of Protein Condensates with Many Components.

Biomolecular condensates, which assemble via the process of liquid-liquid phase separation (LLPS), are multicomponent compartments found ubiquitously inside cells. Experiments and simulations have shown that biomolecular condensates with many components can exhibit multilayered organizations. Using a minimal coarse-grained model for interacting multivalent proteins, we investigate the thermodynamic parameters governing the formation of multilayered condensates through changes in protein valency and binding affinity. We focus on multicomponent condensates formed by scaffold proteins (high-valency proteins that can phase separate on their own via homotypic interactions) and clients (proteins recruited to condensates via heterotypic scaffold-client interactions). We demonstrate that higher valency species are sequestered to the center of the multicomponent condensates, while lower valency proteins cluster towards the condensate interface. Such multilayered condensate architecture maximizes the density of LLPS-stabilizing molecular interactions, while simultaneously reducing the surface tension of the condensates. In addition, multilayered condensates exhibit rapid exchanges of low valency proteins in and out, while keeping higher valency proteins-the key biomolecules involved in condensate nucleation-mostly within. We also demonstrate how modulating the binding affinities among the different proteins in a multicomponent condensate can significantly transform its multilayered structure, and even trigger fission of a condensate into multiple droplets with different compositions.Engineering and Physical Sciences Research Council (EPSRC) scholarship to Ignacio Sanchez-Burgo

Role of Salt, Pressure, and Water Activity on Homogeneous Ice Nucleation.

Pure water can be substantially supercooled below the melting temperature without transforming into ice. The achievable supercooling can be enhanced by adding solutes or by applying hydrostatic pressure. Avoiding ice formation is of great importance in the cryopreservation of food or biological samples. In this Letter, we investigate the similarity between the effects of pressure and salt on ice formation using a combination of state-of-the-art simulation techniques. We find that both hinder ice formation by increasing the energetic cost of creating the ice-fluid interface. Moreover, we examine the widely accepted proposal that the ice nucleation rate for different pressures and solute concentrations can be mapped through the activity of water [ Koop , L. ; Tsias , P. Nature , 2000 , 406 , 611 ]. We show that such a proposal is not consistent with the nucleation rates predicted in our simulations because it does not include all parameters affecting ice nucleation. Therefore, even though salt and pressure have a qualitatively similar effect on ice formation, they cannot be quantitatively mapped onto one another

Antifreeze proteins and homogeneous nucleation: On the physical determinants impeding ice crystal growth

Antifreeze proteins (AFPs) are biopolymers capable of interfering with ice growth. Their antifreeze action is commonly understood considering that the AFPs, by pinning the ice surface, force the crystal–liquid interface to bend forming an ice meniscus, causing an increase in the surface free energy and resulting in a decrease in the freezing point ΔT max. Here, we present an extensive computational study for a model protein adsorbed on a TIP4P/Ice crystal, computing ΔT max as a function of the average distance d between AFPs, with simulations spanning over 1 μs. First, we show that the lower the d, the larger the ΔT max. Then, we find that the water–ice–protein contact angle along the line ΔT max(d) is always larger than 0○ , and we provide a theoretical interpretation. We compute the curvature radius of the stable solid–liquid interface at a given supercooling ΔT ≤ ΔT max, connecting it with the critical ice nucleus at ΔT. Finally, we discuss the antifreeze capability of AFPs in terms of the protein–water and protein–ice interactions. Our findings establish a unified description of the AFPs in the contest of homogeneous ice nucleation, elucidating key aspects of the antifreeze mechanisms and paving the way for the design of novel ice-controlling materials

Effect of a DC Electric field on the melting temperature, nucleation and ice growth rate of the TIP4P/ICE water model

Understanding the effect of electric fields on the thermal stability and phase transitions of water could have potential applications in the food industry, cryopreservation, and environmental science. In this work, we investigate the effect of a static electric field on the melting temperature (Tm), ice nucleation and ice growth rate of two phases of ice, hexagonal ice (Ih) and ferroelectric cubic ice (Icf), for the TIP4P/ICE water model. By means of direct coexistence simulations, we establish that Tm of Ice Ih is shifted toward lower values, whereas Tm of Ice Icf grows, becoming the most stable ice phase for sufficiently largevalues of the applied electric field. We also investigate ice nucleation for both ice phases under an external electric field and find that, for a given supercooling with respect to Tm, while the field slows down the nucleation rate of ice Ih significantly, it barely affects that of ice Icf, due to the enhanced ability of water molecules to orient favorably along the direction of the field in the latter phase. In terms of absolute temperature, overall ice formation is promoted by the electric field because it increases the melting point of ice Icf. Finally, we show how the electric field slows down the crystal growth of Ice Ih and increases that of Ice Icf by a factor of about two

RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins.

Funder: Oppenheimer FellowshipFunder: Roger Ekins FellowshipFunder: Derek Brewer Emmanuel College scholarshipBiomolecular condensates formed via liquid-liquid phase separation (LLPS) play a crucial role in the spatiotemporal organization of the cell material. Nucleic acids can act as critical modulators in the stability of these protein condensates. To unveil the role of RNA length in regulating the stability of RNA binding protein (RBP) condensates, we present a multiscale computational strategy that exploits the advantages of a sequence-dependent coarse-grained representation of proteins and a minimal coarse-grained model wherein proteins are described as patchy colloids. We find that for a constant nucleotide/protein ratio, the protein fused in sarcoma (FUS), which can phase separate on its own-i.e., via homotypic interactions-only exhibits a mild dependency on the RNA strand length. In contrast, the 25-repeat proline-arginine peptide (PR25), which does not undergo LLPS on its own at physiological conditions but instead exhibits complex coacervation with RNA-i.e., via heterotypic interactions-shows a strong dependence on the length of the RNA strands. Our minimal patchy particle simulations suggest that the strikingly different effect of RNA length on homotypic LLPS versus RBP-RNA complex coacervation is general. Phase separation is RNA-length dependent whenever the relative contribution of heterotypic interactions sustaining LLPS is comparable or higher than those stemming from protein homotypic interactions. Taken together, our results contribute to illuminate the intricate physicochemical mechanisms that influence the stability of RBP condensates through RNA inclusion

Size conservation emerges spontaneously in biomolecular condensates formed by scaffolds and surfactant clients

Funder: Junior Research Fellow at Kings CollegeFunder: Ernest Oppenheimer Memorial Trust; doi: http://dx.doi.org/10.13039/501100009978Abstract: Biomolecular condensates are liquid-like membraneless compartments that contribute to the spatiotemporal organization of proteins, RNA, and other biomolecules inside cells. Some membraneless compartments, such as nucleoli, are dispersed as different condensates that do not grow beyond a certain size, or do not present coalescence over time. In this work, using a minimal protein model, we show that phase separation of binary mixtures of scaffolds and low-valency clients that can act as surfactants—i.e., that significantly reduce the droplet surface tension—can yield either a single drop or multiple droplets that conserve their sizes on long timescales (herein ‘multidroplet size-conserved’ scenario’), depending on the scaffold to client ratio. Our simulations demonstrate that protein connectivity and condensate surface tension regulate the balance between these two scenarios. The multidroplet size-conserved scenario spontaneously arises at increasing surfactant-to-scaffold concentrations, when the interfacial penalty for creating small liquid droplets is sufficiently reduced by the surfactant proteins that are preferentially located at the interface. In contrast, low surfactant-to-scaffold concentrations enable continuous growth and fusion of droplets without restrictions. Overall, our work proposes one thermodynamic mechanism to help rationalize how size-conserved coexisting condensates can persist inside cells—shedding light on the roles of protein connectivity, binding affinity, and droplet composition in this process

The local skin cellular immune response determines the clinical outcome of sarcoptic mange in Iberian ibex (Capra pyrenaica)

Sarcoptic mange, caused by Sarcoptes scabiei, is a disease with implications for wildlife conservation and management. Its severity depends on the host's local skin immune response, which is largely unknown in Iberian ibex (Capra pyrenaica), a mountain ungulate dramatically affected by mange. In this species, the clinical outcome of sarcoptic mange varies among individuals, and the local immune response could be key to controlling the infestation. This study aims to characterize the local cellular immune response and its relationship with the clinical outcome. Fourteen Iberian ibexes were experimentally infested with S. scabiei and six more served as controls. Clinical signs were monitored, and skin biopsies were collected from the withers at 26, 46, and 103 days post-infection (dpi). The presence and distribution of macrophages (including M1 and M2 phenotypes), T lymphocytes, B lymphocytes, plasma cells, and interleukine 10 were quantitatively evaluated using immunohistochemical techniques. An inflammatory infiltrate that decreased significantly from 26 to 103 dpi was observed in all the infested ibexes. The predominant inflammatory cell population in the skin of the mangy ibexes was formed by macrophages (mainly the M2 phenotype) followed by T lymphocytes, with lower numbers of B lymphocytes and plasma cells. Three clinical courses were identified: total recovery, partial recovery, and terminal stage. The inflammatory infiltrates were less pronounced in the fully recovered ibexes than in those that progressed to the terminal stage throughout the study. The results suggest an exacerbated but effective Th1-type cellular immune response controlling mange in Iberian ibex. Furthermore, the local immune response appears to determine the variability of the clinical responses to S. scabiei infestation in this species. This first report on the progression of local skin immune cells is relevant not only for individuals but also for population management and conservation