Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userModel for disordered proteins with strongly sequence-dependent liquid phase behavior
175
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Phase separation of intrinsically disordered proteins is important for the formation of membraneless organelles, or biomolecular condensates, which play key roles in the regulation of biochemical processes within cells. In this work, we investigated the phase separation of different sequences of a coarse-grained model for intrinsically disordered proteins and discovered a surprisingly rich phase behavior. We studied both the fraction of total hydrophobic parts and the distribution of hydrophobic parts. Not surprisingly, sequences with larger hydrophobic fractions showed conventional liquid-liquid phase separation. The location of the critical point was systematically influenced by the terminal beads of the sequence, due to changes in interfacial composition and tension. For sequences with lower hydrophobicity, we observed not only conventional liquid-liquid phase separation, but also reentrant phase behavior, in which the liquid phase density decreases at lower temperatures. For some sequences, we observed formation of open phases consisting of aggregates, rather than a normal liquid. These aggregates had overall lower densities than the conventional liquid phases, and exhibited complex geometries with large interconnected string-like or membrane-like clusters. Our findings suggest that minor alterations in the ordering of residues may lead to large changes in the phase behavior of the protein, a fact of significant potential relevance for biology.
rate research
Read More
Bulk properties of ionic liquid crystals are investigated using density functional theory. The liquid crystal molecules are represented by ellipsoidal particles with charges located in their center or at their tails. Attractive interactions are taken into account in terms of the Gay-Berne pair potential. Rich phase diagrams involving vapor, isotropic and nematic liquid, as well as smectic phases are found. The dependence of the phase behavior on various parameters such as the length of the particles and the location of charges on the particles is studied.
Lattice Boltzmann simulations of liquid-gas systems are believed to be restricted to modest density ratios of less than 10. In this article we show that reducing the speed of sound and, just as importantly, the interfacial contributions to the pressure allows lattice Boltzmann simulations to achieve high density ratios of 1000 or more. We also present explicit expressions for the limits of the parameter region in which the method gives accurate results. There are two separate limiting phenomena. The first is the stability of the bulk liquid phase. This consideration is specific to lattice Boltzmann methods. The second is a general argument for the interface discretization that applies to any diffuse interface method.
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to liquid-liquid phase separation, or a via a bridging-induced attraction mechanism. For proteins which interact multivalently, we obtain a phase diagram which includes liquid-like droplets, droplets with absorbed polymer, and coated polymer regimes. Of particular interest is a regime where protein droplets only form due to interaction with the polymer; here, unlike a standard phase separating system, droplet density rather than size varies with the overall protein concentration. We also observe that protein dynamics within droplets slow down as chromatin is absorbed. If the protein-protein interactions have a strictly limited valence, fractal or gel-like condensates are instead observed. Together this provides biologically relevant insights into the nature of protein-chromatin condensates in living cells.
Multicomponent systems are ubiquitous in nature and industry. While the physics of few-component liquid mixtures (i.e., binary and ternary ones) is well-understood and routinely taught in undergraduate courses, the thermodynamic and kinetic properties of $N$-component mixtures with $N>3$ have remained relatively unexplored. An example of such a mixture is provided by the intracellular fluid, in which protein-rich droplets phase separate into distinct membraneless organelles. In this work, we investigate equilibrium phase behavior and morphology of $N$-component liquid mixtures within the Flory-Huggins theory of regular solutions. In order to determine the number of coexisting phases and their compositions, we developed a new algorithm for constructing complete phase diagrams, based on numerical convexification of the discretized free energy landscape. Together with a Cahn-Hilliard approach for kinetics, we employ this method to study mixtures with $N=4$ and $5$ components. We report on both the coarsening behavior of such systems, as well as the resulting morphologies in three spatial dimensions. We discuss how the number of coexisting phases and their compositions can be extracted with Principal Component Analysis (PCA) and K-Means clustering algorithms. Finally, we discuss how one can reverse engineer the interaction parameters and volume fractions of components in order to achieve a range of desired packing structures, such as nested `Russian dolls and encapsulated Janus droplets.
Based on simplifications of previous numerical calculations [Graf and L{o}wen, Phys. Rev. E textbf{59}, 1932 (1999)], we propose algebraic free energy expressions for the smectic-A liquid crystal phase and the crystal phases of hard spherocylinders. Quantitative agreement with simulations is found for the resulting equations of state. The free energy expressions can be used to straightforwardly compute the full phase behavior for all aspect ratios and to provide a suitable benchmark for exploring how attractive interrod interactions mediate the phase stability through perturbation approaches such as free-volume or van der Waals theory.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
