Browse
Submit Data
Databases
API
Help

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Role of Solvent Compatibility in the Phase Behavior of Binary Solutions of Weakly Associating Multivalent Polymers.

ABSTRACT: Condensate formation of biopolymer solutions, prominently those of various intrinsically disordered proteins (IDPs), is often driven by "sticky" interactions between associating residues, multivalently present along the polymer backbone. Using a ternary mean-field "stickers-and-spacers" model, we demonstrate that if sticker association is of the order of a few times the thermal energy, a delicate balance between specific binding and nonspecific polymer-solvent interactions gives rise to a particularly rich ternary phase behavior under physiological circumstances. For a generic system represented by a solution comprising multiassociative scaffold and client polymers, the difference in solvent compatibility between the polymers modulates the nature of isothermal liquid-liquid phase separation (LLPS) between associative and segregative. The calculations reveal regimes of dualistic phase behavior, where both types of LLPS occur within the same phase diagram, either associated with the presence of multiple miscibility gaps or a flip in the slope of the tie-lines belonging to a single coexistence region.

SUBMITTER: Michels JJ

PROVIDER: S-EPMC8753604 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Multivalent polymers can control phase boundary, dynamics, and organization of liquid-liquid phase separation.

Project description:Multivalent polymers are a key structural component of many biocondensates. When interacting with their cognate binding proteins, multivalent polymers such as RNA and modular proteins have been shown to influence the liquid-liquid phase separation (LLPS) boundary to both control condensate formation and to influence condensate dynamics after phase separation. Much is still unknown about the function and formation of these condensed droplets, but changes in their dynamics or phase separation are associated with neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and Alzheimer's Disease. Therefore, investigation into how the structure of multivalent polymers relates to changes in biocondensate formation and maturation is essential to understanding and treating these diseases. Here, we use a coarse-grain, Brownian Dynamics simulation with reactive binding that mimics specific interactions in order to investigate the difference between non-specific and specific multivalent binding polymers. We show that non-specific binding interactions can lead to much larger changes in droplet formation at lower protein-polymer interaction energies than their specific, valence-limited counterparts. We also demonstrate the effects of solvent conditions and polymer length on phase separation, and we present how modulating binding energy to the polymer can change the organization of a droplet in a three component system of polymer, binding protein, and solvent. Finally, we compare the effects of surface tension and polymer binding on the condensed phase dynamics, and show that both lower protein solubilities and higher attraction/affinity of the protein to the polymer result in slower droplet dynamics. This research will help to better understand experimental systems and provides additional insight into how multivalent polymers can control LLPS.

| S-EPMC8575181 | biostudies-literature

Cationic Polymers Remarkably Boost Haloalkane Dehalogenase Activity in Organic Solvent Solutions and the Molecular Implications.

Project description:Applications of haloalkane dehalogenase DhaA in biocatalysis are limited by its unfavorable performance in organic solvents. Our previous work proved that mutations of surface positive-charged residues enhanced the organic solvent resistance of DhaA, which inspired us to explore the effect of cationic polymers on DhaA in organic solvents. Remarkably boosted performance was achieved in different organic solvent solutions by introducing cationic polymers, for example, there was a 6.1-fold activity increase with poly(allylamine hydrochloride) and a 5.5-fold activity increase with poly(ethylene imine) in 40 vol.% dimethylsulfoxide. The presence of cationic polymers protected DhaA from damage by organic solvents and increased the substrate concentration around the enzyme-polymer complex. Fluorescence spectroscopy and molecular dynamics simulations revealed that the binding of cationic polymers onto DhaA weakened the interactions between organic solvents and DhaA, decreased the organic solvent solvation level around DhaA, and enhanced the structural stability of DhaA in organic solvents. This comprehensive understanding of the effect of cationic polymers on DhaA can help to broaden the applications of DhaA in organic solvent-involved biocatalysis.

| S-EPMC10574148 | biostudies-literature

Study on the corrosion behavior and mechanical response of weakly cemented sandstone in alkaline solutions.

Project description:This study examines the corrosion characteristics of weakly cemented sandstone under alkaline conditions, evaluating the effects of varying pH levels on its macroscopic degradation, micro-porosity, and mechanical properties, notably uniaxial compressive strength. Findings reveal that heightened alkalinity exacerbates rock damage, although a temporary alleviation in mass loss occurs between pH 9 and 11 due to pore clogging by complexes formed from cations like Ca2+ and Mg2+.Increased alkalinity induces marked changes in pore features, with an observed rise in pore numbers, transformation of pore shapes from elongated to more spherical, and adjustments in porosity, pore size, and roundness. Furthermore, the study confirms a decline in both the rock's compressive strength and elastic modulus as pH rises. These revelations shed light on the role of pH in the corrosion behavior of weakly cemented sandstone under alkaline conditions, providing a fresh perspective for understanding its corrosion mechanisms in such environments.

| S-EPMC11373863 | biostudies-literature

Superselective targeting using multivalent polymers.

Project description:Despite their importance for material and life sciences, multivalent interactions between polymers and surfaces remain poorly understood. Combining recent achievements of synthetic chemistry and surface characterization, we have developed a well-defined and highly specific model system based on host/guest interactions. We use this model to study the binding of hyaluronic acid functionalized with host molecules to tunable surfaces displaying different densities of guest molecules. Remarkably, we find that the surface density of bound polymer increases faster than linearly with the surface density of binding sites. Based on predictions from a simple analytical model, we propose that this superselective behavior arises from a combination of enthalpic and entropic effects upon binding of nanoobjects to surfaces, accentuated by the ability of polymer chains to interpenetrate.

| S-EPMC3919174 | biostudies-other

Modeling the Phase Equilibria of Associating Polymers in Porous Media with Respect to Chromatographic Applications.

Project description:Associating copolymers self-assemble during their passage through a liquid chromatography (LC) column, and the elution differs from that of common non-associating polymers. This computational study aims at elucidating the mechanism of their unique and intricate chromatographic behavior. We focused on amphiphilic diblock copolymers in selective solvents, performed the Monte Carlo (MC) simulations of their partitioning between a bulk solvent (mobile phase) and a cylindrical pore (stationary phase), and investigated the concentration dependences of the partition coefficient and of other functions describing the phase behavior. The observed abruptly changing concentration dependences of the effective partition coefficient demonstrate the significant impact of the association of copolymers with their partitioning between the two phases. The performed simulations reveal the intricate interplay of the entropy-driven and the enthalpy-driven processes, elucidate at the molecular level how the self-assembly affects the chromatographic behavior, and provide useful hints for the analysis of experimental elution curves of associating polymers.

| S-EPMC9370872 | biostudies-literature

Optimizing the Selectivity of Surface-Adsorbing Multivalent Polymers.

Project description:Multivalent polymers are macromolecules containing multiple chemical moieties designed to bind to complementary moieties on a target; for example, a protein with multiple ligands that have affinity for receptors on a cell surface. Though the individual ligand-receptor bonds are often weak, the combinatorial entropy associated with the different possible ligand-receptor pairs leads to a binding transition that can be very sharp with respect to control parameters, such as temperature or surface receptor concentration. We use mean-field self-consistent field theory to study the binding selectivity of multivalent polymers to receptor-coated surfaces. Polymers that have their ligands clustered into a contiguous domain, either located at the chain end or chain midsection, exhibit cooperative surface adsorption and superselectivity when the polymer concentration is low. On the other hand, when the ligands are uniformly spaced along the chain backbone, selectivity is substantially reduced due to the lack of binding cooperativity and due to crowding of the surface by the inert polymer segments in the chain backbone.

| S-EPMC4229857 | biostudies-other

Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules.

Project description:Molecular interactions of importance to cell biology are subject to sol-gel transitions: large clusters of weakly interacting multivalent molecules (gel phase) are produced at a critical concentration of monomers. Examples include cell-cell and cell-matrix adhesions, nucleoprotein bodies, and cell signaling platforms. We use the term pleomorphic ensembles (PEs) to describe these clusters, because they have dynamic compositions and sizes and have rapid turnover of their molecular constituents; this plasticity can be highly responsive to cellular signals. The classical polymer physical chemistry theory developed by Flory and Stockmayer provides a brilliant framework for treating multivalent interactions for simple idealized systems. But the complexity and variability of PEs challenges existing modeling approaches. Here we describe and validate a computational algorithm that extends the Flory-Stockmayer formalism to overcome the limitations of analytic theories. We divide the problem by deterministically calculating the fraction of bound sites for each type of binding site, followed by the stochastic assignment of the bonds to a finite number of molecules. The method allows for high valency within many different kinds of interacting molecules and site types, permits simulation of steady-state distributions, as well as assembly kinetics, and can treat cooperative binding within one of the interacting molecules. We then apply our method to the analysis of interactions in the nephrin-Nck-N-Wasp signaling system, demonstrating how multivalent layered scaffolds produce PEs at low monomer concentrations despite weak binding interactions. We show how the experimental data for this system are most consistent with synergistic cooperative interactions between Nck and N-Wasp.

| S-EPMC3853317 | biostudies-literature

Control and measurement of the phase behavior of aqueous solutions using microfluidics.

Project description:A microfluidic device denoted the Phase Chip has been designed to measure and manipulate the phase diagram of multicomponent fluid mixtures. The Phase Chip exploits the permeation of water through poly(dimethylsiloxane) (PDMS) in order to controllably vary the concentration of solutes in aqueous nanoliter volume microdrops stored in wells. The permeation of water in the Phase Chip is modeled using the diffusion equation, and good agreement between experiment and theory is obtained. The Phase Chip operates by first creating drops of the water/solute mixture whose composition varies sequentially. Next, drops are transported down channels and guided into storage wells using surface tension forces. Finally, the solute concentration of each stored drop is simultaneously varied and measured. Two applications of the Phase Chip are presented. First, the phase diagram of a polymer/salt mixture is measured on-chip and validated off-chip, and second, protein crystallization rates are enhanced through the manipulation of the kinetics of nucleation and growth.

| S-EPMC2531156 | biostudies-literature

Different Topologies of Hg(II)-Bispidine 1D Coordination Polymers: Dynamic Behavior in Solvent Adsorption and Exchange Processes.

Project description:One-dimensional (1D) coordination polymers (CPs) featuring three different topologies, comprising zig-zag, ribbon-like and poly-[n]-catenane structures, were obtained by reaction of Hg(II) ions with a novel bispidine ligand L3, and structurally characterized by SC- and P-XRD methods. The CPs obtained in the form of microcrystalline powders were tested for their ability to undergo solvent adsorption and exchange by P-XRD and 1 H NMR spectroscopy. The extent of their dynamic behavior was then correlated to their structural features, highlighting the role of interchain interactions established among their constituting linear arrays. Zig-zag CPs proved to be resilient to external chemical stimuli, while they differently respond to thermal treatments, depending on the solvent originally included within the CP. In the case of polycatenated structures, we observed transformations where the original topology was maintained upon guest exchange, but also cases where it changed to zig-zag, even under solid/vapor conditions (i. e., no complete dissolution of the CP). Given the presence of linear interconnected 1D channels, 3 ⋅ ClBz-polycatenanePwd is also able to trap volatile guests such as n-hexane when exposed to its vapors.

| S-EPMC9311696 | biostudies-literature

Layered microporous polymers by solvent knitting method.

Project description:Two-dimensional (2D) nanomaterials, especially 2D organic nanomaterials with unprecedentedly diverse and controlled structure, have attracted decent scientific interest. Among the preparation strategies, the top-down approach is one of the considered low-cost and scalable strategies to obtain 2D organic nanomaterials. However, some factors of their layered counterparts limited the development and potential applications of 2D organic nanomaterials, such as type, stability, and strict synthetic conditions of layered counterparts. We report a class of layered solvent knitting hyper-cross-linked microporous polymers (SHCPs) prepared by improving Friedel-Crafts reaction and using dichloroalkane as an economical solvent, stable electrophilic reagent, and external cross-linker at low temperature, which could be used as layered counterparts to obtain previously unknown 2D SHCP nanosheets by method of ultrasonic-assisted solvent exfoliation. This efficient and low-cost strategy can produce previously unreported microporous organic polymers with layered structure and high surface area and gas storage capacity. The pore structure and surface area of these polymers can be controlled by tuning the chain length of the solvent, the molar ratio of AlCl3, and the size of monomers. Furthermore, we successfully obtain an unprecedentedly high-surface area HCP material (3002 m2 g-1), which shows decent gas storage capacity (4.82 mmol g-1 at 273 K and 1.00 bar for CO2; 12.40 mmol g-1 at 77.3 K and 1.13 bar for H2). This finding provides an opportunity for breaking the constraint of former knitting methods and opening up avenues for the design and synthesis of previously unknown layered HCP materials.

| S-EPMC5376128 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data