Formation Of Protein Clusters Research Articles

Effective interactions in protein solutions with and without clustering

Protein interactions in solution and the question of cluster formation are of paramount importance to a wide range of research fields and industrial applications. Protein clustering can arise due to a delicate interplay between the short-range attraction and the long-range repulsion in the interaction potential. This study employs small angle X-ray scattering (SAXS) to examine the clustering behavior of three protein systems in solution: bovine serum albumin (BSA), bovine β-lactoglobulin (BLG) and lysozyme (LYZ) under varying protein concentrations, ionic strengths and temperatures. The goal is to elucidate the influence of the attractive potential’s nature on clustering behavior. BSA serves as a reference system, where electrostatic repulsions dominate the effective interactions, resulting in a mean protein–protein distance as a function of protein concentration which follows the 1/3 power law and precludes protein cluster formation. In contrast, BLG and LYZ solutions exhibit exponents less than 1/3, indicating concentration-dependent cluster formation. The effective interactions are well described using a two-Yukawa type potential comprising a long-ranged repulsion and a short-ranged attraction. While increasing ionic strength by adding NaCl reduced repulsion and correlation in all three systems, the response of protein solutions to ionic strength differed for clustering systems of BLG and LYZ. BLG solutions exhibited a reduced attraction with increasing ionic strength, leading to cluster dissolution, while LYZ solutions experienced enhanced attraction, favoring larger cluster formation. Notably, BLG solutions showed minimal temperature dependence, while LYZ solutions exhibited increased attraction with decreasing temperature, further promoting cluster formation. These results demonstrate the crucial role of short-ranged attractions of specific nature in determining protein clustering behavior. A thorough understanding of protein interactions is essential for predicting protein clustering and phase behavior.

Protein of yak milk residue: Structure, functionality, and the effects on the quality of non-fat yogurt

The purpose of this study was to compare the structural and functional of protein from yak milk residue, which collected from different elevations (MRP1 and MRP2) in Tibet, as well as their potential for enhancing the quality of non-fat yogurt. The results showed that MRP1 exhibited higher levels of β-sheet, turbidity, particle size, and gel properties. MRP2 had better flexibility, emulsification, foaming, water/oil absorption capacity. The addition of MRP1 (3%) could improve texture and sensory properties of yogurt. Although MRP2 yogurt had higher hardness, gumminess, chewiness and water holding capacity, poor mouthfeel. Rheological test showed that MRPs yogurt exhibited typical gel-like and shear-thinning behavior. Moreover, the fortification of non-fat yogurts with MRP1 brought the formation of larger protein clusters with a more tightly knit network of smaller pores. These results indicate that MRP1 can be used as a fat substitute to improve the quality of non-fat yogurt.

Asymptotic analysis of particle cluster formation in the presence of anchoring sites

The aggregation or clustering of proteins and other macromolecules plays an important role in the formation of large-scale molecular assemblies within cell membranes. Examples of such assemblies include lipid rafts, and postsynaptic domains (PSDs) at excitatory and inhibitory synapses in neurons. PSDs are rich in scaffolding proteins that can transiently trap transmembrane neurotransmitter receptors, thus localizing them at specific spatial positions. Hence, PSDs play a key role in determining the strength of synaptic connections and their regulation during learning and memory. Recently, a two-dimensional (2D) diffusion-mediated aggregation model of PSD formation has been developed in which the spatial locations of the clusters are determined by a set of fixed anchoring sites. The system is kept out of equilibrium by the recycling of particles between the cell membrane and interior. This results in a stationary distribution consisting of multiple clusters, whose average size can be determined using an effective mean-field description of the particle concentration around each anchored cluster. In this paper, we derive corrections to the mean-field approximation by applying the theory of diffusion in singularly perturbed domains. The latter is a powerful analytical method for solving two-dimensional (2D) and three-dimensional (3D) diffusion problems in domains where small holes or perforations have been removed from the interior. Applications range from modeling intracellular diffusion, where interior holes could represent subcellular structures such as organelles or biological condensates, to tracking the spread of chemical pollutants or heat from localized sources. In this paper, we take the bounded domain to be the cell membrane and the holes to represent anchored clusters. The analysis proceeds by partitioning the membrane into a set of inner regions around each cluster, and an outer region where mean-field interactions occur. Asymptotically matching the inner and outer stationary solutions generates an asymptotic expansion of the particle concentration, which includes higher-order corrections to mean-field theory that depend on the positions of the clusters and the boundary of the domain. Motivated by a recent study of light-activated protein oligomerization in cells, we also develop the analogous theory for cluster formation in a three-dimensional (3D) domain. The details of the asymptotic analysis differ from the 2D case due to the contrasting singularity structure of 2D and 3D Green’s functions.Graphical abstract2D model of diffusion-based protein cluster formation in the presence of anchoring cites and particle recycling. a A set of N anchoring sites at positions xj\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\ extbf{x}}_j$$\\end{document}, j=1,…,N\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$j=1,\\ldots ,N$$\\end{document}, in a bounded domain Ω\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\Omega $$\\end{document}. b Diffusing particles accumulate at the anchoring sites resulting in the formation of particle aggregates or clusters Uj\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${{\\mathcal {U}}}_j$$\\end{document}. c The clusters are dynamically maintained by a combination of lateral diffusion outside the clusters and particle recycling

Molecular Dynamics Study of Protein Aggregation at Moving Interfaces.

Repeated compression and dilation of a protein film adsorbed to an interface lead to aggregation and entry of film fragments into the bulk. This is a major mechanism for protein aggregate formation in drug products upon mechanical stress, such as shaking or pumping. To gain a better understanding of these events, we developed a molecular dynamics (MD) setup, which would, in a later stage, allow for in silico formulation optimization. In contrast to previous approaches, the molecules of our model protein human growth hormone displayed realistic shapes, surfaces, and interactions with each other and the interface. This enabled quantitative assessment of protein cluster formation. Simulation outcomes aligned with experimental data on subvisible particles and turbidity, thereby validating the model. Computational and experimental results indicated that compression speed does not affect the aggregation behavior of preformed protein films but rather their regeneration. Protein clusters that formed during compression disassembled upon relaxation, suggesting that the particles originate from a partly compressed state. Desorption studies via steered MD revealed that proteins from compressed systems are more likely to detach as clusters, implying that compression effects at the interface translate into aggregates present in the bulk solution. With the possibility of studying the impact of different variables upon compression and dilation at the interface on a molecular level, our model contributes to the understanding of the mechanisms of protein aggregation at moving interfaces. It also enables further studies to change formulation parameters, interfaces, or proteins.

Separation of protein corona from nanoparticles under intracellular acidic conditions: effect of protonation on nanoparticle-protein and protein-protein interactions.

Protein coronas separate from nanoparticles under intracellular acidic conditions however, competitive adsorption of multiple proteins and their protein network formation under different pH conditions have not yet been systematically studied at the atomic scale. Herein, we report all-atom molecular dynamics simulations of plasma proteins (human serum albumin and immunoglobulin gamma-1 chain C) adsorbed to 10 nm-sized carboxyl-terminated polystyrene (PS) nanoparticles at different protonation states that mimic extracellular and intracellular pH conditions of 7, 6-5, and 4.5. Binding free energies are calculated from umbrella sampling simulations, showing the significantly weakened binding between PS particles and proteins at the protonation state at pH 4.5, in agreement with experiments showing the separation of protein corona from nanoparticles at pH 4.5. Mixtures of multiple proteins and PS particles are also simulated, showing much less protein adsorption and protein cluster formation at the protonation state at pH 4.5 than that at higher pH values, which are further confirmed by calculating the diffusivities and hydrodynamic radii of individual proteins. In particular, electrostatic particle-protein and protein-protein interactions are significantly weakened by a combination of particle and protein protonation rather than by particle protonation alone, to an extent dependent on different proteins. These findings help explain the experimental observations regarding separation of protein corona from nanoparticles under intracellular acidic conditions at pH 4.5 but not at higher pH, supporting that acidification cannot be the only reason for this separation during the process of endosome maturation.

Quantitative real-time in-cell imaging reveals heterogeneous clusters of proteins prior to condensation

Our current understanding of biomolecular condensate formation is largely based on observing the final near-equilibrium condensate state. Despite expectations from classical nucleation theory, pre-critical protein clusters were recently shown to form under subsaturation conditions in vitro; if similar long-lived clusters comprising more than a few molecules are also present in cells, our understanding of the physical basis of biological phase separation may fundamentally change. Here, we combine fluorescence microscopy with photobleaching analysis to quantify the formation of clusters of NELF proteins in living, stressed cells. We categorise small and large clusters based on their dynamics and their response to p38 kinase inhibition. We find a broad distribution of pre-condensate cluster sizes and show that NELF protein cluster formation can be explained as non-classical nucleation with a surprisingly flat free-energy landscape for a wide range of sizes and an inhibition of condensation in unstressed cells.

The Role of Water Hydrogen Bonds in the Formation of Associates and Condensates in Dispersions of Serum Albumin with Shungite Carbon and Quartz Nanoparticles

The role of the network of water hydrogen bonds in the regulation of the intermolecular interaction’s responsible for colloidal stability of dispersions has been studied in order to search for general patterns of interaction between water, nanoparticles, and bio-macromolecules. Raman spectroscopy for mixed dispersions of bovine serum albumin (SA), shungite carbon nanoparticles (ShC NPs), and quartz nanoparticles (quartz NPs) was performed within the wave number range 3200–3600 cm−1. The main spectral lines in this range are caused by the OH stretch vibrations of water molecules. We analyzed the state of the water hydrogen bonding network for dispersions of varied ratios of both fatty acid-containing and fatty acid-free SA macromolecules, ShC NPs, and silica NPs in the range 0.01–10 mg/mL.We used dynamic light scattering to control the sizes of the protein associates and protein associates with ShC NPs and quartz NPs. The strength of the hydrogen bonds in water depends essentially non-linearly, but in a qualitatively similar way, on the concentrations of the dispersion components. The initial strengthening of the bonds is followed by their loosening with a further increase in the concentration of the components. This is accompanied by the association of the dispersion components. We estimate the thickness of the protein corona layer as 20–25 nm for ShC NPs and 28–33 nm for quartz NPs, depending on the SA concentration. Colloidal stability of the aqueous dispersion is determined almost completely by an association of the protein with NPs. In contrast, colloidal stability of a pure protein solution is regulated by the formation of protein clusters of two main types and sizes. The association effects of SA with ShC NPs are evident in microscopic images of condensate films. The structures differ significantly for native and fatty acid-free SA in shape and size.

Galectin-3 Binding to α5β1 Integrin in Pore Suspended Biomembranes.

Galectin-3 (Gal3) is a β-galactoside binding lectin that mediates many physiological functions, including the binding of cells to the extracellular matrix for which the glycoprotein α5β1 integrin is of critical importance. The mechanisms by which Gal3 interacts with membranes have not been widely explored to date due to the complexity of cell membranes and the difficulty of integrin reconstitution within model membranes. Herein, to study their interaction, Gal3 and α5β1 were purified, and the latter reconstituted into pore-suspended lipid bilayers comprised eggPC:eggPA. Using electrochemical impedance and fluorescence lifetime correlation spectroscopy, we found that on incubation with low nanomolar concentrations of wild-type Gal3, the membrane's admittance and fluidity, as well as integrin's lateral diffusivity, were enhanced. These effects were diminished in the following conditions: (i) absence of integrin, (ii) presence of lactose as a competitive inhibitor of glycan-Gal3 interaction, and (iii) use of a Gal3 mutant that lacked the N-terminal oligomerization domain (Gal3ΔNter). These findings indicated that WTGal3 oligomerized on α5β1 integrin in a glycan-dependent manner and that the N-terminal domain interacted directly with membranes in a way that is yet to be fully understood. At concentrations above 10 nM of WTGal3, membrane capacitance started to decrease and very slowly diffusing molecular species appeared, which indicated the formation of protein clusters made from WTGal3-α5β1 integrin assemblies. Overall, our study demonstrates the capacity of WTGal3 to oligomerize in a cargo protein-dependent manner at low nanomolar concentrations. Of note, these WTGal3 oligomers appeared to have membrane active properties that could only be revealed using our sensitive methods. At slightly higher WTGal3 concentrations, the capacity to generate lateral assemblies between cargo proteins was observed. In cells, this could lead to the construction of tubular endocytic pits according to the glycolipid-lectin (GL-Lect) hypothesis or to the formation of galectin lattices, depending on cargo glycoprotein stability at the membrane, the local Gal3 concentration, or plasma membrane intrinsic parameters. The study also demonstrates the utility of microcavity array-suspended lipid bilayers to address the biophysics of transmembrane proteins.

Effects of Commercial Polysaccharides Stabilizers with Different Charges on Textural, Rheological, and Microstructural Characteristics of Set Yoghurts.

The study investigated the preparation of set yoghurts by adding three common commercial polysaccharide stabilizers, namely sodium alginate (SA), gellan gum (GG), and konjac gum (KGM), in milk fermentation to evaluate their effects on the texture, rheology, and microstructure of set yoghurts. The physicochemical properties, water-holding capacity (WHC), texture, low-field nuclear magnetic resonance (LF-NMR), rheology, and microstructure of set yoghurts added with different kinds and quantities of polysaccharides were compared and analyzed. The results showed that the set yoghurts added with anionic polysaccharide GG had more obvious effects on improving WHC, firmness, and rheological properties compared with the set yoghurt added with KGM and SA. The firmness of set yoghurts with 0.02% (w/v) GG increased from 1.17 N to 1.32 N, which significantly improved the gel structure. The transverse relaxation time (T2) of set yoghurts added with GG was the closest to that of the control. Compared with the set yoghurts added with 0.02% SA and KGM, the free water area (A23) of the one added with 0.02% GG decreased most significantly. Moreover, all samples showed shear-thinning behavior, and the apparent elastic and viscous modulus (G′, G″) increased with the increase of GG concentration. The G′ and G″ of set yoghurts with 0.005% SA and KGM were higher than those in the control, decreased when adding 0.010%, and then increased with the increase of SA and KGM. Additionally, the microscopic observation demonstrated that the addition of GG in set yoghurts significantly promoted the formation of larger protein clusters and showed a tighter and more uniform protein network comparing with the other two polysaccharides (SA, KGM).

Neurexins play a crucial role in cerebellar granule cell survival by organizing autocrine machinery for neurotrophins

Neurexins (NRXNs) are key presynaptic cell adhesion molecules that regulate synapse formation and function via trans-synaptic interaction with postsynaptic ligands. Here, we generate cerebellar granule cell (CGC)-specific Nrxn triple-knockout (TKO) mice for complete deletion of all NRXNs. Unexpectedly, most CGCs die in these mice, and this requirement for NRXNs for cell survival is reproduced in cultured CGCs. The axons of cultured Nrxn TKO CGCs that are not in contact with a postsynaptic structure show defects in the formation of presynaptic protein clusters and in action-potential-induced Ca2+ influxes. These cells also show impaired secretion of depolarization-induced, fluorescence-tagged brain-derived neurotrophic factor (BDNF) from their axons, and the cell-survival defect is rescued by the application of BDNF. These results suggest that CGC survival is maintained by autocrine neurotrophic factors and that NRXNs organize the presynaptic protein clusters and the autocrine neurotrophic-factor secretory machinery independent of contact with postsynaptic ligands.

The effect of different lyophilisation pressures on the microbiological stability, physicochemical, microstructural, and sensorial properties of yoghurt powders

This study investigated how different pressures used in the lyophilisation process affected the physicochemical, microstructural, microbiological, and sensory properties of yoghurt powders. To that end, pressures of 0.3 (0.3PY), 0.5 (0.5PY) and 1.0 (1.0PY) mbar were applied to obtain powders. Additionally, some physical and sensory properties of rehydrated yoghurt powders were evaluated. Different pressures did not affect final moisture content and powder yield. According to CLSM examinations, 0.3PY showed finer protein network, while the formation of coarser protein clusters in 0.5PY and 1.0PY was noted. Water activity of powders increased with increasing pressure. The count of Lactobacillus bulgaricus was higher in 0.5PY and 1.0PY, while Streptococcus thermophilus showed 93–95% viability. WHC and viscosity values of all rehydrated yoghurts were found to be considerably lower than fresh yoghurts; however, the best results related to these properties were determined in reconstituted yoghurts of 0.5PY and 1.0PY.

Thermodynamics and Kinetics of Aggregation of Flexible Peripheral Membrane Proteins.

Biomembrane remodeling is essential for cellular trafficking, with membrane-binding peripheral proteins playing a key role in it. Significant membrane remodeling as in endo- and exocytosis is often due to aggregates of many proteins with direct or membrane-mediated interactions. Understanding this process via computer simulations is extremely challenging: protein-membrane systems involve time and length scales that make atomistic simulations impractical, while most coarse-grained models fall short in resolving dynamics and physical effects of protein and membrane flexibility. Here, we develop a coarse-grained model of the bilayer membrane bestrewed with rotationally symmetric flexible proteins, parametrized to reflect local curvatures and lateral dynamics of proteins. We investigate the kinetics, equilibrium distributions, and the free energy landscape governing the formation and breakup of protein clusters on the surface of the membrane. We demonstrate how the flexibility of the proteins as well as their surface concentration play deciding roles in highly selective macroscopic aggregation behavior.

Suppression of human T cell activation by derivatives of glycerol monolaurate

Glycerol monolaurate (GML), a naturally occurring monoglyceride, is widely used commercially for its antimicrobial properties. Interestingly, several studies have shown that GML not only has antimicrobial properties but is also an anti-inflammatory agent. GML inhibits peripheral blood mononuclear cell proliferation and inhibits T cell receptor (TCR)-induced signaling events. In this study, we perform an extensive structure activity relationship analysis to investigate the structural components of GML necessary for its suppression of human T cell activation. Human T cells were treated with analogs of GML, differing in acyl chain length, head group, linkage of acyl chain, and number of laurate groups. Treated cells were then tested for changes in membrane dynamics, LAT clustering, calcium signaling, and cytokine production. We found that an acyl chain with 12–14 carbons, a polar head group, an ester linkage, and a single laurate group at any position are all necessary for GML to inhibit protein clustering, calcium signaling, and cytokine production. Removing the glycerol head group or replacing the ester linkage with a nitrogen prevented derivative-mediated inhibition of protein cluster formation and calcium signaling, while still inhibiting TCR-induced cytokine production. These findings expand our current understanding of the mechanisms of action of GML and the of GML needed to function as a novel immunosuppressant.

Molecular Regulators of Cellular Mechanoadaptation at Cell-Material Interfaces.

Diverse essential cellular behaviors are determined by extracellular physical cues that are detected by highly orchestrated subcellular interactions with the extracellular microenvironment. To maintain the reciprocity of cellular responses and mechanical properties of the extracellular matrix, cells utilize a variety of signaling pathways that transduce biophysical stimuli to biochemical reactions. Recent advances in the micromanipulation of individual cells have shown that cellular responses to distinct physical and chemical features of the material are fundamental determinants of cellular mechanosensation and mechanotransduction. In the process of outside-in signal transduction, transmembrane protein integrins facilitate the formation of focal adhesion protein clusters that are connected to the cytoskeletal architecture and anchor the cell to the substrate. The linkers of nucleoskeleton and cytoskeleton molecular complexes, collectively termed LINC, are critical signal transducers that relay biophysical signals between the extranuclear cytoplasmic region and intranuclear nucleoplasmic region. Mechanical signals that involve cytoskeletal remodeling ultimately propagate into the nuclear envelope comprising the nuclear lamina in assistance with various nuclear membrane proteins, where nuclear mechanics play a key role in the subsequent alteration of gene expression and epigenetic modification. These intracellular mechanical signaling cues adjust cellular behaviors directly associated with mechanohomeostasis. Diverse strategies to modulate cell-material interfaces, including alteration of surface rigidity, confinement of cell adhesive region, and changes in surface topology, have been proposed to identify cellular signal transduction at the cellular and subcellular levels. In this review, we will discuss how a diversity of alterations in the physical properties of materials induce distinct cellular responses such as adhesion, migration, proliferation, differentiation, and chromosomal organization. Furthermore, the pathological relevance of misregulated cellular mechanosensation and mechanotransduction in the progression of devastating human diseases, including cardiovascular diseases, cancer, and aging, will be extensively reviewed. Understanding cellular responses to various extracellular forces is expected to provide new insights into how cellular mechanoadaptation is modulated by manipulating the mechanics of extracellular matrix and the application of these materials in clinical aspects.

INCLUSION BODIES IN BIOTECHNOLOGY

Protein aggregation is commonly observed phenomenon occurring during production of recombinant proteins in genetically engineered organisms over-expressing foreign genes. Aggregation of such recombinant proteins often leads to the formation of insoluble protein clusters named inclusion bodies (IBs). Although usually considered as waste by-products of protein production, over the last decade, this general misconception has been questioned by various studies. Gradual understanding of the structural, molecular and physiological features has revealed promising potential of these so far undesirable cellular products. In the present review we summarize basic characteristics of IBs, their use in antimicrobial peptides production and in various biotechnological fields, including tissue engineering, drug delivery and biocatalysis.

Indirect repulsion between actin binding proteins induces the local pattern formation of protein clusters

A periodic pattern composed of alternating myosin II and α-actinin clusters forms along the stress fibers in live cells. Here, we propose that the indirect repulsion between these proteins is able to lead to the formation of the periodic pattern. We use a coarse-grained Kinetic Monte Carlo method to investigate the effect of the repulsion strength. The simulation results reproduce the phase separation of these proteins as well as the dynamics of the cluster growth observed in experiments. Meanwhile, a double-S feature emerges during the cluster growth when the repulsion strength is high, indicating that the system undergoes a transition from an intermediate state to the final state. The good agreement between our simulations and the published experimental observations suggests that the indirect repulsion might play an important role during the pattern formation of proteins along the stress fibers.

Neuronal BIN1 Regulates Presynaptic Neurotransmitter Release and Memory Consolidation

SUMMARYBIN1, a member of the BAR adaptor protein family, is a significant late-onset Alzheimer disease risk factor. Here, we investigate BIN1 function in the brain using conditional knockout (cKO) models. Loss of neuronal Bin1 expression results in the select impairment of spatial learning and memory. Examination of hippocampal CA1 excitatory synapses reveals a deficit in presynaptic release probability and slower depletion of neurotransmitters during repetitive stimulation, suggesting altered vesicle dynamics in Bin1 cKO mice. Super-resolution and immunoelectron microscopy localizes BIN1 to presynaptic sites in excitatory synapses. Bin1 cKO significantly reduces synapse density and alters presynaptic active zone protein cluster formation. Finally, 3D electron microscopy reconstruction analysis uncovers a significant increase in docked and reserve pools of synaptic vesicles at hippocampal synapses in Bin1 cKO mice. Our results demonstrate a non-redundant role for BIN1 in presynaptic regulation, thus providing significant insights into the fundamental function of BIN1 in synaptic physiology relevant to Alzheimer disease.

Differential Actin Binding Affinity Leads to Protein Sorting in a Reconstituted Active Composite Layer

Various functional cell surface proteins bind to cortical actin and undergo actomyosin driven clustering. GPI-anchored proteins, T-cell receptors, glycoproteins such as CD44, and E-cadherins are some reported examples of such patterning. Given the density and diversity of proteins in the plasma membrane, the question arises how the local accumulation of specific molecules is controlled spatiotemporally. Here we explore the possibility that molecular patterning and cluster formation of membrane proteins arises from the combination of differential binding of surface molecules to actin filaments and non-equilibrium actomyosin dynamics.

A multi-channel in situ light scattering instrument utilized for monitoring protein aggregation and liquid dense cluster formation

Liquid-liquid phase separation (LLPS) phenomena have been observed in vitro as well as in vivo and came in focus of interdisciplinary research activities particularly aiming at understanding the physico-chemical pathways of LLPS and its functionality in recent years. Dynamic light scattering (DLS) has been proven to be a most efficient method to analyze macromolecular clustering in solutions and suspensions with diverse applications in life sciences, material science and biotechnology. For spatially and time-resolved investigations of LLPS, i.e. formation of liquid dense protein clusters (LDCs) and aggregation, a novel eight-channel in situ DLS instrument was designed, constructed and applied. The real time formation of LDCs of glucose isomerase (GI) and bovine pancreatic trypsin inhibitor (BPTI) under different physico-chemical conditions was investigated in situ. Complex shifts in the particle size distributions indicated growth of LDCs up to the μm size regime. Additionally, near-UV circular dichroism spectroscopy was performed to monitor the folding state of the proteins in the process of LDC formation.

Multi-Step Concanavalin A Phase Separation and Early-Stage Nucleation Monitored Via Dynamic and Depolarized Light Scattering

Protein phase separation and protein liquid cluster formation have been observed and analysed in protein crystallization experiments and, in recent years, have been reported more frequently, especially in studies related to membraneless organelles and protein cluster formation in cells. A detailed understanding about the phase separation process preceding liquid dense cluster formation will elucidate what has, so far, been poorly understood—despite intracellular crowding and phase separation being very common processes—and will also provide more insights into the early events of in vitro protein crystallization. In this context, the phase separation and crystallization kinetics of concanavalin A were analysed in detail, which applies simultaneous dynamic light scattering and depolarized dynamic light scattering to obtain insights into metastable intermediate states between the soluble phase and the crystalline form. A multi-step mechanism was identified for ConA phase separation, according to the resultant ACF decay, acquired after an increase in the concentration of the crowding agent until a metastable ConA gel intermediate between the soluble and final crystalline phases was observed. The obtained results also revealed that ConA is trapped in a macromolecular network due to short-range intermolecular protein interactions and is unable to transform back into a non-ergodic solution.