Widespread amyloidogenicity potential of multiple myeloma patient-derived immunoglobulin light chains.

BACKGROUND: In a range of human disorders such as multiple myeloma (MM), immunoglobulin light chains (IgLCs) can be produced at very high concentrations. This can lead to pathological aggregation and deposition of IgLCs in different tissues, which in turn leads to severe and potentially fatal organ damage. However, IgLCs can also be highly soluble and non-toxic. It is generally thought that the cause for this differential solubility behaviour is solely found within the IgLC amino acid sequences, and a variety of individual sequence-related biophysical properties (e.g. thermal stability, dimerisation) have been proposed in different studies as major determinants of the aggregation in vivo. Here, we investigate biophysical properties underlying IgLC amyloidogenicity. RESULTS: We introduce a novel and systematic workflow, Thermodynamic and Aggregation Fingerprinting (ThAgg-Fip), for detailed biophysical characterisation, and apply it to nine different MM patient-derived IgLCs. Our set of pathogenic IgLCs spans the entire range of values in those parameters previously proposed to define in vivo amyloidogenicity; however, none actually forms amyloid in patients. Even more surprisingly, we were able to show that all our IgLCs are able to form amyloid fibrils readily in vitro under the influence of proteolytic cleavage by co-purified cathepsins. CONCLUSIONS: We show that (I) in vivo aggregation behaviour is unlikely to be mechanistically linked to any single biophysical or biochemical parameter and (II) amyloidogenic potential is widespread in IgLC sequences and is not confined to those sequences that form amyloid fibrils in patients. Our findings suggest that protein sequence, environmental conditions and presence and action of proteases all determine the ability of light chains to form amyloid fibrils in patients.

Protein solutions close to liquid-liquid phase separation exhibit a universal osmotic equation of state and dynamical behavior.

Liquid-liquid phase separation (LLPS) of protein solutions is governed by highly complex protein-protein interactions. Nevertheless, it has been suggested that based on the extended law of corresponding states (ELCS), as proposed for colloids with short-range attractions, one can rationalize not only the thermodynamics, but also the structure and dynamics of such systems. This claim is systematically and comprehensively tested here by static and dynamic light scattering experiments. Spinodal lines, the isothermal osmotic compressibility κT and the relaxation rate of concentration fluctuations Γ are determined for protein solutions in the vicinity of LLPS. All these quantities are found to exhibit a corresponding-states behavior. This means that, for different solution conditions, these quantities are essentially the same if considered at similar reduced temperature or second virial coefficient. For moderately concentrated solutions, the volume fraction ϕ dependence of κT and Γ can be consistently described by Baxter's model of adhesive hard spheres. The off-critical, asymptotic T behavior of κT and Γ close to LLPS is consistent with the scaling laws predicted by mean-field theory. Thus, the present work aims at a comprehensive experimental test of the applicability of the ELCS to structural and dynamical properties of concentrated protein solutions.

Phase separation and dynamical arrest of protein solutions dominated by short-range attractions.

The interplay of liquid-liquid phase separation (LLPS) and dynamical arrest can lead to the formation of gels and glasses, which is relevant for such diverse fields as condensed matter physics, materials science, food engineering, and the pharmaceutical industry. In this context, protein solutions exhibit remarkable equilibrium and non-equilibrium behaviors. In the regime where attractive and repulsive forces compete, it has been demonstrated, for example, that the location of the dynamical arrest line seems to be independent of ionic strength, so that the arrest lines at different ionic screening lengths overlap, in contrast to the LLPS coexistence curves, which strongly depend on the salt concentration. In this work, we show that the same phenomenology can also be observed when the electrostatic repulsions are largely screened, and the range and strength of the attractions are varied. In particular, using lysozyme in brine as a model system, the metastable gas-liquid binodal and the dynamical arrest line as well as the second virial coefficient have been determined for various solution conditions by cloud-point measurements, optical microscopy, centrifugation experiments, and light scattering. With the aim of understanding this new experimental phenomenology, we apply the non-equilibrium self-consistent generalized Langevin equation theory to a simple model system with only excluded volume plus short-range attractions, to study the dependence of the predicted arrest lines on the range of the attractive interaction. The theoretical predictions find a good qualitative agreement with experiments when the range of the attraction is not too small compared with the size of the protein.

Modeling the structure and thermodynamics of multicomponent and polydisperse hard-sphere dispersions with continuous potentials.

A model system of identical particles interacting via a hard-sphere potential is essential in condensed matter physics; it helps to understand in and out of equilibrium phenomena in complex fluids, such as colloidal dispersions. Yet, most of the fixed time-step algorithms to study the transport properties of those systems have drawbacks due to the mathematical nature of the interparticle potential. Because of this, mapping a hard-sphere potential onto a soft potential has been recently proposed [Báez et al., J. Chem. Phys. 149, 164907 (2018)]. More specifically, using the second virial coefficient criterion, one can set a route to estimate the parameters of the soft potential that accurately reproduces the thermodynamic properties of a monocomponent hard-sphere system. However, real colloidal dispersions are multicomponent or polydisperse, making it important to find an efficient way to extend the potential model for dealing with such kind of many-body systems. In this paper, we report on the extension and applicability of the second virial coefficient criterion to build a description that correctly captures the phenomenology of both multicomponent and polydisperse hard-sphere dispersions. To assess the accuracy of the continuous potentials, we compare the structure of soft polydisperse systems with their hard-core counterpart. We also contrast the structural and thermodynamic properties of soft binary mixtures with those obtained through mean-field approximations and the Ornstein-Zernike equation for the two-component hard-sphere dispersion.

Layering and packing in confined colloidal suspensions.

Confinement modifies the properties of a fluid. The particle density is no longer uniform but depends on the distance from the walls; parallel to the walls, layers with different particle densities form. This affects the particle packing in the layers. We investigated colloidal fluids with volume fractions between 0.19 and 0.32 confined between rough walls. The particle-particle interactions were dominated by hard-sphere interactions but also contained some electrostatic interactions. The particle locations were determined using confocal microscopy and served to calculate the density profile, radial distribution function, anisotropic and generalized structure factors but also to characterize the arrangement of the wall particles leading to the roughness of the walls. The experiments are complemented by molecular dynamics simulations and fundamental-measure theory. While the particle arrangements are mainly controlled by hard-core interactions, electrostatic interactions become more important as the volume fraction decreases. Furthermore, the structure of the rough walls was varied and found to have a significant effect on the fluid structure. An appropriate representation of the rough walls in the simulations is thus crucial to successfully mimic the experiments.

Universal effective interactions of globular proteins close to liquid-liquid phase separation: Corresponding-states behavior reflected in the structure factor.

Intermolecular interactions in protein solutions, in general, contain many contributions. If short-range attractions dominate, the state diagram exhibits liquid-liquid phase separation (LLPS) that is metastable with respect to crystallization. In this case, the extended law of corresponding states (ELCS) suggests that thermodynamic properties are insensitive to details of the underlying interaction potential. Using lysozyme solutions, we investigate the applicability of the ELCS to the static structure factor and how far effective colloidal interaction models can help to rationalize the phase behavior and interactions of protein solutions in the vicinity of the LLPS binodal. The (effective) structure factor has been determined by small-angle x-ray scattering. It can be described by Baxter's adhesive hard-sphere model, which implies a single fit parameter from which the normalized second virial coefficient b2 is inferred and found to quantitatively agree with previous results from static light scattering. The b2 values are independent of protein concentration but systematically vary with temperature and solution composition, i.e., salt and additive content. If plotted as a function of temperature normalized by the critical temperature, the values of b2 follow a universal behavior. These findings validate the applicability of the ELCS to globular protein solutions and indicate that the ELCS can also be reflected in the structure factor.

ArGSLab: a tool for analyzing experimental or simulated particle networks.

Microscopy and particle-based simulations are both powerful techniques to study aggregated particulate matter such as colloidal gels. The data provided by these techniques often contains information on a wide array of length scales, but structural analysis methods typically focus on the local particle arrangement, even though the data also contains information about the particle network on the mesoscopic length scale. In this paper, we present a MATLAB software package for quantifying mesoscopic network structures in colloidal samples. ArGSLab (Arrested and Gelated Structures Laboratory) extracts a network backbone from the input data, which is in turn transformed into a set of nodes and links for graph theory-based analysis. The routines can process both image stacks from microscopy as well as explicit coordinate data, and thus allows quantitative comparison between simulations and experiments. ArGSLab furthermore enables the accurate analysis of microscopy data where, e.g., an extended point spread function prohibits the resolution of individual particles. We demonstrate the resulting output for example datasets from both microscopy and simulation of colloidal gels, in order to showcase the capability of ArGSLab to quantitatively analyze data from various sources. The freely available software package can be used either with a provided graphical user interface or directly as a MATLAB script.

Interactions in protein solutions close to liquid-liquid phase separation: ethanol reduces attractions via changes of the dielectric solution properties.

Ethanol is a common protein crystallization agent, precipitant, and denaturant, but also alters the dielectric properties of solutions. While ethanol-induced unfolding is largely ascribed to its hydrophobic parts, its effect on protein phase separation and inter-protein interactions remains poorly understood. Here, the effects of ethanol and NaCl on the phase behavior and interactions of protein solutions are studied in terms of the metastable liquid-liquid phase separation (LLPS) and the second virial coefficient B2 using lysozyme solutions. Determination of the phase diagrams shows that the cloud-point temperatures are reduced and raised by the addition of ethanol and salt, respectively. The observed trends can be explained using the extended law of corresponding states as changes of B2. The results for B2 agree quantitatively with those of static light scattering and small-angle X-ray scattering experiments. Furthermore, B2 values calculated based on inter-protein interactions described by the Derjaguin-Landau-Verwey-Overbeek (DLVO) potential and considering the dielectric solution properties and electrostatic screening due to the ethanol and salt content quantitatively agree with the experimentally observed B2 values.

The crystallization enthalpy and entropy of protein solutions: microcalorimetry, van't Hoff determination and linearized Poisson-Boltzmann model of tetragonal lysozyme crystals.

During a first-order phase transition, a thermodynamic system releases or absorbs latent heat. Despite their fundamental importance, the heat or enthalpy change occurring during protein crystallization has been directly measured only in a few cases, and the associated entropy change can only be determined indirectly. This work provides an experimental determination and theoretical analysis of the dependence of the molar crystallization enthalpy of lysozyme solutions, ΔHxtal, on the physicochemical solution parameters. Its value is determined directly by isothermal microcalorimetry and indirectly by a van't Hoff analysis of solubility data, which quantitatively agree. This suggests a two-state crystallization process, in which oligomeric intermediates play a minor role. ΔHxtal is found to be negative on the order of few tens of the thermal energy per molecule. It is independent of protein concentration and stirring speed, but weakly depends on salt (NaCl) concentration and solution pH. Assuming that crystals are electrostatically neutral, these trends are explained by a linearized Poisson-Boltzmann theory. In addition, the molar crystallization entropy, ΔSxtal, is analyzed. The dependence of the van't Hoff entropy on salt concentration and pH is captured by the model, complementing the analysis of crystallization thermodynamics.

Binary colloidal glasses: linear viscoelasticity and its link to the microscopic structure and dynamics.

We study the relation between the microscopic structure and dynamics and the macroscopic rheological response of glass-forming colloidal suspensions, namely binary colloidal hard-sphere mixtures with large size asymmetry (1 : 5) that span a large range of mixture compositions close to the glass transition. The dynamical shear moduli are measured by oscillatory rheology and the structure and dynamics on the single-particle level by confocal microscopy. The data are compared with Brownian Dynamics simulations and predictions from mode-coupling theory based on the Percus-Yevick approximation. Experiments, simulations and theory consistently observe a strong decrease of the intermediate-frequency mechanical moduli combined with faster dynamics at intermediate mixing ratios and hence a non-monotonic dependence of these parameters but a localization of the large particles which decreases monotonically as the fraction of small particles is increased. We find that the Generalized-Stokes Einstein relation applied to the mean square displacements of the two components leads to a reasonable estimate of the shear moduli of the mixtures and hence links the rheological response to the particle dynamics which in turn reflects the microscopic structure.

Different scenarios of dynamic coupling in glassy colloidal mixtures.

Colloidal mixtures represent a versatile model system to study transport in complex environments. They allow for a systematic variation of the control parameters, namely size ratio, total volume fraction and composition. We study the effects of these parameters on the dynamics of dense suspensions using molecular dynamics simulations and differential dynamic microscopy experiments. We investigate the motion of small particles through the matrix of large particles as well as the motion of large particles. A particular focus is on the coupling of the collective dynamics of small and large particles and on the different mechanisms leading to this coupling. For large size ratios, of about 1 : 5, and an increasing fraction of small particles, the dynamics of the two species become increasingly coupled and reflect the structure of the large particles. This is attributed to the dominant effect of the large particles on the motion of the small particles, which is mediated by the increasing crowding of the small particles. Furthermore, for moderate size ratios of about 1 : 3 and sufficiently high fractions of small particles, mixed cages are formed and hence the dynamics are also strongly coupled. Again, the coupling becomes weaker as the fraction of small particles is decreased. In this case, however, the collective intermediate scattering function of the small particles shows a logarithmic decay corresponding to a broad range of relaxation times.

Structure of colloidal gels at intermediate concentrations: the role of competing interactions.

Colloidal gels formed by colloid-polymer mixtures with an intermediate volume fraction (ϕc ≈ 0.4) are investigated by confocal microscopy. In addition, we have performed Monte Carlo simulations based on a simple effective pair potential that includes a short-range attractive contribution representing depletion interactions, and a longer-range repulsive contribution describing the electrostatic interactions due to the presence of residual charges. Despite neglecting non-equilibrium effects, experiments and simulations yield similar gel structures, characterised by, e.g., the pair, angular and bond distribution functions. We find that the structure hardly depends on the strength of the attraction if the electrostatic contribution is fixed, but changes significantly if the electrostatic screening is changed. This delicate balance between attractions and repulsions, which we quantify by the second virial coefficient, also determines the location of the gelation boundary.

Structure of the H-NS-DNA nucleoprotein complex.

Nucleoid associated proteins (NAPs) play a key role in the compaction and expression of the prokaryotic genome. Here we report the organisation of a major NAP, the protein H-NS on a double stranded DNA fragment. For this purpose we have carried out a small angle neutron scattering study in conjunction with contrast variation to obtain the contributions to the scattering (structure factors) from DNA and H-NS. The H-NS structure factor agrees with a heterogeneous, two-state binding model with sections of the DNA duplex surrounded by protein and other sections having protein bound to the major groove. In the presence of magnesium chloride, we observed a structural rearrangement through a decrease in cross-sectional diameter of the nucleoprotein complex and an increase in fraction of major groove bound H-NS. The two observed binding modes and their modulation by magnesium ions provide a structural basis for H-NS-mediated genome organisation and expression regulation.

Tuning protein-protein interactions using cosolvents: specific effects of ionic and non-ionic additives on protein phase behavior.

Cosolvents are routinely used to modulate the (thermal) stability of proteins and, hence, their interactions with proteins have been studied intensely. However, less is known about their specific effects on protein-protein interactions, which we characterize in terms of the protein phase behavior. We analyze the phase behavior of lysozyme solutions in the presence of sodium chloride (NaCl), guanidine hydrochloride (GuHCl), glycerol, and dimethyl sulfoxide (DMSO). We experimentally determined the crystallization boundary (XB) and, in combination with data on the cloud-point temperatures (CPTs), the crystallization gap. In agreement with other studies, our data indicate that the additives might affect the protein phase behavior through electrostatic screening and additive-specific contributions. At high salt concentrations, where electrostatic interactions are screened, both the CPT and the XB are found to be linear functions of the additive concentration. Their slopes quantify the additive-specific changes of the phase behavior and thus of the protein-protein interactions. While the specific effect of NaCl is to induce attractions between proteins, DMSO, glycerol and GuHCl (with increasing strength) weaken attractions and/or induce repulsions. Except for DMSO, changes of the CPT are stronger than those of the XB. Furthermore, the crystallization gap widens in the case of GuHCl and glycerol and narrows in the case of NaCl. We relate these changes to colloidal interaction models, namely square-well and patchy interactions.

Time- and ensemble-averages in evolving systems: the case of Brownian particles in random potentials.

Anomalous diffusion is a ubiquitous phenomenon in complex systems. It is often quantified using time- and ensemble-averages to improve statistics, although time averages represent a non-local measure in time and hence can be difficult to interpret. We present a detailed analysis of the influence of time- and ensemble-averages on dynamical quantities by investigating Brownian particles in a rough potential energy landscape (PEL). Initially, the particle ensemble is randomly distributed, but the occupancy of energy values evolves towards the equilibrium distribution. This relaxation manifests itself in the time evolution of time- and ensemble-averaged dynamical measures. We use Monte Carlo simulations to study particle dynamics in a potential with a Gaussian distribution of energy values, where the long-time limit of the diffusion coefficient is known from theory. In our experiments, individual colloidal particles are exposed to a laser speckle pattern inducing a non-Gaussian roughness and are followed by optical microscopy. The relaxation depends on the kind and degree of roughness of the PEL. It can be followed and quantified by the time- and ensemble-averaged mean squared displacement. Moreover, the heterogeneity of the dynamics is characterized using single-trajectory analysis. The results of this work are relevant for the correct interpretation of single-particle tracking experiments in general.

Colloids exposed to random potential energy landscapes: From particle number density to particle-potential and particle-particle interactions.

Colloidal particles were exposed to a random potential energy landscape that has been created optically via a speckle pattern. The mean particle density as well as the potential roughness, i.e., the disorder strength, were varied. The local probability density of the particles as well as its main characteristics were determined. For the first time, the disorder-averaged pair density correlation function g((1))(r) and an analogue of the Edwards-Anderson order parameter g((2))(r), which quantifies the correlation of the mean local density among disorder realisations, were measured experimentally and shown to be consistent with replica liquid state theory results.

Kinks in experimental diffusion profiles of a dissolving semi-crystalline polymer explained by a concentration-dependent diffusion coefficient.

The dissolution of polyethylene oxide (PEO) tablets in water has been followed in situ by neutron radiography. When in contact with water, the crystalline phase of semi-crystalline PEO melts once a certain water content is attained. Polymer concentration profiles obtained from the neutron transmission images exhibited a pronounced kink which corresponds to a sharp front in the images and which is related to the melting transition. Sharp diffusion fronts and phase transitions are often linked to non-Fickian behaviour. However, by considering the time evolution of the complete concentration profiles in detail it is shown that the dissolution process can be explained using Fickian diffusion equations with a concentration-dependent diffusion coefficient.

Extended law of corresponding states for protein solutions.

The so-called extended law of corresponding states, as proposed by Noro and Frenkel [J. Chem. Phys. 113, 2941 (2000)], involves a mapping of the phase behaviors of systems with short-range attractive interactions. While it has already extensively been applied to various model potentials, here we test its applicability to protein solutions with their complex interactions. We successfully map their experimentally determined metastable gas-liquid binodals, as available in the literature, to the binodals of short-range square-well fluids, as determined by previous as well as new Monte Carlo simulations. This is achieved by representing the binodals as a function of the temperature scaled with the critical temperature (or as a function of the reduced second virial coefficient) and the concentration scaled by the cube of an effective particle diameter, where the scalings take into account the attractive and repulsive contributions to the interaction potential, respectively. The scaled binodals of the protein solutions coincide with simulation data of the adhesive hard-sphere fluid. Furthermore, once the repulsive contributions are taken into account by the effective particle diameter, the temperature dependence of the reduced second virial coefficients follows a master curve that corresponds to a linear temperature dependence of the depth of the square-well potential. We moreover demonstrate that, based on this approach and cloud-point measurements only, second virial coefficients can be estimated, which we show to agree with values determined by light scattering or by Derjaguin-Landau-Verwey-Overbeek (DLVO)-based calculations.

Anomalous front broadening during spontaneous imbibition in a matrix with elongated pores.

During spontaneous imbibition, a wetting liquid is drawn into a porous medium by capillary forces. In systems with comparable pore length and diameter, such as paper and sand, the front of the propagating liquid forms a continuous interface. Sections of this interface advance in a highly correlated manner due to an effective surface tension, which restricts front broadening. Here we investigate water imbibition in a nanoporous glass (Vycor) in which the pores are much longer than they are wide. In this case, no continuous liquid-vapor interface with coalesced menisci can form. Anomalously fast imbibition front roughening is experimentally observed by neutron imaging. We propose a theoretical pore-network model, whose structural details are adapted to the microscopic pore structure of Vycor glass and show that it displays the same large-scale roughening characteristics as observed in the experiment. The model predicts that menisci movements are uncorrelated, indicating that despite the connectivity of the network the smoothening effect of surface tension on the imbibition front roughening is negligible. These results suggest a new universality class of imbibition behavior, which is expected to occur in any matrix with elongated, interconnected pores of random radii.

Effect of glycerol and dimethyl sulfoxide on the phase behavior of lysozyme: theory and experiments.

Salt, glycerol, and dimethyl sulfoxide (DMSO) are used to modify the properties of protein solutions. We experimentally determined the effect of these additives on the phase behavior of lysozyme solutions. Upon the addition of glycerol and DMSO, the fluid-solid transition and the gas-liquid coexistence curve (binodal) shift to lower temperatures and the gap between them increases. The experimentally observed trends are consistent with our theoretical predictions based on the thermodynamic perturbation theory and the Derjaguin-Landau-Verwey-Overbeek model for the lysozyme-lysozyme pair interactions. The values of the parameters describing the interactions, namely the refractive indices, dielectric constants, Hamaker constant and cut-off length, are extracted from literature or are experimentally determined by independent experiments, including static light scattering, to determine the second virial coefficient. We observe that both, glycerol and DMSO, render the potential more repulsive, while sodium chloride reduces the repulsion.