Liquid-Liquid Phase Separation in Oligomeric Peptide Solutions.

Oligomeric peptides exist widely in living organisms and play a role in a broad range of biological functions. We report the first observation of liquid-liquid phase separation (LLPS) in peptide solutions, in particular, solutions of peptides consisting of noncovalent oligomers. We determined the binary phase boundary of the oligomeric peptide solution and compared the result to the well-established phase diagram of globular proteins. We also provide simple theoretical interpretations of the similarities and differences between the phase diagrams of peptides and proteins. Finally, by tuning inter-oligomer interactions using a crowding agent, we demonstrated that LLPS is a universal phenomenon that can be observed under different solution conditions for a variety of peptides.

Evaluation of effects of pH and ionic strength on colloidal stability of IgG solutions by PEG-induced liquid-liquid phase separation.

Colloidal stability of IgG antibody solutions is important for pharmaceutical and medicinal applications. Solution pH and ionic strength are two key factors that affect the colloidal stability of protein solutions. In this work, we use a method based on the PEG-induced liquid-liquid phase separation to examine the effects of pH and ionic strength on the colloidal stability of IgG solutions. We found that at high ionic strength (≥0.25M), the colloidal stability of most of our IgGs is insensitive to pH, and at low ionic strength (≤0.15M), all IgG solutions are much more stable at pH 5 than at pH 7. In addition, the PEG-induced depletion force is less efficient in causing phase separation at pH 5 than at pH 7. In contrast to the native inter-protein interaction of IgGs, the effect of depletion force on phase separation of the antibody solutions is insensitive to ionic strength. Our results suggest that the long-range electrostatic inter-protein repulsion at low ionic strength stabilizes the IgG solutions at low pH. At high ionic strength, the short-range electrostatic interactions do not make a significant contribution to the colloidal stability for most IgGs with a few exceptions. The weaker effect of depletion force at lower pH indicates a reduction of protein concentration in the condensed phase. This work advances our basic understanding of the colloidal stability of IgG solutions and also introduces a practical approach to measuring protein colloidal stability under various solution conditions.

The phase behavior study of human antibody solution using multi-scale modeling.

Phase transformation in antibody solutions is of growing interest in both academia and the pharmaceutical industry. Recent experimental studies have shown that, as in near-spherical proteins, antibodies can undergo a liquid-liquid phase separation under conditions metastable with respect to crystallization. However, the phase diagram of the Y-shaped antibodies exhibits unique features that differ substantially from those of spherical proteins. Specifically, antibody solutions have an exceptionally low critical volume fraction (CVF) and a broader and more asymmetric liquid-liquid coexistence curve than those of spherical proteins. Using molecular dynamics simulation on a series of trimetric Y-shaped coarse-grained models, we investigate the phase behavior of antibody solutions and compare the results with the experimental phase diagram of human immunoglobulin G (IgG), one of the most common Y-shape typical of antibody molecules. With the fitted size of spheres, our simulation reproduces both the low CVF and the asymmetric shape of the experimental coexistence curve of IgG antibodies. The broadness of the coexistence curve can be attributed to the anisotropic nature of the inter-protein interaction. In addition, the repulsion between the inner parts of the spherical domains of IgG dramatically expands the coexistence region in the scaled phase diagram, while the hinge length has only a minor effect on the CVF and the overall shape of the coexistence curve. We thus propose a seven-site model with empirical parameters characterizing the exclusion volume and the hinge length of the IgG molecules, which provides a base for simulation studies of the phase behavior of IgG antibodies.

Transformation of oligomers of lipidated peptide induced by change in pH.

Oligomerization of lipidated peptides is of general scientific interest and is important in biomedical and pharmaceutical applications. We investigated the solution properties of a lipidated peptide, Liraglutide, which is one of the glucagon-like peptide-1 (GLP-1) agonists used for the treatment of type II diabetes. Liraglutide can serve as a model system for studying biophysical and biochemical properties of micelle-like self-assemblies of the lipidated peptides. Here, we report a transformation induced in Liraglutide oligomers by changing pH in the vicinity of pH 7. This fully reversible transformation is characterized by changes in the size and aggregation number of the oligomer and an associated change in the secondary structure of the constituent peptides. This transformation has quite slow kinetics: the equilibrium is reached in a course of several days. Interestingly, while the transformation is induced by changing pH, its kinetics is essentially independent of the final pH. We interpreted these findings using a model in which desorption of the monomer from the oligomer is the rate-limiting step in the transformation, and we determined the rate constant of the monomer desorption.

Aß dimers differ from monomers in structural propensity, aggregation paths and population of synaptotoxic assemblies.

Dimers of Aß (amyloid ß-protein) are believed to play an important role in Alzheimer's disease. In the absence of sufficient brain-derived dimers, we studied one of the only possible dimers that could be produced in vivo, [Aß](DiY) (dityrosine cross-linked Aß). For comparison, we used the Aß monomer and a design dimer cross-linked by replacement of Ser²6 with cystine [AßS26C]2. We showed that similar to monomers, unaggregated dimers lack appreciable structure and fail to alter long-term potentiation. Importantly, dimers exhibit subtly different structural propensities from monomers and each other, and can self-associate to form larger assemblies. Although [Aß](DiY) and [AßS26C]2 have distinct aggregation pathways, they both populate bioactive soluble assemblies for longer durations than Aß monomers. Our results indicate that the link between Aß dimers and Alzheimer's disease results from the ability of dimers to further assemble and form synaptotoxic assemblies that persist for long periods of time.

Pathological crystallization of human immunoglobulins.

Condensation of Igs has been observed in pharmaceutical formulations and in vivo in cases of cryoglobulinemia. We report a study of monoclonal IgG cryoglobulins overexpressed by two patients with multiple myeloma. These cryoglobulins form crystals, and we measured their solubility lines. Depending on the supersaturation, we observed a variety of condensate morphologies consistent with those reported in clinical investigations. Remarkably, the crystallization can occur at quite low concentrations. This suggests that, even within the regular immune response to infections, cryoprecipitation of Ig can be possible.

Quantitative evaluation of colloidal stability of antibody solutions using PEG-induced liquid-liquid phase separation.

Colloidal stability of antibody solutions, i.e., the propensity of the folded protein to precipitate, is an important consideration in formulation development of therapeutic monoclonal antibodies. In a protein solution, different pathways including crystallization, colloidal aggregation, and liquid-liquid phase separation (LLPS) can lead to the formation of precipitates. The kinetics of crystallization and aggregation are often slow and vary from protein to protein. Due to the diverse mechanisms of these protein condensation processes, it is a challenge to develop a standardized test for an early evaluation of the colloidal stability of antibody solutions. LLPS would normally occur in antibody solutions at sufficiently low temperature, provided that it is not preempted by freezing of the solution. Poly(ethylene glycol) (PEG) can be used to induce LLPS at temperatures above the freezing point. Here, we propose a colloidal stability test based on inducing LLPS in antibody solutions and measuring the antibody concentration of the dilute phase. We demonstrate experimentally that such a PEG-induced LLPS test can be used to compare colloidal stability of different antibodies in different solution conditions and can be readily applied to high-throughput screening. We have derived an equation for the effects of PEG concentration and molecular weight on the results of the LLPS test. Finally, this equation defines a binding energy in the condensed phase, which can be determined in the PEG-induced LLPS test. This binding energy is a measure of attractive interactions between antibody molecules and can be used for quantitative characterization of the colloidal stability of antibody solutions.

Phase separation in solutions of monoclonal antibodies and the effect of human serum albumin.

We report the observation of liquid-liquid phase separation in a solution of human monoclonal antibody, IgG2, and the effects of human serum albumin, a major blood protein, on this phase separation. We find a significant reduction of phase separation temperature in the presence of albumin, and a preferential partitioning of the albumin into the antibody-rich phase. We provide a general thermodynamic analysis of the antibody-albumin mixture phase diagram and relate its features to the magnitude of the effective interprotein interactions. Our analysis suggests that additives (HSA in this report), which have moderate attraction with antibody molecules, may be used to forestall undesirable protein condensation in antibody solutions. Our findings are relevant to understanding the stability of pharmaceutical solutions of antibodies and the mechanisms of cryoglobulinemia.

Phase transitions in human IgG solutions.

Protein condensations, such as crystallization, liquid-liquid phase separation, aggregation, and gelation, have been observed in concentrated antibody solutions under various solution conditions. While most IgG antibodies are quite soluble, a few outliers can undergo condensation under physiological conditions. Condensation of IgGs can cause serious consequences in some human diseases and in biopharmaceutical formulations. The phase transitions underlying protein condensations in concentrated IgG solutions is also of fundamental interest for the understanding of the phase behavior of non-spherical protein molecules. Due to the high solubility of generic IgGs, the phase behavior of IgG solutions has not yet been well studied. In this work, we present an experimental approach to study IgG solutions in which the phase transitions are hidden below the freezing point of the solution. Using this method, we have investigated liquid-liquid phase separation of six human myeloma IgGs and two recombinant pharmaceutical human IgGs. We have also studied the relation between crystallization and liquid-liquid phase separation of two human cryoglobulin IgGs. Our experimental results reveal several important features of the generic phase behavior of IgG solutions: (1) the shape of the coexistence curve is similar for all IgGs but quite different from that of quasi-spherical proteins; (2) all IgGs have critical points located at roughly the same protein concentration at ~100 mg/ml while their critical temperatures vary significantly; and (3) the liquid-liquid phase separation in IgG solutions is metastable with respect to crystallization. These features of phase behavior of IgG solutions reflect the fact that all IgGs have nearly identical molecular geometry but quite diverse net inter-protein interaction energies. This work provides a foundation for further experimental and theoretical studies of the phase behavior of generic IgGs as well as outliers with large propensity to condense. The investigation of the phase diagram of IgG solutions is of great importance for the understanding of immunoglobulin deposition diseases as well as for the understanding of the colloidal stability of IgG pharmaceutical formulations.

Phase behavior of mixtures of human lens proteins Gamma D and Beta B1.

We have experimentally determined the coexistence surface characterizing the phase behavior of gammaD-betaB1-water ternary solutions. The coexistence surface fully describes the solution conditions, i.e., temperature, protein concentration, and protein composition, at which liquid-liquid phase separation occurs in a ternary solution. We have observed a significant demixing of gammaD and betaB1 i.e., large difference of composition in the two coexisting phases. This demixing suggests that the energy of the gammaD-betaB1 attractive interaction is significantly smaller than the energy of the gammaD-gammaD attractive interaction. We also observed the lowering of the phase separation temperature upon increasing of the fraction of betaB1 in solution. We provide a theoretical analysis of our experimental data, which enables a quantitative description of our principal experimental findings. In this way, we have evaluated the magnitude and temperature dependence of the relevant interprotein interaction energies. Our findings provide insight into the factors essential for maintaining lens proteins in a single homogeneous phase, thereby enabling lens transparency.

Serum protein profiles predict coronary artery disease in symptomatic patients referred for coronary angiography.

BACKGROUND: More than a million diagnostic cardiac catheterizations are performed annually in the US for evaluation of coronary artery anatomy and the presence of atherosclerosis. Nearly half of these patients have no significant coronary lesions or do not require mechanical or surgical revascularization. Consequently, the ability to rule out clinically significant coronary artery disease (CAD) using low cost, low risk tests of serum biomarkers in even a small percentage of patients with normal coronary arteries could be highly beneficial. METHODS: Serum from 359 symptomatic subjects referred for catheterization was interrogated for proteins involved in atherogenesis, atherosclerosis, and plaque vulnerability. Coronary angiography classified 150 patients without flow-limiting CAD who did not require percutaneous intervention (PCI) while 209 required coronary revascularization (stents, angioplasty, or coronary artery bypass graft surgery). Continuous variables were compared across the two patient groups for each analyte including calculation of false discovery rate (FDR ≤ 1%) and Q value (P value for statistical significance adjusted to ≤ 0.01). RESULTS: Significant differences were detected in circulating proteins from patients requiring revascularization including increased apolipoprotein B100 (APO-B100), C-reactive protein (CRP), fibrinogen, vascular cell adhesion molecule 1 (VCAM-1), myeloperoxidase (MPO), resistin, osteopontin, interleukin (IL)-1ß, IL-6, IL-10 and N-terminal fragment protein precursor brain natriuretic peptide (NT-pBNP) and decreased apolipoprotein A1 (APO-A1). Biomarker classification signatures comprising up to 5 analytes were identified using a tunable scoring function trained against 239 samples and validated with 120 additional samples. A total of 14 overlapping signatures classified patients without significant coronary disease (38% to 59% specificity) while maintaining 95% sensitivity for patients requiring revascularization. Osteopontin (14 times) and resistin (10 times) were most frequently represented among these diagnostic signatures. The most efficacious protein signature in validation studies comprised osteopontin (OPN), resistin, matrix metalloproteinase 7 (MMP7) and interferon γ (IFNγ) as a four-marker panel while the addition of either CRP or adiponectin (ACRP-30) yielded comparable results in five protein signatures. CONCLUSIONS: Proteins in the serum of CAD patients predominantly reflected (1) a positive acute phase, inflammatory response and (2) alterations in lipid metabolism, transport, peroxidation and accumulation. There were surprisingly few indicators of growth factor activation or extracellular matrix remodeling in the serum of CAD patients except for elevated OPN. These data suggest that many symptomatic patients without significant CAD could be identified by a targeted multiplex serum protein test without cardiac catheterization thereby eliminating exposure to ionizing radiation and decreasing the economic burden of angiographic testing for these patients.

Thickness-radius relationship and spring constants of cholesterol helical ribbons.

Using quantitative phase microscopy, we have discovered a quadratic relationship between the radius R and the thickness t of helical ribbons that form spontaneously in multicomponent cholesterol-surfactant mixtures. These helical ribbons may serve as mesoscopic springs to measure or to exert forces on nanoscale biological objects. The spring constants of these helices depend on their submicroscopic thickness. The quadratic relationship (R proportional to t(2)) between radius and thickness is a consequence of the crystal structure of the ribbons and enables a determination of the spring constant of any of our helices solely in terms of its observable geometrical dimensions.

Lysine-specific molecular tweezers are broad-spectrum inhibitors of assembly and toxicity of amyloid proteins.

Amyloidoses are diseases characterized by abnormal protein folding and self-assembly, for which no cure is available. Inhibition or modulation of abnormal protein self-assembly, therefore, is an attractive strategy for prevention and treatment of amyloidoses. We examined Lys-specific molecular tweezers and discovered a lead compound termed CLR01, which is capable of inhibiting the aggregation and toxicity of multiple amyloidogenic proteins by binding to Lys residues and disrupting hydrophobic and electrostatic interactions important for nucleation, oligomerization, and fibril elongation. Importantly, CLR01 shows no toxicity at concentrations substantially higher than those needed for inhibition. We used amyloid ß-protein (Aß) to further explore the binding site(s) of CLR01 and the impact of its binding on the assembly process. Mass spectrometry and solution-state NMR demonstrated binding of CLR01 to the Lys residues in Aß at the earliest stages of assembly. The resulting complexes were indistinguishable in size and morphology from Aß oligomers but were nontoxic and were not recognized by the oligomer-specific antibody A11. Thus, CLR01 binds already at the monomer stage and modulates the assembly reaction into formation of nontoxic structures. The data suggest that molecular tweezers are unique, process-specific inhibitors of aberrant protein aggregation and toxicity, which hold promise for developing disease-modifying therapy for amyloidoses.

C-terminal peptides coassemble into Abeta42 oligomers and protect neurons against Abeta42-induced neurotoxicity.

Alzheimer's disease (AD) is an age-related disorder that threatens to become an epidemic as the world population ages. Neurotoxic oligomers of Abeta42 are believed to be the main cause of AD; therefore, disruption of Abeta oligomerization is a promising approach for developing therapeutics for AD. Formation of Abeta42 oligomers is mediated by intermolecular interactions in which the C terminus plays a central role. We hypothesized that peptides derived from the C terminus of Abeta42 may get incorporated into oligomers of Abeta42, disrupt their structure, and thereby inhibit their toxicity. We tested this hypothesis using Abeta fragments with the general formula Abeta(x-42) (x = 28-39). A cell viability screen identified Abeta(31-42) as the most potent inhibitor. In addition, the shortest peptide, Abeta(39-42), also had high activity. Both Abeta(31-42) and Abeta(39-42) inhibited Abeta-induced cell death and rescued disruption of synaptic activity by Abeta42 oligomers at micromolar concentrations. Biophysical characterization indicated that the action of these peptides likely involved stabilization of Abeta42 in nontoxic oligomers. Computer simulations suggested a mechanism by which the fragments coassembled with Abeta42 to form heterooligomers. Thus, Abeta(31-42) and Abeta(39-42) are leads for obtaining mechanism-based drugs for treatment of AD using a systematic structure-activity approach.

Mechanistic investigation of the inhibition of Abeta42 assembly and neurotoxicity by Abeta42 C-terminal fragments.

Oligomeric forms of amyloid beta-protein (Abeta) are key neurotoxins in Alzheimer's disease (AD). Previously, we found that C-terminal fragments (CTFs) of Abeta42 interfered with assembly of full-length Abeta42 and inhibited Abeta42-induced toxicity. To decipher the mechanism(s) by which CTFs affect Abeta42 assembly and neurotoxicity, here, we investigated the interaction between Abeta42 and CTFs using photoinduced cross-linking and dynamic light scattering. The results demonstrate that distinct parameters control CTF inhibition of Abeta42 assembly and Abeta42-induced toxicity. Inhibition of Abeta42-induced toxicity was found to correlate with stabilization of oligomers with a hydrodynamic radius (R(H)) of 8-12 nm and attenuation of formation of oligomers with an R(H) of 20-60 nm. In contrast, inhibition of Abeta42 paranucleus formation correlated with CTF solubility and the degree to which CTFs formed amyloid fibrils themselves but did not correlate with inhibition of Abeta42-induced toxicity. Our findings provide important insight into the mechanisms by which different CTFs inhibit the toxic effect of Abeta42 and suggest that stabilization of nontoxic Abeta42 oligomers is a promising strategy for designing inhibitors of Abeta42 neurotoxicity.

Despite its role in assembly, methionine 35 is not necessary for amyloid beta-protein toxicity.

An important component of the pathologic process underlying Alzheimer's disease is oxidative stress. Met(35) in amyloid beta-protein (A beta) is prone to participating in redox reactions promoting oxidative stress, and therefore is believed to contribute significantly A beta-induced toxicity. Thus, substitution of Met(35) by residues that do not participate in redox chemistry would be expected to decrease A beta toxicity. Indeed, substitution of Met(35) by norleucine (Nle) was reported to reduce A beta toxicity. Surprisingly, however, substitution of Met(35) by Val was reported to increase toxicity. A beta toxicity is known to be strongly related to its self-assembly. However, neither substitution is predicted to affect A beta assembly substantially. Thus, the effect of these substitutions on toxicity is difficult to explain. We revisited this issue and compared A beta 40 and A beta 42 with analogs containing Met(35)-->Nle or Met(35)-->Val substitutions using multiple biophysical and toxicity assays. We found that substitution of Met(35) by Nle or Val had moderate effects on A beta assembly. Surprisingly, despite these effects, neither substitution changed A beta neurotoxicity significantly in three different assays. These results suggest that the presence of Met(35) in A beta is not important for A beta toxicity, challenging to the prevailing paradigm, which suggests that redox reactions involving Met(35) contribute substantially to A beta-induced toxicity.

Serum biomarker panels for the discrimination of benign from malignant cases in patients with an adnexal mass.

OBJECTIVES: The diagnosis of an adnexal mass is a prevalent issue among women in the United States, although current methods of identifying those at high risk of malignancy remain insufficient. Ineffective triage of women with malignant masses is associated with delayed or inappropriate treatment and a negative effect on disease outcome. METHODS: We performed an evaluation of 65 ovarian cancer-related biomarkers in the circulation of women diagnosed with an adnexal mass. Our subject group consisted of women diagnosed with benign masses and early- and late-stage ovarian cancer. RESULTS: More than half of the biomarkers tested were found to differ significantly between benign and malignant cases. As individual markers, HE4 and CA-125 provided the greatest level of discrimination between benign and malignant cases, and the combination of these two biomarkers provided a higher level of discriminatory power than either marker considered alone. Multivariate statistical analysis identified several multimarker panels that could discriminate early-stage, late-stage, and combined ovarian cancers from benign cases with similar or slightly improved SN/SP levels to the CA-125/HE4 combination; however, these larger panels could not outperform the 2-biomarker panel in an independent validation set. We also identified a 3-biomarker panel with particular utility in premenopausal women. CONCLUSIONS: Our findings serve to advance the development of blood-based screening methods for the discrimination of benign and malignant ovarian masses by confirming and expanding upon the superior utility of the CA-125/HE4 combination.

Quasielastic light scattering study of amyloid beta-protein fibril formation.

Quasielastic light scattering spectroscopy (QLS) is an optical method for the determination of diffusion coefficients of particles in solution. Here we discuss the principles of QLS and explain how the distribution of particle sizes can be reconstructed from the measured correlation function of scattered light. Non-invasive observation of the temporal evolution of particle sizes provides a powerful tool for studying protein assembly. We illustrate practical applications of QLS with examples from studies of fibril formation of the amyloid beta-protein.

The molecular basis for the prolonged blood circulation of lipidated incretin peptides: Peptide oligomerization or binding to serum albumin?

Hybrid incretin peptides are a new generation of drugs for the treatment of diabetes and obesity. Despite their biological potency, the effectiveness of these peptides as drugs is limited by their short circulation time in blood (typically within minutes). In this work, we show that lipid conjugated forms of a GLP-1/GIP/glucagon hybrid peptides stay in circulation for hours. We studied the oligomerization and albumin-binding of the unconjugated hybrid peptide as well as its lipidated variants. These lipidated peptides differ in the N-terminal mutation, the position of lipidation and the linkage to lipid. We found that these lipidated peptides form stable oligomers at concentrations above 1mg/mL. This concentration range is relevant to formulation and storage of the peptides. We observed no binding between the peptide oligomers and human serum albumin. However, at the expected therapeutic concentration range (~10-100ng/mL), the oligomers dissociate into monomers. The monomers of lipidated peptides bind to albumin. We have determined the dissociation constants of binding between the lipidated peptides and serum albumin. The dissociation constants of albumin-binding of our lipidated peptides are all very close and similar to that of the fatty acid binding of albumin. Our findings suggest that the monomeric lipidated peptides bind to HSA mainly by the fatty acid chain. Therefore, albumin binding is likely to be a universal mechanism of the prolonged circulating duration of lipidated pharmaceutical peptides.

Quasielastic light scattering for protein assembly studies.

Quasielastic light scattering (QLS) spectroscopy is an optical method for the determination of diffusion coefficients of particles in solution. In this chapter, we discuss the principles and practice of QLS with respect to protein assembly reactions. Particles undergoing Brownian motion produce fluctuations in scattered light intensity. We describe how the temporal correlation function of these fluctuations can be measured and how this correlation function provides information about the distribution of diffusion coefficients of the particles in solution. We discuss the intricacies of deconvolution of the correlation function and the assumptions incorporated into data analysis procedures. We explain how the Stokes-Einstein relationship can be used to convert distributions of diffusion coefficients into distributions of particle size. Noninvasive observation of the temporal evolution of particles sizes provides a powerful tool for studying protein aggregation and self-assembly. We use examples from studies of Abeta fibrillogenesis to illustrate QLS application for understanding the molecular mechanisms of the nucleation and growth of amyloid fibrils.