Effects of Doxorubicin on the Liquid-Liquid Phase Change Properties of Elastin-Like Polypeptides

Lipidation alters the phase-separation of resilin-like polypeptides

Biology exploits biomacromolecular phase separation to form condensates, known as membraneless organelles. Despite significant advancements in deciphering sequence determinants for phase separation, modulating these features in vivo remains challenging. A promising approach inspired by biology is to use post-translational modifications (PTMs)-to modulate the amino acid physicochemistry instead of altering protein sequences-to control the formation and characteristics of condensates. However, despite the identification of more than 300 types of PTMs, the detailed understanding of how they influence the formation and material properties of protein condensates remains incomplete. In this study, we investigated how modification with myristoyl lipid alters the formation and characteristics of the resilin-like polypeptide (RLP) condensates, a prototypical disordered protein with upper critical solution temperature (UCST) phase behaviour. Using turbidimetry, dynamic light scattering, confocal and electron microscopy, we demonstrated that lipidation-in synergy with the sequence of the lipidation site-significantly influences RLPs' thermodynamic propensity for phase separation and their condensate properties. Molecular simulations suggested these effects result from an expanded hydrophobic region created by the interaction between the lipid and lipidation site rather than changes in peptide rigidity. These findings emphasize the role of "sequence context" in modifying the properties of PTMs, suggesting that variations in lipidation sequences could be strategically used to fine-tune the effect of these motifs. Our study advances understanding of lipidation's impact on UCST phase behaviour, relevant to proteins critical in biological processes and diseases, and opens avenues for designing lipidated resilins for biomedical applications like heat-mediated drug elution.

Modulating Phase Behavior in Fatty Acid-Modified Elastin-like Polypeptides (FAMEs): Insights into the Impact of Lipid Length on Thermodynamics and Kinetics of Phase Separation

Although post-translational lipidation is prevalent in eukaryotes, its impact on the liquid-liquid phase separation of disordered proteins is still poorly understood. Here, we examined the thermodynamic phase boundaries and kinetics of aqueous two-phase system (ATPS) formation for a library of elastin-like polypeptides modified with saturated fatty acids of different chain lengths. By systematically altering the physicochemical properties of the attached lipids, we were able to correlate the molecular properties of lipids to changes in the thermodynamic phase boundaries and the kinetic stability of droplets formed by these proteins. We discovered that increasing the chain length lowers the phase separation temperature in a sigmoidal manner due to alterations in the unfavorable interactions between protein and water and changes in the entropy of phase separation. Our kinetic studies unveiled remarkable sensitivity to lipid length, which we propose is due to the temperature-dependent interactions between lipids and the protein. Strikingly, we found that the addition of just a single methylene group is sufficient to allow tuning of these interactions as a function of temperature, with proteins modified with C7-C9 lipids exhibiting non-Arrhenius dependence in their phase separation, a behavior that is absent for both shorter and longer fatty acids. This work advances our theoretical understanding of protein-lipid interactions and opens avenues for the rational design of lipidated proteins in biomedical paradigms, where precise control over the phase separation is pivotal.

Peptide-based coacervates in therapeutic applications

Coacervates are droplets formed by liquid‒liquid phase separation. An increasing number of studies have reported that coacervates play an important role in living cells, such as in the generation of membraneless organelles, and peptides contribute to condensate droplet formation. Peptides with versatile functional groups and special secondary structures, including α-helices, β-sheets and intrinsically disordered regions, provide novel insights into coacervation, such as biomimetic protocells, neurodegenerative diseases, modulations of signal transmission, and drug delivery systems. In this review, we introduce different types of peptide-based coacervates and the principles of their interactions. Additionally, we summarize the thermodynamic and kinetic mechanisms of peptide-based coacervates and the associated factors, including salt, pH, and temperature, affecting the phase separation process. We illustrate recent studies on modulating the functions of peptide-based coacervates applied in biological diseases. Finally, we propose their promising broad applications and describe the challenges of peptide-based coacervates in the future.

Application of Elastin-Like Polypeptide in Tumor Therapy

Simple Summary

Elastin-like Polypeptide (ELP) are widely applied in protein purification, drug delivery, tissue engineering, and even tumor therapy. Recent studies show that usage of ELP has made great progress in combination with peptide drugs or antibody drugs. The combination of ELP and photosensitizer in cancer therapy or imaging has made more progress and needs to be summarized. In this review, we summarize the specific application of ELP in cancer therapy, especially the latest developments in the combined use of ELP with photosensitizers. We seek to provide the most recent understanding of ELP and its new application in combination with Photosensitizer.

Abstract

Elastin-like polypeptides (ELPs) are stimulus-responsive artificially designed proteins synthesized from the core amino acid sequence of human tropoelastin. ELPs have good biocompatibility and biodegradability and do not systemically induce adverse immune responses, making them a suitable module for drug delivery. Design strategies can equip ELPs with the ability to respond to changes in temperature and pH or the capacity to self-assemble into nanoparticles. These unique tunable biophysicochemical properties make ELPs among the most widely studied biopolymers employed in protein purification, drug delivery, tissue engineering and even in tumor therapy. As a module for drug delivery and as a carrier to target tumor cells, the combination of ELPs with therapeutic drugs, antibodies and photo-oxidation molecules has been shown to result in improved pharmacokinetic properties (prolonged half-life, drug targeting, cell penetration and controlled release) while restricting the cytotoxicity of the drug to a confined infected site. In this review, we summarize the latest developments in the application methods of ELP employed in tumor therapy, with a focus on its conjugation with peptide drugs, antibodies and photosensitizers.

Temperature-Responsive Nano-Biomaterials from Genetically Encoded Farnesylated Disordered Proteins

Despite broad interest in understanding the biological implications of protein farnesylation in regulating different facets of cell biology, the use of this post-translational modification to develop protein-based materials and therapies remains underexplored. The progress has been slow due to the lack of accessible methodologies to generate farnesylated proteins with broad physicochemical diversities rapidly. This limitation, in turn, has hindered the empirical elucidation of farnesylated proteins' sequence-structure-function rules. To address this gap, we genetically engineered prokaryotes to develop operationally simple, high-yield biosynthetic routes to produce farnesylated proteins and revealed determinants of their emergent material properties (nano-aggregation and phase-behavior) using scattering, calorimetry, and microscopy. These outcomes foster the development of farnesylated proteins as recombinant therapeutics or biomaterials with molecularly programmable assembly.

Photocrosslinked, Tunable Protein Vesicles for Drug Delivery Applications

Recombinant proteins have emerged as promising building blocks for vesicle self-assembly because of their versatility through genetic manipulation and biocompatibility. Vesicles composed of thermally responsive elastin-like polypeptide (ELP) fusion proteins encapsulate cargo during assembly. However, vesicle stability in physiological environments remains a significant challenge for biofunctional applications. Here, incorporation of an unnatural amino acid, para-azido phenylalanine, into the ELP domain is reported to enable photocrosslinking of protein vesicles and tuning of vesicle size and swelling. The size of the vesicles can be tuned by changing ELP hydrophobicity and ionic strength. Protein vesicles are assessed for their ability to encapsulate doxorubicin and dually deliver doxorubicin and fluorescent protein in vitro as a proof of concept. The resulting photocrosslinkable vesicles made from full-sized, functional proteins show high potential in drug delivery applications, especially for small molecule/protein combination therapies or targeted therapies.

A multi-step nucleation process determines the kinetics of prion-like domain phase separation

Compartmentalization by liquid-liquid phase separation (LLPS) has emerged as a ubiquitous mechanism underlying the organization of biomolecules in space and time. Here, we combine rapid-mixing time-resolved small-angle X-ray scattering (SAXS) approaches to characterize the assembly kinetics of a prototypical prion-like domain with equilibrium techniques that characterize its phase boundaries and the size distribution of clusters prior to phase separation. We find two kinetic regimes on the micro- to millisecond timescale that are distinguished by the size distribution of clusters. At the nanoscale, small complexes are formed with low affinity. After initial unfavorable complex assembly, additional monomers are added with higher affinity. At the mesoscale, assembly resembles classical homogeneous nucleation. Careful multi-pronged characterization is required for the understanding of condensate assembly mechanisms and will promote understanding of how the kinetics of biological phase separation is encoded in biomolecules.

Evaluation of machine learning algorithms to predict the hydrodynamic radii and transition temperatures of chemo-biologically synthesized copolymers

Elastin-like polypeptides (ELP) belong to a family of recombinant polymers that shows great promise as biocompatible drug delivery and tissue engineering materials. ELPs aggregate above a characteristic transition temperature (Tt). We have previously shown that the Tt and size of the resulting aggregates can be controlled by changing the ELP's solution environment (polymer concentration, salt concentration, and pH). When coupled to a synthetic polyelectrolyte, polyethyleneimine (PEI), ELP retains its Tt behavior and gains the ability to be crosslinked into defined particle sizes. This paper explores several machine learning models to predict the Tt and hydrodynamic radius (Rh) of ELP and two ELP-PEI polymers in varying solution conditions. An exhaustive design of experiments matrix consisting of 81 conditions of interest with varying salt concentration (0, 0.2, 1 M NaCl), pH (3, 7, 10), polymer concentration (0.1, 0.17, 0.3 mg/mL), and polymer type (ELP, ELP-PEI800, ELP-PEI10K) was investigated. The five models used in this study were multiple linear regression, elastic-net, support vector regression, multi-layer perceptron, and random forest. A multi-layer perceptron model was found to have the highest accuracy, with an R2 score of 0.97 for both Rh and Tt. This was followed closely by the random forest model, with an R2 of 0.94 for Rh and 0.95 for Tt. Feature importance was determined using the random forest and linear regression models. Both models showed that salt concentration and polymer type were the two most influential factors that determined Rh, while salt concentration was the dominant factor for Tt.

Adaptable antibody Nanoworms designed for non-Hodgkin lymphoma

Despite advancements in antibody-based therapies for non-Hodgkin lymphoma (NHL), at least two major therapeutic needs remain unmet: i) heterogenous activation of host immunity towards B cell NHL; and ii) lack of antibody-based therapeutics for T cell NHL. This study explores the molecular characteristics of an adaptable modality called antibody Nanoworms and demonstrates their receptor clustering activity as a means to overcome and address abovementioned needs. To test this, four selected therapeutic receptors of B cell (CD19, CD20, HLA-DR10) and T cell (CD3) NHL were targeted by Nanoworms. Regardless of the target or the cell type, Nanoworms inherently clustered bound receptors on the cell-surface through their multivalency and activated intracellular signaling without any secondary crosslinker. As a sole agent, Nanoworms induced apoptosis by clustering CD20 or HLA-DR10, and arrested the cell cycle upon CD19 clustering. Interestingly, CD3 clustering was particularly advantageous in inducing activation-induced cell death (AICD) in an aggressive form of T cell NHL named Sézary syndrome that is fatal, limited in antibody-based therapeutics, and has poor outcomes to traditional chemotherapy. As Nanoworms can be easily designed to target any receptor for which a scFv is available, they may provide solutions and add therapeutic novelty to underserved diseases.

Human Granulocyte-Macrophage Colony-Stimulating Factor Fused to Elastin-Like Polypeptides Assembles Biologically-Active Nanoparticles

Human granulocyte-macrophage colony-stimulating factor (hGMCSF) is crucial in the immune system as it stimulates survival, proliferation, differentiation, and functional activation of myeloid hematopoietic cells. hGMCSF is integral to approved therapies, including monoclonal antibodies against checkpoint inhibitors, chimeric antigen receptors, and prevention of chemotherapy-induced neutropenia. Recombinant hGMCSF can be purified from Escherichia. coli; however, it forms inclusion bodies that require solubilization and refolding. Alternatively, this manuscript describes its fusion with an elastin-like polypeptide (ELP). Previously reported as purification tags and solubility enhancers, ELPs are recombinant polypeptides that undergo reversible temperature-dependent phase separation. This report is the first to show that fusion to an ELP enables direct purification of hGMCSF fusions from the soluble fraction of bacterial lysate. Surprisingly, these ELP-fusions assemble stable, small, spherical nanoparticles that maintain pro-mitotic activity of hGMCSF. These nanoparticles exhibit ELP-mediated phase separation; however, nanoparticle assembly significantly increases the entropic and enthalpic cost of phase separation compared to ELP alone. The attachment of a high molecular weight ELP to a difficult-to-express protein, like hGMCSF, appears to be a useful strategy to stabilize bioactive, protein-based nanoparticles, which may have broad applications in medicine and biology.

FT-IR Spectroscopic Analysis of the Secondary Structures Present during the Desiccation Induced Aggregation of Elastin-Like Polypeptide on Silica

Previously, we found that elastin-like polypeptide (ELP), when dried above the lower critical solution temperature on top of a hydrophilic fused silica disk, exhibited a dynamic coalescence behavior. The ELP initially wet the silica, but over the next 12 h, dewett the surface and formed aggregates of precise sizes and shapes. Using Fourier-transform infrared (FT-IR) spectroscopy, the present study explores the role of secondary structures present in ELP during this progressive desiccation and their effect on aggregate size. The amide I peak (1600-1700 cm-1) in the ELP's FT-IR spectrum was deconvoluted using the second derivative method into eight subpeaks (1616, 1624, 1635, 1647, 1657, 1666, 1680, 1695 cm-1). These peaks were identified to represent extended strands, β-turns, 3(10)-helix, polyproline I, and polyproline II using previous studies on ELP and molecules similar in peptide composition. Positive correlations were established between the various subpeaks, water content, and aggregate size to understand the contributions of the secondary structures in particle formation. The positive correlations suggest that type II β-turns, independent of the water content, contributed to the growth of the aggregates at earlier time points (1-3.5 h). At later time points (6-12 h), the aggregate growth was attributed to the formation of 3(10)-helices that relied on a decrease in water content. Understanding these relationships gives greater control in creating precisely sized aggregates and surface coatings with varying roughness.

Brachytherapy using elastin-like polypeptide with different concentrations of 131I for treatment of VX2 liver tumor in rabbits

BACKGROUND

Brachytherapy is a targeted radiation therapy for cancer. The elastin-like peptide (ELP) is a genetically engineered peptide that has unique advantages such as self-assembly, temperature responsiveness, and non-immunogenicity, which make it possible to become the carrier of the radionuclide ¹³¹I.

AIM

To evaluate the effectiveness of brachytherapy in a rabbit model of VX2 liver tumor using elastin-like polypeptide as a radionuclide ¹³¹I carrier and compare the effectiveness of ¹³¹I-ELP at different radioactive concentrations to provide evidence for its clinical application.

METHODS

ELP as a carrier was labeled with ¹³¹I by the iodogen method, and different concentrations of ¹³¹I-ELP were prepared. Under ultrasound guidance, different concentrations of ¹³¹I-ELP and ELP solution were randomly injected into 15 rabbits with VX2 liver tumor for brachytherapy and blank control observation. The rabbits were divided into the following groups: high-dose radiation group (injection with 100 mCi/mL ¹³¹I-ELP; group H, n = 5); low-dose radiation group (injection with 50 mCi/mL ¹³¹I-ELP; group L, n = 5); and blank control group (injection with ELP solution; group C, n = 5). Periodic biochemical and sonographic examinations were performed to assess the therapeutic efficacy after treatment. Single-photon emission computed tomography/computed tomography (SPECT/CT) was additionally performed in the treatment groups. The natural survival time of animals in the three groups was determined. In addition, histopathological examination was performed.

RESULTS

The survival time of animals was the longest in group H (61.4 d ± 10.50 d) and the shortest (39.2 d ± 5.63 d) in group C. The survival time of animals in group L was 52.6 d ± 8.85 d. Significant differences were observed in the survival time among the three groups (P < 0.05). At 7 and 14 d after treatment, SPECT/CT showed that ¹³¹I-ELP was continuously localized in liver tumors in groups H and L. The tumor growth rates in groups H and L were significantly lower than that in group C (P < 0.05). Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) at 14 d after treatment in groups H and L were significantly lower than those in group C (P < 0.05). At 7 d after treatment, ALT level in group L was significantly lower than that in group H (P < 0.05). At 14 d after treatment, AST value in group L was significantly lower than that in group H (P < 0.05), suggesting that group L is better than group H with regard to ameliorating ALT and AST levels (P < 0.05). There were no significant differences in Hb or RBC levels between the three groups at 7 and 14 d after treatment. Histopathological examination showed that normal tissues around the tumor in group H were destroyed; proliferation of cord-like fibers, expansion of hepatic sinus, and dilatation of small bile ducts in the portal area were observed. In group L, no radioactive damage was observed in normal liver tissues around the tumor.

CONCLUSION

¹³¹I-ELP brachytherapy has curative effects in inhibiting tumor growth. ¹³¹I-ELP at a radiation dose of 100 mCi/mL inhibits tumor growth better than ¹³¹I-ELP at a radiation dose of 50 mCi/mL; however, the higher dose causes greater radiation damage to normal liver tissues around the tumor.

Single Amino Acid Substitutions in Stickers, but Not Spacers, Substantially Alter UBQLN2 Phase Transitions and Dense Phase Material Properties

UBQLN2 450-624 oligomerizes and undergoes temperature-responsive liquid-liquid phase transitions following a closed-loop temperature-concentration phase diagram. We recently showed that disease-linked mutations to UBQLN2 450-624 impart highly varying effects to its phase behavior, ranging from little change to significant decrease of saturation concentration and formation of gels and aggregates. However, how single mutations lead to these properties is unknown. Here, we use UBQLN2 450-624 as a model system to study the sequence determinants of phase separation. We hypothesized that UBQLN2 450-624 regions previously identified to promote its oligomerization are the "stickers" that drive interchain interactions and phase separation. We systematically investigated how phase behavior is affected by all 19 possible single amino acid substitutions at three sticker and two "spacer" (sequences separating stickers) positions. Overall, substitutions to stickers, but not spacers, substantially altered the shape of the phase diagram. Within the sticker regions, increasing hydrophobicity decreased saturation concentrations at low temperatures and enhanced oligomerization propensity and viscoelasticity of the dense phase. Conversely, substitutions to acidic residues at all positions greatly increased saturation concentrations. Our data demonstrate that single amino acid substitutions follow a molecular code to tune phase transition behavior of biopolymers.

Macro- and Microphase Separated Protein-Polyelectrolyte Complexes: Design Parameters and Current Progress

Protein-containing polyelectrolyte complexes (PECs) are a diverse class of materials, composed of two or more oppositely charged polyelectrolytes that condense and phase separate near overall charge neutrality. Such phase-separation can take on a variety of morphologies from macrophase separated liquid condensates, to solid precipitates, to monodispersed spherical micelles. In this review, we present an overview of recent advances in protein-containing PECs, with an overall goal of defining relevant design parameters for macro- and microphase separated PECs. For both classes of PECs, the influence of protein characteristics, such as surface charge and patchiness, co-polyelectrolyte characteristics, such as charge density and structure, and overall solution characteristics, such as salt concentration and pH, are considered. After overall design features are established, potential applications in food processing, biosensing, drug delivery, and protein purification are discussed and recent characterization techniques for protein-containing PECs are highlighted.