Label-Free Analysis of Protein Aggregation and Phase Behavior

Label-free visualization of unfolding and crosslinking mediated protein aggregation in nonenzymatically glycated proteins

Nonenzymatic glycation (NEG) unfolds and crosslinks proteins, resulting in aggregation. Label-free evaluation of such structural changes, without disturbing molecular integrity, would be beneficial for understanding the fundamental mechanisms of protein aggregation. The current study demonstrates the assessment of NEG-induced protein aggregation by combining autofluorescence (AF) spectroscopy and imaging. The methylglyoxal (MG) induced protein unfolding and the formation of cross-linking advanced glycation end-products (AGEs) leading to aggregation were evaluated using deep-UV-induced-autofluorescence (dUV-AF) spectroscopy in proteins with distinct structural characteristics. Since the AGEs formed on proteins are fluorescent, the study demonstrated the possibility of autofluorescence imaging of NEG-induced protein aggregates. Autofluorescence spectroscopy can potentially reveal molecular alterations such as protein unfolding and cross-linking. In contrast, AGE-based autofluorescence imaging offers a means to visually explore the structural arrangement of aggregates, regardless of whether they are amyloid or non-amyloid in nature.

Amyloid formation and depolymerization of tumor suppressor p16INK4a are regulated by a thiol-dependent redox mechanism

The conversion of a soluble protein into polymeric amyloid structures is a process that is poorly understood. Here, we describe a fully redox-regulated amyloid system in which cysteine oxidation of the tumor suppressor protein p16INK4a leads to rapid amyloid formation. We identify a partially-structured disulfide-bonded dimeric intermediate species that subsequently assembles into fibrils. The stable amyloid structures disassemble when the disulfide bond is reduced. p16INK4a is frequently mutated in cancers and is considered highly vulnerable to single-point mutations. We find that multiple cancer-related mutations show increased amyloid formation propensity whereas mutations stabilizing the fold prevent transition into amyloid. The complex transition into amyloids and their structural stability is therefore strictly governed by redox reactions and a single regulatory disulfide bond.

β-Lactoglobulin-based aerogels: Facile preparation and sustainable removal of organic contaminants from water

Economically and efficiently removing organic pollutants from water is still a challenge in wastewater treatment. Utilizing environmentally friendly and readily available protein-based natural polymers to develop aerogels with effective removal performance and sustainable regeneration capability is a promising strategy for adsorbent design. Here, a robust and cost-effective method using inexpensive β-lactoglobulin (BLG) as raw material was proposed to fabricate BLG-based aerogels. Firstly, photocurable BLG-based polymers were synthesized by grafting glycidyl methacrylate. Then, a cross-linking reaction, including photo-crosslinking and salting-out treatment, was applied to prepared BLG-based hydrogels. Finally, the BLG-based aerogels with high porosity and ultralight weight were obtained after freeze-drying. The outcomes revealed that the biocompatible BLG-based aerogels exhibited effective removal performance for a variety of organic pollutants under perfectly quiescent conditions, and could be regenerated and reused many times via a simple and rapid process of acid washing and centrifugation. Overall, this work not only demonstrates that BLG-based aerogels are promising adsorbents for water purification but also provides a potential way for the sustainable utilization of BLG.

Highly sensitive absorbance measurement using droplet microfluidics integrated with an oil extraction and long pathlength detection flow cell

In droplet microfluidics, UV-Vis absorption spectroscopy along with colorimetric assays have been widely used for chemical and biochemical analysis. However, the sensitivity of the measurement can be limited by the short optical pathlength. Here we report a novel design to enhance the sensitivity by removing oil and converting the droplets into a single-phase aqueous flow, which can be measured within a U-shape channel with long optical pathlength. The flow cells were fabricated via 3D printing. The calibration results have demonstrated complete oil removal and effective optical pathlengths similar to the designed channel lengths (from 5 to 20 mm). The flow cell was further employed in a droplet microfluidic-based phosphate sensing system. The measured phosphate levels displayed excellent consistency with data obtained from traditional UV spectroscopy analysis. This flow cell design overcomes the limitations of short optical pathlengths in droplet microfluidics and has the potential to be used for in situ and continuous monitoring.

The immune-evasive proline-283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure

Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. NP also determines the sensitivity of influenza to myxovirus resistance protein 1 (MxA), an innate immunity factor that restricts influenza replication. A few critical MxA-resistant mutations have been identified in NP, including the highly conserved proline-283 substitution. This essential proline-283 substitution impairs influenza growth, a fitness defect that becomes particularly prominent at febrile temperature (39°C) when host chaperones are depleted. Here, we biophysically characterize proline-283 NP and serine-283 NP to test whether the fitness defect is caused by the proline-283 substitution introducing folding defects. We show that the proline-283 substitution changes the folding pathway of NP, making NP more aggregation prone during folding, but does not alter the native structure of the protein. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape.

Real-time and quantitative protein detection via polyacrylamide gel electrophoresis and online intrinsic fluorescence imaging

The detection of intrinsic protein fluorescence is a powerful tool for studying proteins in their native state. Thanks to its label-free and stain-free feature, intrinsic fluorescence detection has been introduced to polyacrylamide gel electrophoresis (PAGE), a fundamental and ubiquitous protein analysis technique, to avoid the tedious detection process. However, the reported methods of intrinsic fluorescence detection were incompatible with online PAGE detection or standard slab gel. Here, we fulfilled online intrinsic fluorescence imaging (IFI) of the standard slab gel to develop a PAGE-IFI method for real-time and quantitative protein detection. To do so, we comprehensively investigated the arrangement of the deep-UV light source to obtain a large imaging area compatible with the standard slab gel, and then designed a semi-open gel electrophoresis apparatus (GEA) to scaffold the gel for the online UV irradiation and IFI with low background noise. Thus, we achieved real-time monitoring of the protein migration, which enabled us to determine the optimal endpoint of PAGE run to improve the sensitivity of IFI. Moreover, online IFI circumvented the broadening of protein bands to enhance the separation resolution. Because of the low background noise and the optimized endpoint, we showcased the quantitative detection of bovine serum albumin (BSA) with a limit of detection (LOD) of 20 ng. The standard slab gel provided a high sample loading volume that allowed us to attain a wide linear range of 0.03-10 μg. These results indicate that the PAGE-IFI method can be a promising alternative to conventional PAGE and can be widely used in molecular biology labs.

Investigating the synergistic effects of high-pressure homogenization and pH shifting on the formation of tryptophan-rich nanoparticles

A combined treatment of high-pressure homogenization (HPH) and pH-shifting on the mixture of α-lactalbumin (α-LA) and tryptophan (Trp) was used to fabricate nanoparticles (α-LA-Trp-NP). The optimal α-LA/Trp ratio (5:1), HPH pressure (206.8 MPa), and recirculation time (40 min) was found to produce small α-LA-Trp-NP (243.0 ± 7.2 nm) with a narrow particle size distribution. Comparing the size and morphology of α-LA-NPs with α-LA-Trp-NPs indicated that the presence of Trp significantly affected the size and morphology of the NPs in the dry form. The stability of the α-LA-Trp-NPs was improved by using the combination of HPH and pH-shifting. The α-LA-Trp-NPs showed better freeze-thaw stability and retained the particle characteristics with heat treatment at 63 °C, 30 min after the freeze-thaw cycle. α-LA-Trp-NPs were also observed to have remarkable stability against pH changes and thermal treatments at 63 °C, 30 min, and 90 °C, 2 min.

Protein classification by autofluorescence spectral shape analysis using machine learning

Depending on the relative numbers and spatial arrangement of Tryptophan (Trp; W) and Tyrosine (Tyr; Y) residues, different proteins produce distinct autofluorescence (AF) spectral shapes when excited at ∼280 nm. Yet, considering the vast number and heterogeneous forms in nature, visual analysis and precise identification of proteins based on their AF spectra is challenging and further compounded in cases when different proteins produce substantially similar AF spectral shapes. There is, thus, a serious need to develop a methodology to address this problem. The current study proposes a practical technology to quickly identify proteins using machine learning (ML) algorithms based on their AF spectra. Specifically, AF spectra of fifteen different standard proteins of varying origin with distinct structural and Trp/Tyr compositions were recorded; based on the spectral features selected by the Minimum-Redundancy-Maximum-Relevance (mRMR) algorithm, a multiclass Support Vector Machine (SVM) learning model with Radial Basis Function (RBF), Polynomial, and Linear kernels classified the proteins with high accuracy of 99.06%, 99.03%, and 98.29% respectively. Since protein identification is the key to understand biological functions and disease diagnosis, the proposed methodology could offer a viable alternative to and improve the existing protein identification techniques.

Ultraviolet Resonant Nanogap Antennas with Rhodium Nanocube Dimers for Enhancing Protein Intrinsic Autofluorescence

Plasmonic optical nanoantennas offer compelling solutions for enhancing light-matter interactions at the nanoscale. However, until now, their focus has been mainly limited to the visible and near-infrared regions, overlooking the immense potential of the ultraviolet (UV) range, where molecules exhibit their strongest absorption. Here, we present the realization of UV resonant nanogap antennas constructed from paired rhodium nanocubes. Rhodium emerges as a robust alternative to aluminum, offering enhanced stability in wet environments and ensuring reliable performance in the UV range. Our results showcase the nanoantenna's ability to enhance the UV autofluorescence of label-free streptavidin and hemoglobin proteins. We achieve significant enhancements of the autofluorescence brightness per protein by up to 120-fold and reach zeptoliter detection volumes, enabling UV autofluorescence correlation spectroscopy (UV-FCS) at high concentrations of several tens of micromolar. We investigate the modulation of fluorescence photokinetic rates and report excellent agreement between the experimental results and numerical simulations. This work expands the applicability of plasmonic nanoantennas to the deep UV range, unlocking the investigation of label-free proteins at physiological concentrations.

Small molecule fluorescent probes for the study of protein phase separation

Liquid-liquid phase separation (LLPS) and liquid-solid phase transitions (LSPT) play crucial roles in biological systems, including sorting biomolecules, facilitate the transport of substrates for assembly, and accelerate the formation of metabolic and signaling complexes. Efforts towards improved characterization and quantification of phase separated species remain of outstanding interest and priority. In this review, we cover recent advances and the strategies used with small molecule fluorescent probes for the study of phase separation.

Non-Pore Dependent and MMP-9 Responsive Gelatin/Silk Fibroin Composite Microparticles as Universal Delivery Platform for Inhaled Treatment of Lung Cancer

Developing a drug delivery platform that possesses universal drug loading capacity to meet various requirements of cancer treatment is a challenging yet interesting task. Herein, a self-assembled gelatin/silk fibroin composite (GSC) particle based drug delivery system is developed via microphase separation followed by desolvation process. Thanks to its preassembled microphase stage, this GSC system is suitable for varying types of drugs. The desolvation process fix drugs inside GSC rapidly and densify the GSC structure, thereby achieving efficient drug loading and providing comprehensive protection for loaded drugs. Actually, the size of this brand-new non-pore dependent drug delivery system can be easily adjusted from 100 nm to 20 µm to fit different scenarios. This work selects GSC with 3 µm diameter as the universal inhaled drug delivery platform, which shows an excellent transmucosal penetration and lung retention ability. Additionally, the MMP-9 sensitive degradation property of GSC enhances the targeted efficiency of drugs and reduces side effects. Intestinally, GSC can self-amplify the regulation of innate immunity to reverse the cancerous microenvironment into an antitumor niche, significantly improving the therapeutic effect of drugs. This study of GSC universal drug platform provides a new direction to develop the next-generation of drug delivery system for lung cancer.

The Immune-Evasive Proline 283 Substitution in Influenza Nucleoprotein Increases Aggregation Propensity Without Altering the Native Structure

Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. In human cells, the interferon induced Myxovirus resistance protein 1 (MxA) binds to NP and restricts influenza replication. This selection pressure has caused NP to evolve a few critical MxA-resistant mutations, particularly the highly conserved Pro283 substitution. Previous work showed that this essential Pro283 substitution impairs influenza growth, and the fitness defect becomes particularly prominent at febrile temperature (39 °C) when host chaperones are depleted. Here, we biophysically characterize Pro283 NP and Ser283 NP to test if the fitness defect is owing to Pro283 substitution introducing folding defects. We show that the Pro283 substitution changes the folding pathway of NP without altering the native structure, making NP more aggregation prone during folding. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape.

Teaser

Pro283 substitution in flu nucleoprotein introduces folding defects, and makes influenza uniquely dependent on host chaperones.

Role of conformational dynamics in pathogenic protein aggregation

The accumulation of pathogenic protein oligomers and aggregates is associated with several devastating amyloid diseases. As protein aggregation is a multi-step nucleation-dependent process beginning with unfolding or misfolding of the native state, it is important to understand how innate protein dynamics influence aggregation propensity. Kinetic intermediates composed of heterogeneous ensembles of oligomers are frequently formed on the aggregation pathway. Characterization of the structure and dynamics of these intermediates is critical to the understanding of amyloid diseases since oligomers appear to be the main cytotoxic agents. In this review, we highlight recent biophysical studies of the roles of protein dynamics in driving pathogenic protein aggregation, yielding new mechanistic insights that can be leveraged for design of aggregation inhibitors.

Kinetic Analysis Reveals the Role of Secondary Nucleation in Regenerated Silk Fibroin Self-Assembly

Silk proteins obtained from the Bombyx mori silkworm have been extensively studied due to their remarkable mechanical properties. One of the major structural components of this complex material is silk fibroin, which can be isolated and processed further in vitro to form artificial functional materials. Due to the excellent biocompatibility and rich self-assembly behavior, there has been sustained interest in such materials formed through the assembly of regenerated silk fibroin feedstocks. The molecular mechanisms by which the soluble regenerated fibroin molecules self-assemble into protein nanofibrils remain, however, largely unknown. Here, we use the framework of chemical kinetics to connect macroscopic measurements of regenerated silk fibroin self-assembly to the underlying microscopic mechanisms. Our results reveal that the aggregation of regenerated silk fibroin is dominated by a nonclassical secondary nucleation processes, where the formation of new fibrils is catalyzed by the existing aggregates in an autocatalytic manner. Such secondary nucleation pathways were originally discovered in the context of polymerization of disease-associated proteins, but the present results demonstrate that this pathway can also occur in functional assembly. Furthermore, our results show that shear flow induces the formation of nuclei, which subsequently accelerate the process of aggregation through an autocatalytic amplification driven by the secondary nucleation pathway. Taken together, these results allow us to identify the parameters governing the kinetics of regenerated silk fibroin self-assembly and expand our current understanding of the spinning of bioinspired protein-based fibers, which have a wide range of applications in materials science.

Current Lifetime of Single-Nanoparticle Electrochemical Collision for In Situ Monitoring Nanoparticles Agglomeration and Aggregation

In situ monitoring of the agglomeration/aggregation process of nanoparticles (NPs) is crucial because it seriously affects cell entry, biosafety, catalytic performance of NPs, and so on. Nevertheless, it remains hard to monitor the solution phase agglomeration/aggregation of NPs via conventional techniques such as electron microscopy, which requires sample pretreatment and cannot represent native state NPs in solution. Considering that single-nanoparticle electrochemical collision (SNEC) is powerful to detect NPs in solution at the single-particle level, and the current lifetime, which refers to the time that current intensity decays to 1/e of the original value, is skilled in distinguishing different sized NPs, herein, a current lifetime-based SNEC has been developed to distinguish a single Au NP (d = 18 nm) from its agglomeration/aggregation. Based on this, the agglomeration/aggregation process of small-sized NPs and the discrimination of agglomeration vs aggregation have been carefully investigated at the single-particle level. Results showed that the agglomeration/aggregation of Au NPs (d = 18 nm) in 0.8 mM HClO₄ climbed from 19% to 69% over two hours, whereas there was no visible granular sediment, and Au NPs tended to agglomerate rather than aggregate irreversibly under normal conditions. Hence, the proposed current lifetime-based SNEC could serve as a complementary method to in situ monitor the agglomeration/aggregation of small-sized NPs in solution at the single-particle level and provide effective guidance for the practical application of NPs.

Ultraviolet Nanophotonics Enables Autofluorescence Correlation Spectroscopy on Label-Free Proteins with a Single Tryptophan

Using the ultraviolet autofluorescence of tryptophan amino acids offers fascinating perspectives to study single proteins without the drawbacks of fluorescence labeling. However, the low autofluorescence signals have so far limited the UV detection to large proteins containing several tens of tryptophan residues. This limit is not compatible with the vast majority of proteins which contain only a few tryptophans. Here we push the sensitivity of label-free ultraviolet fluorescence correlation spectroscopy (UV-FCS) down to the single tryptophan level. Our results show how the combination of nanophotonic plasmonic antennas, antioxidants, and background reduction techniques can improve the signal-to-background ratio by over an order of magnitude and enable UV-FCS on thermonuclease proteins with a single tryptophan residue. This sensitivity breakthrough unlocks the applicability of UV-FCS technique to a broad library of label-free proteins.

A chip-based supersonic microfluidic nebulizer for efficient sample introduction into inductively coupled plasma - Mass spectrometry

As the use of microfluidic chips for handling biological samples is increasing, so is the need for combining them with powerful analytical techniques for metal determination such as inductively-coupled plasma mass spectrometry (ICP-MS). So far, coupling a microfluidic chip to an ICP-MS has been demonstrated mainly through the use of conventional pneumatic micro-flow nebulizers. However, disadvantages associated with the use of such nebulizers entail dead volume issues and liquid suction exerted on the outlet channel of the chip. Herein, we propose that a microfluidic chip, bearing a pneumatic nozzle for liquid nebulization, has the potential to advance metal determination in chip-based ICP-MS. More specifically, we demonstrate for the first time that the coupling of a chip-based supersonic microfluidic nebulizer (chip-μf-Neb) to an ICP-MS can be conveniently achieved through the use of a spray chamber with a laminar flow makeup gas. Operation of the combined system was evaluated at low liquid flow rates across 0.5-20 μL min^-1, while nebulization and makeup argon (Ar) gas flow rates were optimized with respect to maximizing indium (In) sensitivity and minimizing oxide formation; a maximum sensitivity of 40000 cps (μg L^-1)^-1 was achieved at 10 μL min^-1. The system was further evaluated for its performance in single-particle analysis, featuring a transport efficiency of 46% for Ag nanoparticles. Finally, the capabilities for conducting single-cell analysis were demonstrated with the detection of ⁸⁰Se and ⁷⁵As in individual Chlamydomas reinhardtii cells, which were previously incubated in 20 μM of selenate and 300 μM of arsenate, respectively. Efficient operation at low liquid flow rates along with the absence of self-aspiration render this nebulizer a promising tool for combining the powerful field of microfluidics with metal quantitation by means of ICP-MS.

Label-free monitoring of proteins in optofluidic hollow-core photonic crystal fibres

The fluorescent detection of proteins without labels or stains, which affect their behaviour and require additional genetic or chemical preparation, has broad applications to biological research. However, standard approaches require large sample volumes or analyse only a small fraction of the sample. Here we use optofluidic hollow-core photonic crystal fibres to detect and quantify sub-microlitre volumes of unmodified bovine serum albumin (BSA) protein down to 100 nM concentrations. The optofluidic fibre's waveguiding properties are optimised for guidance at the (auto)fluorescence emission wavelength, enabling fluorescence collection from a 10 cm long excitation region, increasing sensitivity. The observed spectra agree with spectra taken from a conventional cuvette-based fluorimeter, corrected for the guidance properties of the fibre. The BSA fluorescence depended linearly on BSA concentration, while only a small hysteresis effect was observed, suggesting limited biofouling of the fibre sensor. Finally, we briefly discuss how this method could be used to study aggregation kinetics. With small sample volumes, the ability to use unlabelled proteins, and continuous flow, the method will be of interest to a broad range of protein-related research.

Direct observation of heterogeneous formation of amyloid spherulites in real-time by super-resolution microscopy

Protein misfolding in the form of fibrils or spherulites is involved in a spectrum of pathological abnormalities. Our current understanding of protein aggregation mechanisms has primarily relied on the use of spectrometric methods to determine the average growth rates and diffraction-limited microscopes with low temporal resolution to observe the large-scale morphologies of intermediates. We developed a REal-time kinetics via binding and Photobleaching LOcalization Microscopy (REPLOM) super-resolution method to directly observe and quantify the existence and abundance of diverse aggregate morphologies of human insulin, below the diffraction limit and extract their heterogeneous growth kinetics. Our results revealed that even the growth of microscopically identical aggregates, e.g., amyloid spherulites, may follow distinct pathways. Specifically, spherulites do not exclusively grow isotropically but, surprisingly, may also grow anisotropically, following similar pathways as reported for minerals and polymers. Combining our technique with machine learning approaches, we associated growth rates to specific morphological transitions and provided energy barriers and the energy landscape at the level of single aggregate morphology. Our unifying framework for the detection and analysis of spherulite growth can be extended to other self-assembled systems characterized by a high degree of heterogeneity, disentangling the broad spectrum of diverse morphologies at the single-molecule level.

Real-time super-resolution microscopy analysis reveals the growth kinetics, morphology, and abundance of human insulin amyloid spherulites with different growth pathways.

Adsorption free energy predicts amyloid protein nucleation rates

Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer's and Parkinson's diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process.

Shear Stress Induces α-Synuclein Aggregation Due to a Less Strained Protein Backbone and Protein Tyrosyl Groups Do Not Intervene in the Aggregation

Parkinson’s disease (PD) is an increasingly prevalent and currently incurable neurodegenerative disorder. The aggregation of the amyloid disordered protein α-synuclein (Syn) has been implicated in the development of PD. In the literature, it has been suggested that tyrosine residues of Syn play an important role in the interactions established during the fibrillation process. Herein, the prevalence of the referred interactions under shear stress conditions of Nα-acetyl-L-tyrosinamide (NAYA) and of Syn solutions by using membrane centrifugal filters with different cut-off of 200 nm, 100 kDa, 50 kDa and 30 kDa, under centrifugation conditions, were investigated. In order to determine the nature of the interactions involving the protein tyrosine residues the NAYA compound, which mimics the peptide bonds in protein and also possesses a tyrosyl group similar to the tyrosyl groups found in the Syn protein molecular structure, was used. It is expected that for a small molecule, such as NAYA, no molecular association occurs, contrary to what exists in the Syn protein solutions, which can more adequately retrieve the type of interactions formed, involving the tyrosyl group. Therefore, sensing the tyrosyl group absorption, spectroscopic techniques, in particular, were used. For NAYA, an intramolecular interaction between the tyrosyl group and the peptide bond was evidenced. For NAYA and Syn, it was observed that decreasing the membrane centrifugal filters pore size, under centrifugation conditions, was concomitant with the minimization of the intramolecular interactions between the tyrosyl group and the peptide bond. With this, it is likely to assume that shear stress conditions in the Syn solutions propel protein aggregation by a less strained protein backbone. Contrary to the centrifugation of NAYA solutions, centrifuging Syn solutions revealed molecular association and a progressive exposure of protein tyrosyl groups to water. Thus, we can also infer that shear stress conditions in the Syn solutions cause the protein tyrosyl groups to not intervene in the protein aggregation.

A comprehensive review on LED-induced fluorescence in diagnostic pathology

Sensitivity, specificity, mobility, and affordability are important criteria to consider for developing diagnostic instruments in common use. Fluorescence spectroscopy has been demonstrating substantial potential in the clinical diagnosis of diseases and evaluating the underlying causes of pathogenesis. A higher degree of device integration with appropriate sensitivity and reasonable cost would further boost the value of the fluorescence techniques in clinical diagnosis and aid in the reduction of healthcare expenses, which is a key economic concern in emerging markets. Light-emitting diodes (LEDs), which are inexpensive and smaller are attractive alternatives to conventional excitation sources in fluorescence spectroscopy, are gaining a lot of momentum in the development of affordable, compact analytical instruments of clinical relevance. The commercial availability of a broad range of LED wavelengths (255-4600 nm) has opened up new avenues for targeting a wide range of clinically significant molecules (both endogenous and exogenous), thereby diagnosing a range of clinical illnesses. As a result, we have specifically examined the uses of LED-induced fluorescence (LED-IF) in preclinical and clinical evaluations of pathological conditions, considering the present advancements in the field.

Using quantitative reconstitution to investigate multicomponent condensates

Many biomolecular condensates are thought to form via liquid-liquid phase separation (LLPS) of multivalent macromolecules. For those that form through this mechanism, our understanding has benefitted significantly from biochemical reconstitutions of key components and activities. Reconstitutions of RNA-based condensates to date have mostly been based on relatively simple collections of molecules. However, proteomics and sequencing data indicate that natural RNA-based condensates are enriched in hundreds to thousands of different components, and genetic data suggest multiple interactions can contribute to condensate formation to varying degrees. In this Perspective, we describe recent progress in understanding RNA-based condensates through different levels of biochemical reconstitutions as a means to bridge the gap between simple in vitro reconstitution and cellular analyses. Complex reconstitutions provide insight into the formation, regulation, and functions of multicomponent condensates. We focus on two RNA-protein condensate case studies: stress granules and RNA processing bodies (P bodies), and examine the evidence for cooperative interactions among multiple components promoting LLPS. An important concept emerging from these studies is that composition and stoichiometry regulate biochemical activities within condensates. Based on the lessons learned from stress granules and P bodies, we discuss forward-looking approaches to understand the thermodynamic relationships between condensate components, with the goal of developing predictive models of composition and material properties, and their effects on biochemical activities. We anticipate that quantitative reconstitutions will facilitate understanding of the complex thermodynamics and functions of diverse RNA-protein condensates.

Accelerating Reaction Rates of Biomolecules by Using Shear Stress in Artificial Capillary Systems

Biomimetics is a design principle within chemistry, biology, and engineering, but chemistry biomimetic approaches have been generally limited to emulating nature's chemical toolkit while emulation of nature's physical toolkit has remained largely unexplored. To begin to explore this, we designed biophysically mimetic microfluidic reactors with characteristic length scales and shear stresses observed within capillaries. We modeled the effect of shear with molecular dynamics studies and showed that this induces specific normally buried residues to become solvent accessible. We then showed using kinetics experiments that rates of reaction of these specific residues in fact increase in a shear-dependent fashion. We applied our results in the creation of a new microfluidic approach for the multidimensional study of cysteine biomarkers. Finally, we used our approach to establish dissociation of the therapeutic antibody trastuzumab in a reducing environment. Our results have implications for the efficacy of existing therapeutic antibodies in blood plasma as well as suggesting in general that biophysically mimetic chemistry is exploited in biology and should be explored as a research area.

Formation of β-Lactoglobulin Self-Assemblies via Liquid-Liquid Phase Separation for Applications beyond the Biological Functions

Proteins are like miracle machines, playing important roles in living organisms. They perform vital biofunctions by further combining together and/or with other biomacromolecules to form assemblies or condensates such as membraneless organelles. Therefore, studying the self-assembly of biomacromolecules is of fundamental importance. In addition to their biological activities, protein assemblies also exhibit extra properties that enable them to achieve applications beyond their original functions. Herein, this study showed that in the presence of monosaccharides, ethylene glycols, and amino acids, β-lactoglobulin (β-LG) can form assemblies with specific structures, which were highly reproducible. The mechanism of the assembly process was studied through multi-scale observations and theoretical analysis, and it was found that the assembling all started from the formation of solute-rich liquid droplets via liquid-liquid phase separation (LLPS). These droplets then combined together to form condensates with elaborate structures, and the condensates finally evolved to form assemblies with various morphologies. Such a mechanism of the assembly is valuable for studying the assembly processes that frequently occur in living organisms. Detailed studies concerning the properties and applications of the obtained β-LG assemblies showed that the assemblies exhibited significantly better performances than the protein itself in terms of autofluorescence, antioxidant activity, and metal ion absorption, which indicates broad applications of these assemblies in bioimaging, biodetection, biodiagnosis, health maintenance, and pollution treatment. This study revealed that biomacromolecules, especially proteins, can be assembled via LLPS, and some unexpected application potentials could be found beyond their original biological functions.

Sequential storage and release of microdroplets

Droplet microfluidic methods have opened up the possibility of studying a plethora of phenomena ranging from biological to physical or chemical processes at ultra low volumes and high throughput. A key component of such approaches is the ability to trap droplets for observation, and many device architectures for achieving this objective have been developed. A challenge with such approaches is, however, recovering the droplets following their confinement for applications involving further analysis. Here, we present a device capable of generating, confining and releasing microdroplets in a sequential manner. Through a combination of experimental and computational simulations, we shed light on the key features required for successful droplet storage and retrieval. Moreover, we explore the effect of the flow rate of the continuous phase on droplet release, determining that a critical rate is needed to ensure complete droplet deformation through constrictions holding the droplets in place prior to release. Finally, we find that once released, droplets can be retrieved and collected off chip. The ability to generate, store and sequentially release droplets renders such a device particularly promising for future applications where reactions may not only be monitored on-chip, but droplets can also be retrieved for further analysis, facilitating new exploratory avenues in the fields of analytical chemistry and biology.

Peptide Amphiphilic-Based Supramolecular Structures with Anti-HIV-1 Activity

In a previous work, we defined a novel HIV-1 fusion inhibitor peptide (E1P47) with a broad spectrum of activity against viruses from different clades, subtypes, and tropisms. With the aim to enhance its efficacy, in the present work we address the design and synthesis of several peptide amphiphiles (PAs) based on the E1P47 peptide sequence to target the lipid rafts of the cell membrane where the cell–cell fusion process takes place. We report the synthesis of novel PAs having a hydrophobic moiety covalently attached to the peptide sequence through a hydrophilic spacer of polyethylene glycol. Characterization of self-assembly in condensed phase and aqueous solution as well as their interaction with model membranes was analyzed by several biophysical methods. Our results demonstrated that the length of the spacer of polyethylene glycol, the position of the peptide conjugation as well as the type of the hydrophobic residue determine the antiviral activity of the construct. Peptide amphiphiles with one alkyl tail either in C-terminus (C-PA_monoalkyl) or in N-terminus (N-PA_monoalkyl) showed the highest anti-HIV-1 activities in the cellular model of TZM-bl cells or in a preclinical model of the human mucosal tissue explants.

Toward the equilibrium and kinetics of amyloid peptide self-assembly

Several devastating human diseases are linked to peptide self-assembly, but our understanding their onset and progression is not settled. This is a sign of the complexity of the aggregation process, which is prevented, catalyzed, or retarded by numerous factors in body fluids and cells, varying in time and space. Biophysical studies of pure peptide solutions contribute insights into the underlying steps in the process and quantitative parameters relating to rate constants (energy barriers) and equilibrium constants (population distributions). This requires methods to quantify the concentration of at least one species in the process. Translation to an in vivo situation poses an enormous challenge, and the effects of selected components (bottom up) or entire body fluids (top down) need to be quantified.

From Protein Building Blocks to Functional Materials

Proteins are the fundamental building blocks for high-performance materials in nature. Such materials fulfill structural roles, as in the case of silk and collagen, and can generate active structures including the cytoskeleton. Attention is increasingly turning to this versatile class of molecules for the synthesis of next-generation green functional materials for a range of applications. Protein nanofibrils are a fundamental supramolecular unit from which many macroscopic protein materials are formed. In this Review, we focus on the multiscale assembly of such protein nanofibrils formed from naturally occurring proteins into new supramolecular architectures and discuss how they can form the basis of material systems ranging from bulk gels, films, fibers, micro/nanogels, condensates, and active materials. We review current and emerging approaches to process and assemble these building blocks in a manner which is different to their natural evolutionarily selected role but allows the generation of tailored functionality, with a focus on microfluidic approaches. We finally discuss opportunities and challenges for this class of materials, including applications that can be involved in this material system which consists of fully natural, biocompatible, and biodegradable feedstocks yet has the potential to generate materials with performance and versatility rivalling that of the best synthetic polymers.

Evidence of the existence of micellar-like aggregates for α-synuclein

We have been investigating the early stages of α-synuclein (Syn) aggregation, a small presynaptic protein implicated in Parkinson's disease. We previously reported that for pH jumps (1000 s) from pH 7 to pH 2 the variation of the Syn intrinsic fluorescence intensity did not change in the concentration range of ca. 10-50 μM (ref. 16). Additionally, I reported dynamic light scattering (DLS) experiments revealing the formation of early large Syn aggregates (ref. 7). These reported results mean that some molecular entity is being early formed. Herein, it was decided to investigate in detail these early Syn aggregates by using light scattering. By DLS analysis, these aggregates exhibited a hydrodynamic diameter of ca. 420 nm along with a high scattering intensity, characteristic of micellar-like aggregates formation. The critical micelle concentration (CMC) at which the Syn micellar-like aggregates are formed was ca. 10 μM. DLS analysis has also revealed that the micellar-like aggregates for Syn evolved, for protein concentrations >100 μM, to the formation of smaller aggregates (hydrodynamic diameter of ca. 165 nm), possibly Syn oligomers. The Syn micellar-like aggregates formed at pH 7 solutions seem to be active species and to have a role in this protein aggregation mechanism.

Label-Free Protein Analysis Using Liquid Chromatography with Gravimetric Detection

The detection and analysis of proteins in a label-free manner under native solution conditions is an increasingly important objective in analytical bioscience platform development. Common approaches to detect native proteins in solution often require specific labels to enhance sensitivity. Dry mass sensing approaches, by contrast, using mechanical resonators, can operate in a label-free manner and offer attractive sensitivity. However, such approaches typically suffer from a lack of analyte selectivity as the interface between standard protein separation techniques and micro-resonator platforms is often constrained by qualitative mechanical sensor performance in the liquid phase. Here, we describe a strategy that overcomes this limitation by coupling liquid chromatography with a quartz crystal microbalance (QCM) platform by using a microfluidic spray dryer. We explore a strategy which allows first to separate a protein mixture in a physiological buffer solution using size exclusion chromatography, permitting specific protein fractions to be selected, desalted, and subsequently spray-dried onto the QCM for absolute mass analysis. By establishing a continuous flow interface between the chromatography column and the spray device via a flow splitter, simultaneous protein mass detection and sample fractionation is achieved, with sensitivity down to a 100 μg/mL limit of detection. This approach for quantitative label-free protein mixture analysis offers the potential for detection of protein species under physiological conditions.

Potential of Microfluidics and Lab-on-Chip Platforms to Improve Understanding of "prion-like" Protein Assembly and Behavior

Human aging is accompanied by a relevant increase in age-associated chronic pathologies, including neurodegenerative and metabolic diseases. The appearance and evolution of numerous neurodegenerative diseases is paralleled by the appearance of intracellular and extracellular accumulation of misfolded proteins in affected brains. In addition, recent evidence suggests that most of these amyloid proteins can behave and propagate among neural cells similarly to infective prions. In order to improve understanding of the seeding and spreading processes of these "prion-like" amyloids, microfluidics and 3D lab-on-chip approaches have been developed as highly valuable tools. These techniques allow us to monitor changes in cellular and molecular processes responsible for amyloid seeding and cell spreading and their parallel effects in neural physiology. Their compatibility with new optical and biochemical techniques and their relative availability have increased interest in them and in their use in numerous laboratories. In addition, recent advances in stem cell research in combination with microfluidic platforms have opened new humanized in vitro models for myriad neurodegenerative diseases affecting different cellular targets of the vascular, muscular, and nervous systems, and glial cells. These new platforms help reduce the use of animal experimentation. They are more reproducible and represent a potential alternative to classical approaches to understanding neurodegeneration. In this review, we summarize recent progress in neurobiological research in "prion-like" protein using microfluidic and 3D lab-on-chip approaches. These approaches are driven by various fields, including chemistry, biochemistry, and cell biology, and they serve to facilitate the development of more precise human brain models for basic mechanistic studies of cell-to-cell interactions and drug discovery.

Collagen-Inspired Helical Peptide Coassembly Forms a Rigid Hydrogel with Twisted Polyproline II Architecture

Collagen, the most abundant protein in mammals, possesses notable cohesion and elasticity properties and efficiently induces tissue regeneration. The Gly-Pro-Hyp canonical tripeptide repeating unit of the collagen superhelix has been well-characterized. However, to date, the shortest tripeptide repeat demonstrated to attain a helical conformation contained 3-10 peptide repeats. Here, taking a minimalistic approach, we studied a single repeating unit of collagen in its protected form, Fmoc-Gly-Pro-Hyp. The peptide formed single crystals displaying left-handed polyproline II superhelical packing, as in the native collagen single strand. The crystalline assemblies also display head-to-tail H-bond interactions and an "aromatic zipper" arrangement at the molecular interface. The coassembly of this tripeptide, with Fmoc-Phe-Phe, a well-studied dipeptide hydrogelator, produced twisted helical fibrils with a polyproline II conformation and improved hydrogel mechanical rigidity. The design of these peptides illustrates the possibility to assemble superhelical nanostructures from minimal collagen-inspired peptides with their potential use as functional motifs to introduce a polyproline II conformation into hybrid hydrogel assemblies.

Analysis of biomolecular condensates and protein phase separation with microfluidic technology

An increasing body of evidence shows that membraneless organelles are key components in cellular organization. These observations open a variety of outstanding questions about the physico-chemical rules underlying their assembly, disassembly and functions. Some molecular determinants of biomolecular condensates are challenging to probe and understand in complex in vivo systems. Minimalistic in vitro reconstitution approaches can fill this gap, mimicking key biological features, while maintaining sufficient simplicity to enable the analysis of fundamental aspects of biomolecular condensates. In this context, microfluidic technologies are highly attractive tools for the analysis of biomolecular phase transitions. In addition to enabling high-throughput measurements on small sample volumes, microfluidic tools provide for exquisite control of self-assembly in both time and space, leading to accurate quantitative analysis of biomolecular phase transitions. Here, with a specific focus on droplet-based microfluidics, we describe the advantages of microfluidic technology for the analysis of several aspects of phase separation. These include phase diagrams, dynamics of assembly and disassembly, rheological and surface properties, exchange of materials with the surrounding environment and the coupling between compartmentalization and biochemical reactions. We illustrate these concepts with selected examples, ranging from simple solutions of individual proteins to more complex mixtures of proteins and RNA, which represent synthetic models of biological membraneless organelles. Finally, we discuss how this technology may impact the bottom-up fabrication of synthetic artificial cells and for the development of synthetic protein materials in biotechnology.

Interfacial ion specificity modulates hydrophobic interaction

HYPOTHESIS

Ion specificity is crucial in assembly and aggregation of polymers in water driven by hydrophobic interaction. An increasing number of studies have suggested that specific ion adsorption and consequent impact on interfacial water molecules should play an important role in modulating hydrophobic interaction.

EXPERIMENTS

Here, bubble probe atomic force microscopy (AFM) combined with theoretical modeling analysis was applied to quantify hydrophobic interactions involving three model polymers in solutions containing different ions.

FINDINGS

For polystyrene, the hydrophobic interaction's decay length D₀ was reduced from 0.75 nm to 0.60 nm by introducing weakly hydrated cations (e.g., K⁺ and NH₄⁺), while varying anion type had little effect. For poly(methyl methacrylate) and polydimethylsiloxane, anion specificity was demonstrated more evident in shortening the hydrophobic interaction range, with D₀ decreasing from 0.63 nm to 0.50 nm and from 0.72 nm to 0.58 nm respectively when strongly hydrated F^- or Cl^- was replaced by weakly hydrated I^-. Such results could arise from specific ion adsorption at water/polymer interface which disrupts the water structuring effect. From the nanomechanical perspective, this work has revealed the importance of interfacial ion specificity in modulating hydrophobic interaction, which offers novel implications for tuning assembly behavior of macromolecules in relevant engineering applications such as micelle formation and foam stabilization.

Microfluidic approaches for the analysis of protein-protein interactions in solution

Exploration and characterisation of the human proteome is a key objective enabling a heightened understanding of biological function, malfunction and pharmaceutical design. Since proteins typically exhibit their behaviour by binding to other proteins, the challenge of probing protein-protein interactions has been the focus of new and improved experimental approaches. Here, we review recently developed microfluidic techniques for the study and quantification of protein-protein interactions. We focus on methodologies that utilise the inherent strength of microfluidics for the control of mass transport on the micron scale, to facilitate surface and membrane-free interrogation and quantification of interacting proteins. Thus, the microfluidic tools described here provide the capability to yield insights on protein-protein interactions under physiological conditions. We first discuss the defining principles of microfluidics, and methods for the analysis of protein-protein interactions that utilise the diffusion-controlled mixing characteristic of fluids at the microscale. We then describe techniques that employ electrophoretic forces to manipulate and fractionate interacting protein systems for their biophysical characterisation, before discussing strategies that use microdroplet compartmentalisation for the analysis of protein interactions. We conclude by highlighting future directions for the field, such as the integration of microfluidic experiments into high-throughput workflows for the investigation of protein interaction networks.

Multi-scale microporous silica microcapsules from gas-in water-in oil emulsions

Controlling the surface area, pore size and pore volume of microcapsules is crucial for modulating their activity in applications including catalytic reactions, delivery strategies or even cell culture assays, yet remains challenging to achieve using conventional bulk techniques. Here we describe a microfluidics-based approach for the formation of monodisperse silica-coated micron-scale porous capsules of controllable sizes. Our method involves the generation of gas-in water-in oil emulsions, and the subsequent rapid precipitation of silica which forms around the encapsulated gas bubbles resulting in hollow silica capsules with tunable pore sizes. We demonstrate that by varying the gas phase pressure, we can control both the diameter of the bubbles formed and the number of internal bubbles enclosed within the silica microcapsule. Moreover, we further demonstrate, using optical and electron microscopy, that these silica capsules remain stable under particle drying. Such a systematic manner of producing silica-coated microbubbles and porous microparticles thus represents an attractive class of biocompatible material for biomedical and pharmaceutical related applications.

Biocompatible Hybrid Organic/Inorganic Microhydrogels Promote Bacterial Adherence and Eradication in Vitro and in Vivo

Self-assembling peptides and proteins have the potential to serve as multifunctional building blocks for the generation of versatile materials for a wide range of biomedical applications. In particular, supramolecular hydrogels comprised of self-assembled protein nanofibrils, have been used in contexts ranging from tissue engineering to drug delivery. Due to the rapid emergence of multidrug resistant bacteria, development of biomaterials with intrinsic antimicrobial properties has been continuously increasing. Here, we describe hybrid organic/inorganic nanofibrillar silk microgels decorated with silver nanoparticles that display potent antimicrobial activity in vitro and in vivo and are able to adhere bacterial cells to their surfaces while subsequently eradicating them, through a two-step mechanism of action. Importantly, in contrast to treatments involving conventional silver, these silk-silver microgels are nonhemolytic and noncytotoxic toward mammalian cell lines. Finally, we show that these hybrid microgels display substantial efficacy as topical antimicrobial agents in a murine model of surgical site infections.