Dynamic light scattering: a practical guide and applications in biomedical sciences

High Selectivity and Sensitivity of Oligomeric p-Phenylene Ethynylenes for Detecting Fibrillar and Prefibrillar Amyloid Protein Aggregates

Misfolding and aggregation of amyloid proteins into fibrillar aggregates is a central pathogenic event in neurodegenerative disorders such as Alzheimer's (AD) and Parkinson's diseases (PD). Currently, there is a lack of reliable sensors for detecting the range of protein aggregates involved in disease etiology, particularly the prefibrillar aggregate conformations that are more neurotoxic. In this study, the fluorescent sensing of two novel oligomeric p-phenylene ethynylenes (OPEs), anionic OPE1- and cationic OPE2+, for detecting prefibrillar and fibrillar aggregates of AD-associated amyloid-β (Aβ40 and Aβ42) and PD-associated α-synuclein proteins (wildtype, and single mutants A30P, E35K, and A53T) over their monomeric counterparts, were tested. Furthermore, the performance of OPEs was evaluated and compared to thioflavin T (ThT), the most widely used fibril dye. Our results show that OPE1- and OPE2+ exhibited aggregate-specific binding inducing large fluorescence turn-on and spectral shifts based on a combination of backbone planarization, hydrophobic unquenching, and superluminescent OPE complex formation sensing modes. OPEs exhibited higher selectivity, higher binding affinity, and comparable limits of detection for Aβ40 fibrils compared to ThT. OPE2+ exhibited the largest fluorescence turn-on and highest sensitivity. Significantly, OPEs detected prefibrillar aggregates of Aβ42 and α-synuclein that ThT failed to detect. The superior sensing performance, the nonprotein specific detection, and the ability to selectively detect fibrillar and prefibrillar amyloid protein aggregates point to the potential of OPEs to overcome the limitations of existing probes and promise significant advancement in the detection of the myriad of protein aggregates involved in the early stages of AD and PD.

In-Solution Microscopic Imaging of Fractal Aggregates of a Stressed Therapeutic Antibody

Aggregates of therapeutic proteins that can contaminate drug products during manufacture is a growing concern for the pharmaceutical industry because the aggregates are potentially immunogenic. Electron microscopy is a typical, indispensable method for imaging nanometer- to micrometer-sized structures. Nevertheless, it is not ideal because it must be performed with ex situ monitoring under high-vacuum conditions, where the samples could be altered by staining and drying. Here, we introduce a scanning electron-assisted dielectric microscopy (SE-ADM) technique for in-solution imaging of monoclonal immunoglobulin G (IgG) aggregates without staining and drying. Remarkably, SE-ADM allowed assessment of the size and morphology of the IgG aggregates in solution by completely excluding drying-induced artifacts. SE-ADM was also beneficial to study IgG aggregation caused by temporary acid exposure followed by neutralization, pH-shift stress. A box-counting analysis of the SE-ADM images provided fractal dimensions of the larger aggregates, which complemented the fractal dimensions of the smaller aggregates measured by light scattering. The scale-free or self-similarity nature of the fractal aggregates indicated that a common mechanism for antibody aggregation existed between the smaller and larger aggregates. Consequently, SE-ADM is a useful method for characterizing protein aggregates to bridge the gaps that occur among conventional analytical methods, such as those related to in situ/ ex situ techniques or size/morphology assessments.

Navigating the Landscape of Tumor Extracellular Vesicle Heterogeneity

The last decade has seen a rapid expansion of interest in extracellular vesicles (EVs) released by cells and proposed to mediate intercellular communication in physiological and pathological conditions. Considering that the genetic content of EVs reflects that of their respective parent cell, many researchers have proposed EVs as a source of biomarkers in various diseases. So far, the question of heterogeneity in given EV samples is rarely addressed at the experimental level. Because of their relatively small size, EVs are difficult to reliably isolate and detect within a given sample. Consequently, standardized protocols that have been optimized for accurate characterization of EVs are lacking despite recent advancements in the field. Continuous improvements in pre-analytical parameters permit more efficient assessment of EVs, however, methods to more objectively distinguish EVs from background, and to interpret multiple single-EV parameters are lacking. Here, we review EV heterogeneity according to their origin, mode of release, membrane composition, organelle and biochemical content, and other factors. In doing so, we also provide an overview of currently available and potentially applicable methods for single EV analysis. Finally, we examine the latest findings from experiments that have analyzed the issue at the single EV level and discuss potential implications.

Evaluation of colloidal platinum on cytotoxicity, oxidative stress and barrier permeability across the gut epithelium

Colloidal platinum (Pt) is widely consumed due to its health promoting benefits. However, the exact biological effects of these nanoparticles have not been studied in detail, particularly in the gut. In the present study we observed that colloidal Pt was not cytotoxic towards three different epithelial colon cancer cell lines. Co-treatment of the colon cancer cell line Caco-2 with the oxidative stress inducing agent hydrogen peroxide (H2O2) and colloidal Pt resulted in a significant decrease in H2O2 induced oxidative stress. Colloidal Pt by itself did not induce any oxidative stress. Additionally, both overnight pretreatment of Caco-2 cells with colloidal Pt followed by 1 h treatment with H2O2, or co-treatment of cells for 1 h with colloidal Pt and H2O2 resulted in a significant recovery of cell death. Of note, the same protective effects of colloidal Pt were not observed when the oxidative stress was induced in the presence of 2, 2-azobis (2-amidinopropane) dihydrochloride, indicating that the source of free radicals may define the outcome of anti-oxidant activity of colloidal Pt. Colloidal Pt was also able to cross a model intestinal barrier formed in vitro with differentiated Caco-2 cells easily. Overall, our data indicate that colloidal Pt was not toxic towards intestinal epithelial cells, reduced H2O2 induced oxidative stress, protected from oxidative stress related death of intestinal epithelial cells and could pass a model gut barrier easily. Colloidal Pt can therefore be consumed orally for its anti-oxidant and other health promoting benefits.

Validation of Size Estimation of Nanoparticle Tracking Analysis on Polydisperse Macromolecule Assembly

As the physicochemical properties of drug delivery systems are governed not only by the material properties which they are compose of but by their size that they conform, it is crucial to determine the size and distribution of such systems with nanometer-scale precision. The standard technique used to measure the size distribution of nanometer-sized particles in suspension is dynamic light scattering (DLS). Recently, nanoparticle tracking analysis (NTA) has been introduced to measure the diffusion coefficient of particles in a sample to determine their size distribution in relation to DLS results. Because DLS and NTA use identical physical characteristics to determine particle size but differ in the weighting of the distribution, NTA can be a good verification tool for DLS and vice versa. In this study, we evaluated two NTA data analysis methods based on maximum-likelihood estimation, namely finite track length adjustment (FTLA) and an iterative method, on monodisperse polystyrene beads and polydisperse vesicles by comparing the results with DLS. The NTA results from both methods agreed well with the mean size and relative variance values from DLS for monodisperse polystyrene standards. However, for the lipid vesicles prepared in various polydispersity conditions, the iterative method resulted in a better match with DLS than the FTLA method. Further, it was found that it is better to compare the native number-weighted NTA distribution with DLS, rather than its converted distribution weighted by intensity, as the variance of the converted NTA distribution deviates significantly from the DLS results.

Genetic code ambiguity modulates the activity of a C. albicans MAP kinase linked to cell wall remodeling

The human fungal pathogen Candida albicans ambiguously decodes the universal leucine CUG codon predominantly as serine but also as leucine. C. albicans has a high capacity to survive and proliferate in adverse environments but the rate of leucine incorporation fluctuates in response to different stress conditions. C. albicans is adapted to tolerate this ambiguous translation through a mechanism that combines drastic decrease in CUG usage and reduction of CUG-encoded residues in conserved positions in the protein sequences. However, in a few proteins, the residues encoded by CUG codons are found in strictly conserved positions, suggesting that this genetic code alteration might have a functional impact. One such example is Cek1, a central signaling protein kinase that contains a single CUG-encoded residue at a conserved position, whose identity might regulate the correct flow of information across the MAPK cascade. Here we show that insertion of a leucine at the CUG-encoded position decreases the stability of Cek1, apparently without major structural alterations. In contrast, incorporation of a serine residue at the CUG position induces the autophosphorylation of the conserved tyrosine residue of the Cek1 ²³¹TEY²³³ motif, and increases its intrinsic kinase activity in vitro. These findings show that CUG ambiguity modulates the activity of Cek1, a key kinase directly linked to morphogenesis and virulence in C. albicans.

Gold nanoparticle-carboxymethyl cellulose nanocolloids for detection of human immunodeficiency virus type-1 (HIV-1) using laser light scattering immunoassay

It is estimated that over 100 million people have been infected with human immunodeficiency virus (HIV-1) resulting in approximately 30 million deaths globally. Herein, we designed and developed novel nano-immunoconjugates using gold nanoparticles (AuNPs) and carboxymethylcellulose (CMC) biopolymer, which performed simultaneously as an eco-friendly in situ reducing agent and surface stabilizing ligand for the aqueous colloidal process. These AuNPs-CMC nanocolloids were biofunctionalized with the gp41 glycoprotein receptor (AuNPs-CMC-gp41) or HIV monoclonal antibodies (AuNPs-CMC_PolyArg-abHIV) for detection using the laser light scattering immunoassay (LIA). These AuNPs-CMC bioengineered nanoconjugates were extensively characterized by morphological and physicochemical methods, which demonstrated the formation of spherical nanocrystalline colloidal AuNPs with the average size from 12 to 20 nm and surface plasmon resonance peak at 520 nm. Thus, stable nanocolloids were formed with core-shell nanostructures composed of AuNPs and biomacromolecules of CMC-gp41, which were cytocompatible based on in vitro cell viability results. The AuNPs-CMC-gp41 nanoconjugates were tested against HIV monoclonal antibodies conjugates (AuNPs-CMC_PolyArg-abHIV) using the light scattering immunoassay (LIA) where they behaved as active nanoprobes for the detection at nM level of HIV-1 antigenic proteins. This strategy offers a novel nanoplatform for creating bioprobes using green nanotechnology for the detection of HIV-1 and other virus-related diseases.

Nanodelivery of doxorubicin for age-related macular degeneration

OBJECTIVE

Polymeric nanoparticles (NPs) containing doxorubicin (DOX) were prepared for the inhibition of hypoxia-induced factor 1α (HIF-1α).

SIGNIFICANCE

HIF-1α is responsible for the upregulation of several angiogenic factors, including vascular endothelial growth factor (VEGF). DOX inhibits HIF-1α but is highly toxic. By encapsulating DOX in NPs, drug delivery will be sustained and toxicity will be reduced without limiting efficacy.

METHODS

DOX NPs were prepared using both polylactic coglycolic acid (PLGA) and chitosan. PLGA NPs were prepared via nanoprecipitation (NPC) and single and double emulsion diffusion (SE; DE). Chitosan NPs were formulated using ionic gelation (IG), and complex coacervation (CC). Size, polydispersity index (PDI), and zeta potential (ZP) were determined via dynamic light scattering (DLS) (n = 3). The encapsulation efficiency (EE), drug loading capacity (DLC) (n = 3) and in vitro drug release profiles (IVR) at 37 °C (n = 4) were analyzed via spectroscopy at 480 nm (λ_max). The cytotoxicity of each formulation as well as free DOX solution in ARPE-19 cells was determined via MTT assay after 24 h (n = 3). HIF-1α and VEGF inhibition in ARPE-19 cells were measured via ELISA (n = 3).

RESULTS

The results were consistent with the hypothesis; the NP formulations decreased HIF-1α and VEGF-A expression in ARPE-19 cells with reduced cytotoxicity. SE, DE, and CC demonstrated low ZP as well as the most rapid drug release of the tested formulations. FTIR confirmed the presence of DOX on the SE NP surface, indicating instability.

CONCLUSIONS

SE, DE, and CC destabilized. NPC was the most efficient formulation for the nanodelivery of DOX for AMD.

Early stages of aggregation of engineered α-synuclein monomers and oligomers in solution

α-Synuclein is a protein that aggregates as amyloid fibrils in the brains of patients with Parkinson's disease and dementia with Lewy bodies. Small oligomers of α-synuclein are neurotoxic and are thought to be closely associated with disease. Whereas α-synuclein fibrillization and fibril morphologies have been studied extensively with various methods, the earliest stages of aggregation and the properties of oligomeric intermediates are less well understood because few methods are able to detect and characterize early-stage aggregates. We used fluorescence spectroscopy to investigate the early stages of aggregation by studying pairwise interactions between α-synuclein monomers, as well as between engineered tandem oligomers of various sizes (dimers, tetramers, and octamers). The hydrodynamic radii of these engineered α-synuclein species were first determined by fluorescence correlation spectroscopy and dynamic light scattering. The rate of pairwise aggregation between different species was then monitored using dual-color fluorescence cross-correlation spectroscopy, measuring the extent of association between species labelled with different dyes at various time points during the early aggregation process. The aggregation rate and extent increased with tandem oligomer size. Self-association of the tandem oligomers was found to be the preferred pathway to form larger aggregates: interactions between oligomers occurred faster and to a greater extent than interactions between oligomers and monomers, indicating that the oligomers were not as efficient in seeding further aggregation by addition of monomers. These results suggest that oligomer-oligomer interactions may play an important role in driving aggregation during its early stages.

Physicochemical Response of Gelatin in a Coulombic Soup of Monovalent Salt: A Molecular Simulation and Experimental Study

The effect of salt on the static properties of aqueous solution of gelatin is studied by molecular dynamics simulation at pH = 1.2, 7, and 10. At the isoelectric point (pH = 7), a monotonic increase in size of the polymer is obtained with the addition of sodium chloride ions. In the positive polyelectrolyte regime (pH = 1.2), collapse of gelatin is observed with increase in salt concentration. In the negative polyelectrolyte regime, we observe an interesting collapse-reexpansion behavior. This is due to the screening of repulsion between the excess charges followed by the screening of attraction of oppositely charged ions as the salt concentration is increased. This mechanism is very different from the charge inversion mechanism which causes the reexpansion in the presence of multivalent ions. The location of salt concentration corresponding to the minimum size of the chain is comparable to the theoretical estimate. The shift in the peak of radial distribution function calculated between monomers and salt ions confirms this spatial reorganization. The predictions from the simulation are verified by dynamic light scattering(DLS) and small-angle X-ray scattering (SAXS) experiments. The size of the hydrodynamic "clusters" obtained from DLS confirms the simulation predictions. Persistence length of the gelatin is calculated from SAXS to get single chain statistics, which also agrees well with the simulation results.

West Nile Virus Capsid Protein Interacts With Biologically Relevant Host Lipid Systems

West Nile and dengue viruses are closely related flaviviruses, originating mosquito-borne viral infections for which there are no effective and specific treatments. Their capsid proteins sequence and structure are particularly similar, forming highly superimposable α-helical homodimers. Measuring protein-ligand interactions at the single-molecule level yields detailed information of biological and biomedical relevance. In this work, such an approach was successfully applied on the characterization of the West Nile virus capsid protein interaction with host lipid systems, namely intracellular lipid droplets (an essential step for dengue virus replication) and blood plasma lipoproteins. Dynamic light scattering measurements show that West Nile virus capsid protein binds very low-density lipoproteins, but not low-density lipoproteins, and this interaction is dependent of potassium ions. Zeta potential experiments show that the interaction with lipid droplets is also dependent of potassium ions as well as surface proteins. The forces involved on the binding of the capsid protein with lipid droplets and lipoproteins were determined using atomic force microscopy-based force spectroscopy, proving that these interactions are K⁺-dependent rather than a general dependence of ionic strength. The capsid protein interaction with host lipid systems may be targeted in future therapeutic strategies against different flaviviruses. The biophysical and nanotechnology approaches employed in this study may be applied to characterize the interactions of other important proteins from different viruses, in order to understand their life cycles, as well as to find new strategies to inhibit them.

Preclinical Safety Evaluation of HIV-1 gp120 Responsive Microbicide Delivery System in C57BL/6 Female Mice

Many novel vaginal/rectal microbicide formulations failed clinically due to safety concerns, indicating the need for the early investigation of lead microbicide formulations. In this study, the preclinical safety of an HIV-1 gp120 and mannose responsive microbicide delivery system (MRP) is evaluated in C57BL/6 mice. MRP was engineered through the layer-by-layer coating of calcium carbonate (CaCO₃) with Canavalia ensiformis lectin (Con A) and glycogen. MRP mean particle diameter and zeta potential were 857.8 ± 93.1 nm and 2.37 ± 4.12 mV, respectively. Tenofovir (TFV) encapsulation and loading efficiencies in MRP were 70.1% and 16.3% w/w, respectively. When exposed to HIV-1 rgp120 (25 μg/mL), MRP released a significant amount of TFV (∼5-fold higher) in vaginal and seminal fluid mixture compared to the control (pre-exposure) level (∼59 μg/mL) in vaginal fluid alone. Unlike the positive control treated groups (e.g., nonoxynol-9), no significant histological damages and CD45+ cells infiltration were observed in the vaginal and major reproductive organ epithelial layers. This was probably due to MRP biocompatibility and its isosmolality (304.33 ± 0.58 mOsm/kg). Furthermore, compared to negative controls, there was no statistically significant increase in pro-inflammatory cytokines such as IL1α, Ilβ, IL7, IP10, and TNFα. Collectively, these data suggest that MRP is a relatively safe nanotemplate for HIV-1 gp120 stimuli responsive vaginal microbicide delivery system.

Bacterial bioreactors: Outer membrane vesicles for enzyme encapsulation

Bacterial membrane vesicles, whether naturally occurring or engineered for enhanced functionality, have significant potential as tools for bioremediation, enzyme catalysis, and the development of therapeutics such as vaccines and adjuvants. In many instances, the vesicles themselves and the naturally occurring proteins are sufficient to lend functionality. Alternatively, additional function can be conveyed to these biological nanoparticles through the directed packaging of peptides and proteins, specifically recombinant enzymes chosen to mediate a specific reaction or facilitate a controlled response. Here we will detail mechanisms for directing the packaging of recombinant proteins and peptides into the nascent membrane vesicles (MVs) of Gram-negative bacteria with a focus on both active and passive packaging using both cellular machinery and engineered molecular systems. Additionally, we detail some of the more common methods for bacterial MVs purification, quantitation, and characterization as these methods are requisite for any subsequent experimentation or processing of MV reagents.

Discovery of a New Xanthone against Glioma: Synthesis and Development of (Pro)liposome Formulations

Following our previous work on the antitumor activity of acetylated flavonosides, a new acetylated xanthonoside, 3,6-bis(2,3,4,6-tetra-O-acetyl-β-glucopyranosyl)xanthone (2), was synthesized and discovered as a potent inhibitor of tumor cell growth. The synthesis involved the glycosylation of 3,6-di-hydroxyxanthone (1) with acetobromo-α-d-glucose. Glycosylation with silver carbonate decreased the amount of glucose donor needed, comparative to the biphasic glycosylation. Xanthone 2 showed a potent anti-growth activity, with GI₅₀ < 1 μM, in human cell lines of breast, lung, and glioblastoma cancers. Current treatment for invasive brain glioma is still inadequate and new agents against glioblastoma with high brain permeability are urgently needed. To overcome these issues, xanthone 2 was encapsulated in a liposome. To increase the well-known low stability of these drug carriers, a proliposome formulation was developed using the spray drying method. Both formulations were characterized and compared regarding three months stability and in vitro anti-growth activity. While the proliposome formulation showed significantly higher stability, it was at the expense of losing its biocompatibility as a drug carrier in higher concentrations. More importantly, the new xanthone 2 was still able to inhibit the growth of glioblastoma cells after liposome formulation.

Extracellular Vesicle Quantification and Characterization: Common Methods and Emerging Approaches

Extracellular vesicles (EVs) are a family of small membrane vesicles that carry information about cells by which they are secreted. Growing interest in the role of EVs in intercellular communication, but also in using their diagnostic, prognostic and therapeutic potential in (bio) medical applications, demands for accurate assessment of their biochemical and physical properties. In this review, we provide an overview of available technologies for EV analysis by describing their working principles, assessing their utility in EV research and summarising their potential and limitations. To emphasise the innovations in EV analysis, we also highlight the unique possibilities of emerging technologies with high potential for further development.

Nanosuspension Technology: Recent Patents on Drug Delivery and their Characterizations

BACKGROUND

Nanosuspension has arisen as a remunerative, lucrative as well as a potent approach to improve the solubility and bioavailability of poorly aqueous soluble drug entities. Several challenges are still present in this approach which need more research. The prime aim of this review is to identify such challenges that can be rectified in the future.

METHODS

Through this review, we enlighten the recent patents and advancement in nanosuspension technology that utilize the different drug moieties, instruments and characterization parameters.

RESULTS

Nanosuspension has been found to possess great potential to rectify the several issues related to poor bioavailability, site-specific drug delivery, dosing frequency, etc. In the past decade, nanosuspension approach has been complementarily utilized to solve the developed grievances, arisen from poorly soluble drugs. But this field still needs more attention to new discoveries.

CONCLUSION

Nanosuspension contributes a crucial role in administering the different drug entities through a variety of routes involving oral, transdermal, ocular, parenteral, pulmonary, etc. with solving the different issues. This review also confirms the significance of nanosuspension in safety, efficacy, and communal as well as the economic expense associated with healthcare.

Extracellular vesicles and vesicle-free secretome of the protozoa Acanthamoeba castellanii under homeostasis and nutritional stress and their damaging potential to host cells

Acanthamoeba castellanii (Ac) are ubiquitously distributed in nature, and by contaminating medical devices such as heart valves and contact lenses, they cause a broad range of clinical presentations to humans. Although several molecules have been described to play a role in Ac pathogenesis, including parasite host-tissue invasion and escaping of host-defense, little information is available on their mechanisms of secretion. Herein, we describe the molecular components secreted by Ac, under different protein availability conditions to simulate host niches. Ac extracellular vesicles (EVs) were morphologically and biochemically characterized. Dynamic light scattering analysis of Ac EVs identified polydisperse populations, which correlated to electron microscopy measurements. High-performance thin liquid chromatography of Ac EVs identified phospholipids, steryl-esters, sterol and free-fatty acid, the last two also characterized by GC-MS. Secretome composition (EVs and EVs-free supernatants) was also determined and proteins biological functions classified. In peptone-yeast-glucose (PYG) medium, a total of 179 proteins were identified (21 common proteins, 89 exclusive of EVs and 69 in EVs-free supernatant). In glucose alone, 205 proteins were identified (134 in EVs, 14 common and 57 proteins in EVs-free supernatant). From those, stress response, oxidative and protein and amino acid metabolism proteins prevailed. Qualitative differences were observed on carbohydrate metabolism enzymes from Krebs cycle and pentose phosphate shunt. Serine proteases and metalloproteinases predominated. Analysis of the cytotoxicity of Ac EVs (upon uptake) and EVs-free supernatant to epithelial and glioblastoma cells revealed a dose-dependent effect. Therefore, the Ac secretome differs depending on nutrient conditions, and is also likely to vary during infection.

Aldolase Does Not Show Enhanced Diffusion in Dynamic Light Scattering Experiments

Recent experimental studies have measured a 30-80% increase of the diffusion coefficient when various enzymes, including aldolase, are catalytically active. This observation has been supported by several theoretical explanations; however, other theoretical studies argue against the possibility of enhanced diffusion, and two of them ascribe the experimental observations to potential artifacts arising in fluorescence correlation spectroscopy (FCS) measurements. Here, we utilized dynamic light scattering (DLS) to measure the diffusion coefficient of aldolase in the absence and presence of its substrate. The DLS measurements have an experimental error of 3% and do not find a statistically significant change of the aldolase diffusion coefficient even at a saturating substrate concentration. This finding lends support to the contention that photophysical artifacts may have affected the FCS measurements and challenges the idea that enzymes can be self-propelled by their catalytic activity.

A Comparative Study of Dynamic Light and X-ray Scatterings on Micelles of Topological Polymer Amphiphiles

Micelles were prepared in organic solvents by using three topological polymer amphiphiles: (i) cyclic poly(n-decyl glycidyl ether-block-2-(2-(2-methoxyethoxy)ethoxy)ethyl glycidyl ether) (c-PDGE-b-PTEGGE) and (ii) its linear analogue (l-PDGE-b-PTEGGE); (iii) linear poly(6-phosphorylcholinehexylthiopropyl glycidyl ether-block-n-dodecanoyl glycidyl ether) (l-PPCGE-b-PDDGE). For the individual micelle solutions, the size and distribution were determined by dynamic light scattering (DLS) and synchrotron X-ray scattering analyses. The synchrotron X-ray scattering analysis further found that c-PDGE-b-PTEGGE forms oblate ellipsoidal micelle in an ethanol/water mixture, l-PDGE-b-PTEGGE makes prolate ellipsoidal micelle in an ethanol/water mixture, and l-PPCGE-b-PDDGE forms cylindrical micelle in chloroform. This comparative study found that there are large differences in the size and distribution results extracted by DLS and X-ray scattering analyses. All possible factors to cause such large differences are discussed. Moreover, a better use of the DLS instrument with keeping its merits is proposed.

Probing Polymer Chain Conformation and Fibril Formation of Peptide Conjugates

Covalent conjugates between a synthetic polymer and a peptide hormone were used to probe the molecular extension of these macromolecules and how the polymer modifies the fibril formation of the hormone. NMR spectroscopy of ¹⁵ N labeled parathyroid hormone (PTH) was employed to visualize the conformation of the conjugated synthetic polymer, triggered by small temperature changes via its lower critical solution temperature. A shroud-like polymer conformation dominated the molecular architecture of the conjugated chimeras. PTH readily forms amyloid fibrils, which is probably the physiological storage form of the hormone. The polyacrylate based polymers stimulated the nucleation processes of the peptide.

Synthesis and Optimization of Chitosan Nanoparticles Loaded with L-Ascorbic Acid and Thymoquinone

The combination of compounds with different classes (hydrophobic and hydrophilic characters) in single chitosan carrier is a challenge due to the hydrophilicity of chitosan. Utilization of l-ascorbic acid (LAA) and thymoquinone (TQ) compounds as effective antioxidants is marred by poor bioavailability and uptake. Nanoparticles (NPs) solved the problem by functioning as a carrier for them because they have high surface areas for more efficient delivery and uptake by cells. This research, therefore, synthesized chitosan NPs (CNPs) containing LAA and TQ, CNP-LAA-TQ via ionic gelation routes as the preparation is non-toxic. They were characterized using electron microscopy, zetasizer, UV⁻VIS spectrophotometry, and infrared spectroscopy. The optimum CNP-LAA-TQ size produced was 141.5 ± 7.8 nm, with a polydispersity index (PDI) of 0.207 ± 0.013. The encapsulation efficiency of CNP-LAA-TQ was 22.8 ± 3.2% for LAA and 35.6 ± 3.6% for TQ. Combined hydrophilic LAA and hydrophobic TQ proved that a myriad of highly efficacious compounds with poor systemic uptake could be encapsulated together in NP systems to increase their pharmaceutical efficiency, indirectly contributing to the advancement of medical and pharmaceutical sectors.

Challenges in the Structural-Functional Characterization of Multidomain, Partially Disordered Proteins CBP and p300: Preparing Native Proteins and Developing Nanobody Tools

The structural and functional characterization of large multidomain signaling proteins containing long disordered linker regions represents special methodological and conceptual challenges. These proteins show extreme structural heterogeneity and have complex posttranslational modification patterns, due to which traditional structural biology techniques provide results that are often difficult to interpret. As demonstrated through the example of two such multidomain proteins, CREB-binding protein (CBP) and its paralogue, p300, even the expression and purification of such proteins are compromised by their extreme proteolytic sensitivity and structural heterogeneity. In this chapter, we describe the effective expression of CBP and p300 in a eukaryotic host, Sf9 insect cells, followed by their tandem affinity purification based on two terminal tags to ensure their structural integrity. The major focus of this chapter is on the development of novel accessory tools, single-domain camelid antibodies (nanobodies), for structural-functional characterization. Specific nanobodies against full-length CBP and p300 can specifically target their different regions and can be used for their marking, labeling, and structural stabilization in a broad range of in vitro and in vivo studies. Here, we describe four high-affinity nanobodies binding to the KIX and the HAT domains, either mimicking known interacting partners or revealing new functionally relevant conformations. As immunization of llamas results in nanobody libraries with a great sequence variation, deep sequencing and interaction analysis with different regions of the proteins provide a novel approach toward developing a panel of specific nanobodies.

Methods for Physical Characterization of Phase-Separated Bodies and Membrane-less Organelles

Membrane-less organelles are cellular structures which arise through the phenomenon of phase separation. This process enables compartmentalization of specific sets of macromolecules (e.g., proteins, nucleic acids), thereby regulating cellular processes by increasing local concentration, and modulating the structure and dynamics of their constituents. Understanding the connection between structure, material properties and function of membrane-less organelles requires inter-disciplinary approaches, which address length and timescales that span several orders of magnitude (e.g., Ångstroms to micrometer, picoseconds to hours). In this review, we discuss the wide variety of methods that have been applied to characterize the morphology, rheology, structure and dynamics of membrane-less organelles and their components, in vitro and in live cells.

Pervasive tertiary structure in the dengue virus RNA genome

RNA virus genomes are efficient and compact carriers of biological information, encoding information required for replication both in their primary sequences and in higher-order RNA structures. However, the ubiquity of RNA elements with higher-order folds-in which helices pack together to form complex 3D structures-and the extent to which these elements affect viral fitness are largely unknown. Here we used single-molecule correlated chemical probing to define secondary and tertiary structures across the RNA genome of dengue virus serotype 2 (DENV2). Higher-order RNA structures are pervasive and involve more than one-third of nucleotides in the DENV2 genomic RNA. These 3D structures promote a compact overall architecture and contribute to viral fitness. Disrupting RNA regions with higher-order structures leads to stable, nonreverting mutants and could guide the development of vaccines based on attenuated RNA viruses. The existence of extensive regions of functional RNA elements with tertiary folds in viral RNAs, and likely many other messenger and noncoding RNAs, means that there are significant regions with pocket-containing surfaces that may serve as novel RNA-directed drug targets.

Assembly of Multicomponent Protein Filaments Using Engineered Subunit Interfaces

Exploiting the ability of proteins to self-assemble into architectural templates may provide novel routes for the positioning of functional molecules in nanotechnology. Here we report the engineering of multicomponent protein templates composed of distinct monomers that assemble in repeating orders into a dynamic functional structure. This was achieved by redesigning the protein-protein interfaces of a molecular chaperone with helical sequences to create unique subunits that assemble through orthogonal coiled-coils into filaments up to several hundred nanometers in length. Subsequently, it was demonstrated that functional proteins could be fused to the subunits to achieve ordered alignment along filaments. Importantly, the multicomponent filaments had molecular chaperone activity and could prevent other proteins from thermal-induced aggregation, a potentially useful property for the scaffolding of enzymes. The design in this work is presented as proof-of-concept for the creation of modular templates that could potentially be used to position functional molecules, stabilize other proteins such as enzymes, and enable controlled assembly of nanostructures with unique topologies.

Electrospraying as a suitable method for nanoencapsulation of the hydrophilic bioactive dihydrochalcone, aspalathin

The bioactive hydrophilic dihydrochalcone, aspalathin, has poor stability and bioavailability hampering its use in functional food ingredients with standardised aspalathin content. The aim of the study was to produce nanoparticles with controlled release to overcome these obstacles. Nanoencapsulation was investigated using both natural (chitosan and lecithin) and synthetic (poly(lactide-co-glycolide) and Eudragit S100® (ES100)) polymers by suitable conventional methods and electrospraying for all polymers. All polymer-method combinations produced particles smaller than 1.1 µm. Electrospraying produced more favourable results than conventional methods for the synthetic polymers, resulting in spherical particles with higher (p < 0.05) encapsulation efficiencies (>50%) and loading capacities (>10%). Opposite trends were observed for natural polymers. An in vitro release study revealed biphasic aspalathin release profiles at pH 7.4 with ES100 electrosprayed nanoparticles having the slowest (p < 0.05) release rate (1.67 h^-1). Overall, ES100 electrosprayed nanoparticles showed the most favourable combination of parameters.

Structural flexibility in the Helicobacter pylori peptidyl-prolyl cis,trans-isomerase HP0175 is achieved through an extension of the chaperone helices

Helicobacter pylori infects the gastric epithelium of half the global population, where infections can persist into adenocarcinomas and peptic ulcers. H. pylori secretes several proteins that lend to its pathogenesis and survival including VacA, CagA, γ-glutamyltransferase and HP0175. HP0175, also known as HpCBF2, classified as a peptidyl-prolyl cis,trans-isomerase, has been shown to induce apoptosis through a cascade of mechanisms initiated though its interaction with toll like receptor 4 (TLR4). Here, we report the structure of apo-HP0175 at 2.09 Å with a single monomer in the asymmetric unit. Chromatographic, light scattering and mass spectrometric analysis of HP0175 in solution indicate that the protein is mainly monomeric under low salt conditions, while increasing ionic interactions facilitates protein dimerization. A comparison of the apo-HP0175 structure to that of the indole-2-carboxylic acid-bound form shows movement of the N- and C-terminal helices upon interaction of the catalytic residues in the binding pocket. Helix extension of the N/C chaperone domains between apo and I2CA-bound HP0175 supports previous findings in parvulin PPIases for their role in protein stabilization (and accommodation of variable protein lengths) of those undergoing catalysis.

Shape and size of non-spherical silver nanoparticles: implications for calculating nanoparticle number concentrations

The international drive to measure accurate number concentrations of nanoparticles is impeded by the typically heterogeneous populations of non-spherical nanoparticles. The irregular shape and size of "50 nm" silver nanoparticles is studied using Electron Tomography. It is evidenced that even for highly symmetrical particles the volume can be over 20% less than that of the circumscribed sphere; more irregularly shaped particles can have volumes of over 45% less. On this basis, criteria are provided to determine the particle sphericity from 2D projections obtained from Electron Microscopy, including an empirical method for particle volume estimation. The results allow the visualisation of irregularly shaped particles, revealing the presence of previously unseen voids in the nanoparticle structure. Comparison of tomographic data with other commonly used particle-sizing methods exposes the limitations of these methods in studying nanoparticle populations that exhibit heterogeneity.

Enhancing Coupled Enzymatic Activity by Colocalization on Nanoparticle Surfaces: Kinetic Evidence for Directed Channeling of Intermediates

Multistep enzymatic cascades are becoming more prevalent in industrial settings as engineers strive to synthesize complex products and pharmaceuticals in economical, environmentally friendly ways. Previous work has shown that immobilizing enzymes on nanoparticles can enhance their activity significantly due to localized interfacial effects, and this enhancement remains in place even when that enzyme's activity is coupled to another enzyme that is still freely diffusing. Here, we investigate the effects of displaying two enzymes with coupled catalytic activity directly on the same nanoparticle surface. For this, the well-characterized enzymes pyruvate kinase (PykA) and lactate dehydrogenase (LDH) were utilized as a model system; they jointly convert phosphoenolpyruvate to lactate in two sequential steps as part of downstream glycolysis. The enzymes were expressed with terminal polyhistidine tags to facilitate their conjugation to semiconductor quantum dots (QDs) which were used here as prototypical nanoparticles. Characterization of enzyme coassembly to two different sized QDs showed a propensity to cross-link into nanoclusters consisting of primarily dimers and some trimers. Individual and joint enzyme activity in this format was extensively investigated in direct comparison to control samples lacking the QD scaffolds. We found that QD association enhances LDH activity by >50-fold and its total turnover by at least 41-fold, and that this high activation appears to be largely due to stabilization of its quarternary structure. When both enzymes are simultaneously bound to the QD surfaces, their colocalization leads to >100-fold improvements in the overall rates of coupled activity. Experimental results in conjunction with detailed kinetic simulations provide evidence that this significant improvement in coupled activity is partially attributable to a combination of enhanced enzymatic activity and stabilization of LDH. More importantly, experiments aimed at disrupting channeled processes and further kinetic modeling suggest that the bulk of the performance enhancement arises from intermediary "channeling" between the QD-colocalized enzymes. A full understanding of the underlying processes that give rise to such enhancements from coupled enzymatic activity on nanoparticle scaffolds can provide design criteria for improved biocatalytic applications.

Membrane Active Peptides and Their Biophysical Characterization

In the last 20 years, an increasing number of studies have been reported on membrane active peptides. These peptides exert their biological activity by interacting with the cell membrane, either to disrupt it and lead to cell lysis or to translocate through it to deliver cargos into the cell and reach their target. Membrane active peptides are attractive alternatives to currently used pharmaceuticals and the number of antimicrobial peptides (AMPs) and peptides designed for drug and gene delivery in the drug pipeline is increasing. Here, we focus on two most prominent classes of membrane active peptides; AMPs and cell-penetrating peptides (CPPs). Antimicrobial peptides are a group of membrane active peptides that disrupt the membrane integrity or inhibit the cellular functions of bacteria, virus, and fungi. Cell penetrating peptides are another group of membrane active peptides that mainly function as cargo-carriers even though they may also show antimicrobial activity. Biophysical techniques shed light on peptide–membrane interactions at higher resolution due to the advances in optics, image processing, and computational resources. Structural investigation of membrane active peptides in the presence of the membrane provides important clues on the effect of the membrane environment on peptide conformations. Live imaging techniques allow examination of peptide action at a single cell or single molecule level. In addition to these experimental biophysical techniques, molecular dynamics simulations provide clues on the peptide–lipid interactions and dynamics of the cell entry process at atomic detail. In this review, we summarize the recent advances in experimental and computational investigation of membrane active peptides with particular emphasis on two amphipathic membrane active peptides, the AMP melittin and the CPP pVEC.

Methods for Lipid Droplet Biophysical Characterization in Flaviviridae Infections

Lipid droplets (LDs) are intracellular organelles for neutral lipid storage, originated from the endoplasmic reticulum. They play an essential role in lipid metabolism and cellular homeostasis. In fact, LDs are complex organelles, involved in many more cellular processes than those initially proposed. They have been extensively studied in the context of LD-associated pathologies. In particular, LDs have emerged as critical for virus replication and assembly. Viruses from the Flaviviridae family, namely dengue virus (DENV), hepatitis C virus (HCV), West Nile virus (WNV), and Zika virus (ZIKV), interact with LDs to usurp the host lipid metabolism for their own viral replication and pathogenesis. In general, during Flaviviridae infections it is observed an increasing number of host intracellular LDs. Several viral proteins interact with LDs during different steps of the viral life cycle. The HCV core protein and DENV capsid protein, extensively interact with LDs to regulate their replication and assembly. Detailed studies of LDs in viral infections may contribute for the development of possible inhibitors of key steps of viral replication. Here, we reviewed different techniques that can be used to characterize LDs isolated from infected or non-infected cells. Microscopy studies have been commonly used to observe LDs accumulation and localization in infected cell cultures. Fluorescent dyes, which may affect LDs directly, are widely used to probe LDs but there are also approaches that do not require the use of fluorescence, namely stimulated Raman scattering, electron and atomic force microscopy-based approaches. These three are powerful techniques to characterize LDs morphology. Raman scattering microscopy allows studying LDs in a single cell. Electron and atomic force microscopies enable a better characterization of LDs in terms of structure and interaction with other organelles. Other biophysical techniques, such as dynamic light scattering and zeta potential are also excellent to characterize LDs in terms of size in a simple and fast way and test possible LDs interaction with viral proteins. These methodologies are reviewed in detail, in the context of viral studies.

How to Study the Uptake and Toxicity of Nanoparticles in Cultured Brain Cells: The Dos and Don't Forgets

Due to their exciting properties, engineered nanoparticles have obtained substantial attention over the last two decades. As many types of nanoparticles are already used for technical and biomedical applications, the chances that cells in the brain will encounter nanoparticles have strongly increased. To test for potential consequences of an exposure of brain cells to engineered nanoparticles, cell culture models for different types of neural cells are frequently used. In this review article we will discuss experimental strategies and important controls that should be used to investigate the physicochemical properties of nanoparticles for the cell incubation conditions applied as well as for studies on the biocompatibility and the cellular uptake of nanoparticles in neural cells. The main focus of this article will be the interaction of cultured neural cells with iron oxide nanoparticles, but similar considerations are important for studying the consequences of an exposure of other types of cultured cells with other types of nanoparticles. Our article aims to improve the understanding of the special technical challenges of working with nanoparticles on cultured neural cells, to identify potential artifacts and to prevent misinterpretation of data on the potential adverse or beneficial consequences of a treatment of cultured cells with nanoparticles.

Dynamic Light Scattering of Biopharmaceutics-Can Analytical Performance Be Enhanced by Laser Power?

Background: Dynamic light scattering (DLS) is an important tool to characterize colloidal systems and adequate sizing is particularly critical in the field of protein formulations. Among the different factors that can influence the measurement result, the effect of laser power has so far not been studied thoroughly. Methods: The sensitivity of a DLS instrument was first considered on a theoretical level, followed by experiments using DLS instruments, equipped with two different lasers of (nominal) 45 mW, and 100 mW, respectively. This work analyzes dilute colloidal dispersions of lysozyme as model protein. Results: Theoretical findings agreed with experiments in that only enhanced laser power of 100 mW laser allowed measuring a 0.1 mg/mL protein dispersion in a reliable manner. Results confirmed the usefulness of the presented theoretical considerations in improving a general understanding of the limiting factors in DLS. Conclusions: Laser power is a critical aspect regarding adequate colloidal analysis by DLS. Practical guidance is provided to help scientists specifically with measuring dilute samples to choose both an optimal instrument configuration as well as a robust experimental procedure.

Physico-chemical characterization of self-emulsifying drug delivery systems

Self-emulsifying drug delivery systems (SEDDS) are regarded as a potential implement for oral delivery of water insoluble APIs to overcome their poor and irregular bioavailability. The correlation between the physicochemical parameters and the behavior of self-emulsifying drug delivery systems was established. The objective of this study was to summarize these physicochemical factors characterized SEDDS. Determination of self-emulsification process and ternary phase diagram are the basis of preparations. The position of APIs in SEDDS inclusion can be determined by dye solubilisation test. The end point of self-emulsification was controlled by turbimetric evaluation. Optimisation of droplet size and zeta potential are crucial parameters because they can influence i.e. the dissolution rate of APIs and the stability of SEDDS. Besides the basic methods in the characterization of SEDDS such as dispersibility tests, turbidimetric evaluation, viscosity tests, determinations with complex instruments such as photon correlation spectroscopy or dynamic light-scattering, electro kinetic potential measurement, non-destructive spectroscopic techniques (LFDS, FTIR, RS) and various microscopic techniques (SEM, PLM, EDS) has also been described.

Application of Light Scattering Techniques to Nanoparticle Characterization and Development

Over the years, the scientific importance of nanoparticles for biomedical applications has increased. The high stability and biocompatibility, together with the low toxicity of the nanoparticles developed lead to their use as targeted drug delivery systems, bioimaging systems, and biosensors. The wide range of nanoparticles size, from 10 nm to 1 μm, as well as their optical properties, allow them to be studied using microscopy and spectroscopy techniques. In order to be effectively used, the physicochemical properties of nanoparticle formulations need to be taken into account, namely, particle size, surface charge distribution, surface derivatization and/or loading capacity, and related interactions. These properties need to be optimized considering the final nanoparticle intended biodistribution and target. In this review, we cover light scattering based techniques, namely dynamic light scattering and zeta-potential, used for the physicochemical characterization of nanoparticles. Dynamic light scattering is used to measure nanoparticles size, but also to evaluate their stability over time in suspension, at different pH and temperature conditions. Zeta-potential is used to characterize nanoparticles surface charge, obtaining information about their stability and surface interaction with other molecules. In this review, we focus on nanoparticle characterization and application in infection, cancer and cardiovascular diseases.

Calcium Sulfate Nanoparticles with Unusual Dispersibility in Organic Solvents for Transparent Film Processing

Calcium sulfate is one of the most important construction materials. Today it is employed as high-performance compound in medical applications and cement mixtures. We report a synthesis for calcium sulfate nanoparticles with outstanding dispersibility properties in organic solvents without further functionalization. The nanoparticles (amorphous with small γ-anhydrite crystallites, 5-50 nm particle size) form long-term stable dispersions in acetone without any sign of precipitation. ¹H NMR spectroscopic techniques and Fourier-transform infrared spectroscopy (FTIR) reveal absorbed 2-propanol on the particle surfaces that induce the unusual dispersibility. Adding water to the nanoparticle dispersion leads to immediate precipitation. A phase transformation to gypsum via bassanite was monitored by an in situ kinetic FT-IR spectroscopic study and transmission electron microscopy (TEM). The dispersibility in a volatile organic solvent and the crystallization upon contact with water open a broad field of applications for the CaSO₄ nanoparticles, e.g., as nanogypsum for coatings or the fabrication of hybrid composites.

Transport of nano-objects in narrow channels: influence of Brownian diffusion, confinement and particle nature

This paper presents experimental results about transport of dilute suspensions of nano-objects in silicon-glass micrometric and sub-micrometric channels. Two kinds of objects are used: solid, rigid latex beads and spherical capsule-shaped, soft polymersomes. They are tracked using fluorescence microscopy. Three aspects are studied: confinement (ratio between particle diameter and channel depth), Brownian diffusion and particle nature. The aim of this work is to understand how these different aspects affect the transport of suspensions in narrow channels and to understand the different mechanisms at play. Concerning the solid beads we observe the appearance of two regimes, one where the experimental mean velocity is close to the expected one and another where this velocity is lower. This is directly related to a competition between confinement, Brownian diffusion and advection. These two regimes are shown to be linked to the inhomogeneity of particles distribution in the channel depth, which we experimentally deduce from velocity distributions. This inhomogeneity appears during the entrance process into the sub-micrometric channels, as for hydrodynamic separation or deterministic lateral displacement. Concerning the nature of the particles we observed a shift of transition towards the second regime likely due to the relationships between shear stress and polymersomes mechanical properties which could reduce the inhomogeneity imposed by the geometry of our device.

Metal-binding polymorphism in late embryogenesis abundant protein AtLEA4-5, an intrinsically disordered protein

Late embryogenesis abundant (LEA) proteins accumulate in plants during adverse conditions and their main attributed function is to confer tolerance to stress. One of the deleterious effects of the adverse environment is the accumulation of metal ions to levels that generate reactive oxygen species, compromising the survival of cells. AtLEA4-5, a member of group 4 of LEAs in Arabidopsis, is an intrinsically disordered protein. It has been shown that their N-terminal region is able to undergo transitions to partially folded states and prevent the inactivation of enzymes. We have characterized metal ion binding to AtLEA4-5 by circular dichroism, electronic absorbance spectroscopy (UV–vis), electron paramagnetic resonance, dynamic light scattering, and isothermal titration calorimetry. The data shows that AtLEA4-5 contains a single binding site for Ni(II), while Zn(II) and Cu(II) have multiple binding sites and promote oligomerization. The Cu(II) interacts preferentially with histidine residues mostly located in the C-terminal region with moderate affinity and different coordination modes. These results and the lack of a stable secondary structure formation indicate that an ensemble of conformations remains accessible to the metal for binding, suggesting the formation of a fuzzy complex. Our results support the multifunctionality of LEA proteins and suggest that the C-terminal region of AtLEA4-5 could be responsible for antioxidant activity, scavenging metal ions under stress conditions while the N-terminal could function as a chaperone.

Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge

The identification of four-stranded G-quadruplexes (G4s) has highlighted the fact that DNA has additional spatial organisations at its disposal other than double-stranded helices. Recently, it became clear that the formation of G4s is not limited to the traditional G3+NL1G3+NL2G3+NL3G3+ sequence motif. Instead, the G3 triplets can be interrupted by deoxythymidylate (DNA) or uridylate (RNA) where the base forms a bulge that loops out from the G-quadruplex core. Here, we report the first high-resolution X-ray structure of a unique unimolecular DNA G4 with a cytosine bulge. The G4 forms a dimer that is stacked via its 5'-tetrads. Analytical ultracentrifugation, static light scattering and small angle X-ray scattering confirmed that the G4 adapts a predominantly dimeric structure in solution. We provide a comprehensive comparison of previously published G4 structures containing bulges and report a special γ torsion angle range preferentially populated by the G4 core guanylates adjacent to bulges. Since the penalty for introducing bulges appears to be negligible, it should be possible to functionalize G4s by introducing artificial or modified nucleotides at such positions. The presence of the bulge alters the surface of the DNA, providing an opportunity to develop drugs that can specifically target individual G4s.