Amphiphilic dendrons as supramolecular holdase chaperones

The aggregation of incompletely or incorrectly folded proteins is implicated in diseases including Alzheimer's, cataracts, and other maladies. Natural systems express protein chaperones to prevent or even reverse harmful protein aggregation. Synthetic chaperone-like systems have sought to mimic the action of their biological counterparts but typically require substantial optimization and high concentrations to be functional, or lack programmability that would enable the targeting of specific protein substrates. Here we report a series of amphiphilic dendrons that undergo assembly and inhibit the aggregation of fragment 16-22 amyloid β protein (Aβ16-22). We show that monodisperse dendrons with hydrophilic tetraethylene glycol chains and a hydrophobic core based on naphthyl and benzyl ethers undergo supramolecular assembly in aqueous solutions to form sphere-like particles. The solubility of these dendrons and their assemblies is tuned by varying the relative sizes of their hydrophilic and hydrophobic regions. Two water-soluble dendrons are discovered and shown, via fluorescence experiments with rhodamine 6G, to generate a hydrophobic environment. Furthermore, we demonstrate that sub-stoichiometric concentrations of these amphiphilic dendrons stabilize Aβ16-22 peptide with respect to aggregation, mimicking the activity of holdase chaperones. Our results highlight the potential of these amphiphilic molecules as the basis for a novel approach to artificial chaperones that may address many of the challenges associated with existing synthetic chaperone mimics.

Quantitative characterizations of the cholesterol-related pathways in the retina and brain of hamsters

The retina and brain are separated from the systemic circulation by the anatomical barriers, which are permeable (the outer blood-retinal barrier) and impermeable (the blood-brain and inner blood-retina barriers) to cholesterol. Herein we investigated whether the whole-body cholesterol maintenance affects cholesterol homeostasis in the retina and brain. We used hamsters, whose whole-body cholesterol handling is more similar to those in humans than in mice and conducted separate administrations of deuterated water and deuterated cholesterol. We assessed the quantitative significance of the retinal and brain pathways of cholesterol input and compared the results with those from our previous studies in mice. The utility of the measurements in the plasma of deuterated 24-hydroxycholesterol, the major cholesterol elimination product from the brain, was investigated as well. We established that despite a 7-fold higher serum LDL to HDL ratio and other cholesterol-related differences, in situ biosynthesis remained the major source of cholesterol for hamster retina, although its quantitative significance was reduced to 53% as compared to 72-78% in mouse retina. In the brain, the principal pathway of cholesterol input was also the same, in situ biosynthesis, accounting for 94% of the total brain cholesterol input (96% in mice); the interspecies differences pertained to the absolute rates of the total cholesterol input and turnover. We documented the correlations between deuterium enrichments of the brain 24-hydroxycholesterol, brain cholesterol, and plasma 24-hydroxycholesterol, which suggested that deuterium enrichment of plasma 24-hydroxycholesteol could be an in vivo marker of cholesterol elimination and turnover in the brain.

Multifunctional synthetic nano-chaperone for peptide folding and intracellular delivery

Artificial, synthetic chaperones have attracted much attention in biomedical research due to their ability to control the folding of proteins and peptides. Here, we report bio-inspired multifunctional porous nanoparticles to modulate proper folding and intracellular delivery of therapeutic α-helical peptide. The Synthetic Nano-Chaperone for Peptide (SNCP) based on porous nanoparticles provides an internal hydrophobic environment which contributes in stabilizing secondary structure of encapsulated α-helical peptides due to the hydrophobic internal environments. In addition, SNCP with optimized inner surface modification not only improves thermal stability for α-helical peptide but also supports the peptide stapling methods in situ, serving as a nanoreactor. Then, SNCP subsequently delivers the stabilized therapeutic α-helical peptides into cancer cells, resulting in high therapeutic efficacy. SNCP improves cellular uptake and bioavailability of the anti-cancer peptide, so the cancer growth is effectively inhibited in vivo. These data indicate that the bio-inspired SNCP system combining nanoreactor and delivery carrier could provide a strategy to expedite the development of peptide therapeutics by overcoming existing drawbacks of α-helical peptides as drug candidates.

Molecular chaperones play an important part in protein folding and delivery in nature. Here, the authors report on the creation of a synthetic chaperone to control the folding of therapeutic peptides from random coil to alpha helix and demonstrate enhanced therapeutic potential in an in vivo tumour model.

Engineering Nanointerfaces of Au25 Clusters for Chaperone-Mediated Peptide Amyloidosis

Synthetic nanomaterials possessing biomolecular-chaperone functions are good candidates for modulating physicochemical interactions in many bioapplications. Despite extensive research, no general principle to engineer nanomaterial surfaces is available to precisely manipulate biomolecular conformations and behaviors, greatly limiting attempts to develop high-performance nanochaperone materials. Here, we demonstrate that, by quantifying the length (-SC_xR^±, x = 3-11) and charges (R^- = -COO^-, R⁺ = -NH₃⁺) of ligands on Au₂₅ gold nanochaperones (AuNCs), simulating binding sites and affinities of amyloid-like peptides with AuNCs, and probing peptide folding and fibrillation in the presence of AuNCs, it is possible to precisely manipulate the peptides' conformations and, thus, their amyloidosis via customizing AuNCs nanointerfaces. We show that intermediate-length liganded AuNCs with a specific charge chaperone peptides' native conformations and thus inhibit their fibrillation, while other types of AuNCs destabilize peptides and promote their fibrillation. We offer a microscopic molecular insight into peptide identity on AuNCs and provide a guideline in customizing nanochaperones via manipulating their nanointerfaces.

Engineered Nanoparticle-Protein Interactions Influence Protein Structural Integrity and Biological Significance

Engineered nanoparticles (ENPs) are artificially synthesized particles with unique physicochemical properties. ENPs are being extensively used in several consumer items, elevating the probability of ENP exposure to biological systems. ENPs interact with various biomolecules like lipids, proteins, nucleic acids, where proteins are most susceptible. The ENP-protein interactions are mostly studied for corona formation and its effect on the bio-reactivity of ENPs, however, an in-depth understanding of subsequent interactive effects on proteins, such as alterations in their structure, conformation, free energy, and folding is still required. The present review focuses on ENP-protein interactions and the subsequent effects on protein structure and function followed by the therapeutic potential of ENPs for protein misfolding diseases.

Dissolution-enhanced emission of 1,3,6,8-tetrakis(p-benzoic acid)pyrene for selectively detecting protamine and “on-to-on” heparin detection in water

A small molecule TBAPy was used as a turn-on fluorescent probe to selectively detect protamine and heparin based on the dissolution-enhanced emission (DEE) phenomenon.

Stacking of nanorings to generate nanotubes for acceleration of protein refolding

Self-assembly and photoisomerization of azobenzene-based amphiphilic molecules produced nanorings with an inner diameter of 25 nm and lengths of <40 nm. The nanorings, which consisted of a single bilayer membrane of the amphiphiles, retained their morphology in the presence of a stacking inhibitor; whereas in the absence of the inhibitor, the nanorings stacked into short nanotubes (<500 nm). When subjected to mild heat treatment, these nanotubes joined end-to-end to form nanotubes with lengths of several tens of micrometers. The nanorings and the short and long nanotubes were able to encapsulate proteins and thereby suppress aggregation induced by thermal denaturation. In addition, the nanotubes accelerated refolding of denatured proteins by encapsulating them and then releasing them into the bulk solution; refolding occurred simultaneously with release. In contrast, the nanorings did not accelerate protein refolding. Refolding efficiency increased with increasing nanotube length, indicating that the re-aggregation of the proteins was strictly inhibited by lowering the concentration of the proteins in the bulk solution as the result of the slow release from the longer nanotubes. The migration of the proteins through the long, narrow nanochannels during the release process will also contribute to refolding.

Common Gene Expression Patterns in Environmental Model Organisms Exposed to Engineered Nanomaterials: A Meta-Analysis

The use of omics is gaining importance in the field of nanoecotoxicology; an increasing number of studies are aiming to investigate the effects and modes of action of engineered nanomaterials (ENMs) in this way. However, a systematic synthesis of the outcome of such studies regarding common responses and toxicity pathways is currently lacking. We developed an R-scripted computational pipeline to perform reanalysis and functional analysis of relevant transcriptomic data sets using a common approach, independent from the ENM type, and across different organisms, including Arabidopsis thaliana, Caenorhabditis elegans, and Danio rerio. Using the pipeline that can semiautomatically process data from different microarray technologies, we were able to determine the most common molecular mechanisms of nanotoxicity across extremely variable data sets. As expected, we found known mechanisms, such as interference with energy generation, oxidative stress, disruption of DNA synthesis, and activation of DNA-repair but also discovered that some less-described molecular responses to ENMs, such as DNA/RNA methylation, protein folding, and interference with neurological functions, are present across the different studies. Results were visualized in radar charts to assess toxicological response patterns allowing the comparison of different organisms and ENM types. This can be helpful to retrieve ENM-related hazard information and thus fill knowledge gaps in a comprehensive way in regard to the molecular underpinnings and mechanistic understanding of nanotoxicity.

Elemental Silver Nanoparticles: Biosynthesis and Bio Applications

The data on the specifics of synthesis of elemental silver nanoparticles (Ag-NP) having various geometric shapes (pseudo spherical, prismatic, cubic, trigonal-pyramidal, etc.), obtained by using various biological methods, and their use in biology and medicine have been systematized and generalized. The review covers mainly publications published in the current 21st century. Bibliography: 262 references.

Refolding of thermally denatured cholesterol oxidases by magnetic nanoparticles

Proteins are prone to unfolding and subsequent denaturation by changes in temperature, pH and other harsh conditions. Nanoparticles act as artificial 'chaperones' due to favourable orientation of the proteins on their scaffold which prevents aggregation and reconfigures denatured proteins into their native functional state. In the present study, thermal denaturation of Cholesterol oxidases from Pseudomonas aeruginosa PseA, Rhodococcus erythropolis MTCC 3951 and Streptomyces sp. were studied at temperatures 50-70 °C. Further, these thermally denatured proteins were refolded using functionalized Magnetic Iron (II, III) oxide nanoparticles which was confirmed using DLS, Zeta Potential Measurements, fluorescence and CD spectroscopy. The refolded proteins were found to regain their secondary structure and activity to a great extent.

Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications

Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO₂, SiO₂, and GeO₂ has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.

Glycolipid-based nanostructures with thermal-phase transition behavior functioning as solubilizers and refolding accelerators for protein aggregates

The self-assembly of synthetic glycolipids produced nanostructures such as vesicles and nanotubes consisting of bilayer membranes, which underwent a gel-to-liquid crystalline thermal phase transition. Vesicles formed at temperatures above the thermal phase transition temperatures (T_g-l) could solubilize aggregates of denatured proteins by trapping them in the fluid bilayer membranes. Cooling to temperatures below T_g-l caused a morphological transformation into nanotubes that accompanied the thermal phase transition from the fluid to the solid state. This phenomenon allowed the trapped proteins to be quickly released into the bulk solution and simultaneously facilitated the refolding of the proteins. The refolding efficiency strongly depended on the electrostatic attraction between the bilayer membranes of the nanostructures and the proteins. Because of the long shape (>400 nm) of the nanotubes, simple membrane filtration through a pore size of 200 nm led to complete separation and recovery of the refolded proteins (3-9 nm sizes).

Selective Uptake and Refolding of Globular Proteins in Coacervate Microdroplets

Intrinsic differences in the molecular sequestration of folded and unfolded proteins within poly(diallyldimethylammonium) (PDDA)/poly(acrylate) (PAA) coacervate microdroplets are exploited to establish membrane-free microcompartments that support protein refolding, facilitate the recovery of secondary structure and enzyme activity, and enable the selective uptake and exclusion of folded and unfolded biomolecules, respectively. Native bovine serum albumin, carbonic anhydrase, and α-chymotrypsin are preferentially sequestered within positively charged coacervate microdroplets, and the unfolding of these proteins in the presence of increasing amounts of urea results in an exponential decrease in the equilibrium partition constants as well as the kinetic release of unfolded molecules from the droplets into the surrounding continuous phase. Slow refolding in the presence of positively charged microdroplets leads to the resequestration of functional proteins and the restoration of enzymatic activity; however, fast refolding results in protein aggregation at the droplet surface. In contrast, slow and fast refolding in the presence of negatively charged PDDA/PAA droplets gives rise to reduced protein aggregation and misfolding by interactions at the droplet surface to give increased levels of protein renaturation. Together, our observations provide new insights into the bottom-up design and construction of self-assembling microcompartments capable of supporting the selective uptake and refolding of globular proteins.

Effect of Photoinduced Size Changes on Protein Refolding and Transport Abilities of Soft Nanotubes

Self-assembly of azobenzene-modified amphiphiles (Glyn Azo, n=1-3) in water at room temperature in the presence of a protein produced nanotubes with the protein encapsulated in the channels. The Gly2 Azo nanotubes (7 nm internal diameter [i.d.]) promoted refolding of some encapsulated proteins, whereas the Gly3 Azo nanotubes (13 nm i.d.) promoted protein aggregation. Although the 20 nm i.d. channels of the Gly1 Azo nanotubes were too large to influence the encapsulated proteins, narrowing of the i.d. to 1 nm by trans-to-cis photoisomerization of the azobenzene units of the Gly1 Azo monomers packed in the solid bilayer membranes led to a squeezing out of the proteins into the bulk solution and simultaneously enhanced their refolding ratios. In contrast, photoinduced transformation of the Gly2 Azo nanotubes to short nanorings (<40 nm) with a large i.d. (28 nm) provided no further refolding assistance. We thus demonstrate that pertubation by the solid bilayer membrane wall of the nanotubes is important to accelerate refolding of the denatured proteins during their transport in the narrow nanotube channels.

Enhanced protein adsorption and facilitated refolding of like-charged protein with highly charged silica nanoparticles fabricated by sequential double modifications

Silica nanoparticles (SNPs) were sequentially modified with poly(ethylenimine) (PEI) and 2-diethylaminoethyl chloride (DEAE) to prepare a series of positively charged SNPs-PEI and SNPs-PEI-DEAE. The sequential double-modification strategy produced a charge density as high as 1740 μmol/g (4524 μmol/mL), which offered a very high adsorption capacity for bovine serum albumin (314 mg/g). Most importantly, the highly charged SNPs-PEI and SNPs-PEI-DEAE could efficiently facilitate the refolding of like-charged protein at extremely low utilization. For instance, in the refolding of 1 mg/mL lysozyme, the refolding yield reached 75% with only 3.3 μL/mL SNPs-PEI-DEAE. The bead consumption was reduced by nearly 96% as compared to that of the charged microspheres used previously to reach a similar yield. The results proved that the polyelectrolyte-modified SNPs were promising for applications in facilitating like-charged protein refolding, and the research opened up a new way for biotechnology applications of highly charged nanoparticles.

Soft nanotube hydrogels functioning as artificial chaperones

Self-assembly of rationally designed asymmetric amphiphilic monomers in water produced nanotube hydrogels in the presence of chemically denatured proteins (green fluorescent protein, carbonic anhydrase, and citrate synthase) at room temperature, which were able to encapsulate the proteins in the one-dimensional channel of the nanotube consisting of a monolayer membrane. Decreasing the concentrations of the denaturants induced refolding of part of the encapsulated proteins in the nanotube channel. Changing the pH dramatically reduced electrostatic attraction between the inner surface mainly covered with amino groups of the nanotube channel and the encapsulated proteins. As a result, the refolded proteins were smoothly released into the bulk solution without specific additive agents. This recovery procedure also transformed the encapsulated proteins from an intermediately refolding state to a completely refolded state. Thus, the nanotube hydrogels assisted the refolding of the denatured proteins and acted as artificial chaperones. Introduction of hydrophobic sites such as a benzyloxycarbony group and a tert-butoxycarbonyl group onto the inner surface of the nanotube channels remarkably enhanced the encapsulation and refolding efficiencies based on the hydrophobic interactions between the groups and the surface-exposed hydrophobic amino acid residues of the intermediates in the refolding process. Refolding was strongly dependent on the inner diameters of the nanotube channels. Supramolecular nanotechnology allowed us to not only precisely control the diameters of the nanotube channels but also functionalize their surfaces, enabling us to fine-tune the biocompatibility. Hence, these nanotube hydrogel systems should be widely applicable to various target proteins of different molecular weights, charges, and conformations.