Yunxiang Sun

Chemically tailoring coal to fluorescent carbon dots with tuned size and their capacity for Cu(II) detection.

The desired control of size, structure, and optical properties of fluorescent carbon dots (CDs) is critical for understanding the fluorescence mechanism and exploring their potential application. Herein, a top-down strategy to chemically tailor the inexpensive coal to fluorescent CDs by a combined method of carbonization and acidic oxidation etching is reported. The size and optical properties of the as-made CDs are tuned by controlling the structures of graphitic crystallites in the starting precursor. The coal-derived CDs exhibit two different distinctive emission modes, where the intensity of the short-wavelength emission is significantly enhanced by partial reduction treatment. The evolution of the electronic structure and the surface states analysis show that two different types of fluorescence centers, nano-sized sp(2) carbon domains and surface defects, are responsible for the observed emission characteristics. The reduced CDs are demonstrated as an effective fluorescent sensing material for label-free and selective detection of Cu(II) ions with a detection limit as low as 2.0 nM, showing a great promise for real-world sensor applications.

Modulating protein amyloid aggregation with nanomaterials

Direct exposure or intake of nanopaticles (NPs) to the human body can invoke a series of biological responses, some of which are deleterious, and as such the role of NPs in vivo requires thorough examination. Over the past decade, it has been established that biomolecules such as proteins can bind NPs to form a corona, where the structures and dynamics of NP-associated proteins can assign new functionality, systemic distribution and toxicity. However, the behavior and fate of NPs in biological systems are still far from being fully understood. Growing evidence has shown that some natural or artificial NPs could either up- or down-regulate protein amyloid aggregation, which is associated with neurodegenerative diseases like Alzheimers and Parkinsons diseases, as well as metabolic diseases such as type 2 diabetes. These effects can be either indirect (e.g., through a crowding effect) or direct, depending on the NP composition, size, shape and surface chemistry. However, efforts to design anti-amyloid NPs for biomedical applications have been largely hindered by insufficient understanding of the complex processes, even though proof-of-concept experiments have been conducted. Therefore, exploring the general mechanisms of NP-meditated protein aggregation marks an emerging field in bio-nano research and a new stage of handling nanotechnology that not only aids in elucidating the origin of nanotoxicity, but also provides a foundation for engineering de novo anti-amyloid nanomedicines. In this review, we summarize research on NP-mediated protein amyloid aggregation, with the goal of contributing to sustained nanotechnology and safe nanomedicine against amyloid diseases.

Cofibrillization of Pathogenic and Functional Amyloid Proteins with Gold Nanoparticles against Amyloidogenesis

Biomimetic nanocomposites and scaffolds hold the key to a wide range of biomedical applications. Here we show, for the first time, a facile scheme of cofibrillizing pathogenic and functional amyloid fibrils via gold nanoparticles (AuNPs) and their applications against amyloidogenesis. This scheme was realized by β-sheet stacking between human islet amyloid polypeptide (IAPP) and the β-lactoglobulin corona of the AuNPs, as revealed by transmission electron microscopy, 3D atomic force microscopy, circular dichroism spectroscopy, and molecular dynamics simulations. The biomimetic AuNPs eliminated IAPP toxicity, enabled X-ray destruction of IAPP amyloids, and allowed dark-field imaging of pathogenic amyloids and their immunogenic response by human T cells. In addition to providing a viable new nanotechnology against amyloidogenesis, this study has implications for understanding the in vivo cross-talk between amyloid proteins of different pathologies.

Islet Amyloid Polypeptide Promotes Amyloid-Beta Aggregation by Binding-Induced Helix-Unfolding of the Amyloidogenic Core

Amyloid aggregation of amyloid-beta (Aβ) and islet amyloid polypeptide (IAPP) is associated with Alzheimers disease (AD) and type-2 diabetes (T2D), respectively. With T2D being the risk factor for AD and the ability of IAPP to cross the blood-brain barrier, the coaggregation of Aβ and IAPP has been explored to understand the cross-talk between the two diseases. Recent studies demonstrated that soluble IAPP could significantly accelerate the aggregation of Aβ while preformed amyloids of IAPP were poor seeds for Aβ aggregation. Here, we apply all-atom discrete molecular dynamics simulations to investigate possible molecular mechanisms for the accelerated coaggregation of IAPP and Aβ42 comparing to Aβ42 aggregation alone, which was confirmed by the complementary thioflavin-T fluorescence assay. Our simulation results suggest that peptides in the mixture tend to form heterodimers as the first step toward their coaggregation. Strong interpeptide interactions with IAPP in the heterodimer shift the helical conformation of Aβ42 in its amyloidogenic central hydrophobic core, residues 16-22 (Aβ16-22), to the extended conformation ready to form β-sheets. Our study suggests that the unfolding of Aβ16-22 helix contributes to the aggregation free-energy barrier and corresponds to the rate-limiting conformational change for Aβ42 aggregation. Therefore, we propose that soluble IAPP promotes the aggregation of Aβ42 by binding-induced conformational change of Aβ42 in its amyloidogenic core and thus reduced aggregation free-energy barrier.

β-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-β Aggregates

Oligomers populated during the early amyloid aggregation process are more toxic than mature fibrils, but pinpointing the exact toxic species among highly dynamic and heterogeneous aggregation intermediates remains a major challenge. β-barrel oligomers, structurally-determined recently for a slow-aggregating peptide derived from αB crystallin, are attractive candidates for exerting amyloid toxicity due to their well-defined structures as therapeutic targets and compatibility to the “amyloid-pore” hypothesis of toxicity. To assess whether β-barrel oligomers are common intermediates to amyloid peptides - a necessary step toward associating β-barrel oligomers with general amyloid cytotoxicity, we computationally studied the oligomerization and fibrillization dynamics of seven well-studied fragments of amyloidogenic proteins with different experimentally-determined aggregation morphologies and cytotoxicity. In our molecular dynamics simulations, β-barrel oligomers were only observed in five peptides self-assembling into the characteristic cross-β aggregates, but not the other two that formed polymorphic β-rich aggregates as reported experimentally. Interestingly, the latter two peptides were previously found nontoxic. Hence, the observed correlation between β-barrel oligomers formation and cytotoxicity supports the hypothesis of β-barrel oligomers as the common toxic intermediates of amyloid aggregation.

Structures and dynamics of β-barrel oligomer intermediates of amyloid-beta16-22 aggregation

Accumulating evidence suggests that soluble oligomers are more toxic than final fibrils of amyloid aggregations. Among the mixture of inter-converting intermediates with continuous distribution of sizes and secondary structures, oligomers in the β-barrel conformation - a common class of protein folds with a closed β-sheet - have been postulated as the toxic species with well-defined three-dimensional structures to perform pathological functions. A common mechanism for amyloid toxicity, therefore, implies that all amyloid peptides should be able to form β-barrel oligomers as the aggregation intermediates. Here, we applied all-atom discrete molecular dynamics (DMD) simulations to evaluate the formation of β-barrel oligomers and characterize their structures and dynamics in the aggregation of a seven-residue amyloid peptide, corresponding to the amyloid core of amyloid-β with a sequence of 16KLVFFAE22 (Aβ16-22). We carried out aggregation simulations with various numbers of peptides to study the size dependence of aggregation dynamics and assembly structures. Consistent with previous computational studies, we observed the formation of β-barrel oligomers in all-atom DMD simulations. Using a network-based approach to automatically identify β-barrel conformations, we systematically characterized β-barrels of various sizes. Our simulations revealed the conformational inter-conversion between β-barrels and double-layer β-sheets due to increased structural strains upon forming a closed β-barrel while maximizing backbone hydrogen bonds. The potential of mean force analysis further characterized the free energy barriers between these two states. The obtained structural and dynamic insights of β-barrel oligomers may help better understand the molecular mechanism of oligomer toxicities and design novel therapeutics targeting the toxic β-barrel oligomers. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.

Mitigating Human IAPP Amyloidogenesis In Vivo with Chiral Silica Nanoribbons

Amyloid fibrils generally display chirality, a feature which has rarely been exploited in the development of therapeutics against amyloid diseases. This study reports, for the first time, the use of mesoscopic chiral silica nanoribbons against the in vivo amyloidogenesis of human islet amyloid polypeptide (IAPP), the peptide whose aggregation is implicated in type 2 diabetes. The thioflavin T assay and transmission electron microscopy show accelerated IAPP fibrillization through elimination of the nucleation phase and shortening of the elongation phase by the nanostructures. Coarse-grained simulations offer complementary molecular insights into the acceleration of amyloid aggregation through their nonspecific binding and directional seeding with the nanostructures. This accelerated IAPP fibrillization translates to reduced toxicity, especially for the right-handed silica nanoribbons, as revealed by cell viability, helium ion microscopy, as well as zebrafish embryo survival, developmental, and behavioral assays. This study has implicated the potential of employing chiral nanotechnologies against the mesoscopic enantioselectivity of amyloid proteins and their associated diseases.

Graphene quantum dots against human IAPP aggregation and toxicity in vivo

The development of biocompatible nanomaterials has become a new frontier in the detection, treatment and prevention of human amyloid diseases. Here we demonstrated the use of graphene quantum dots (GQDs) as a potent inhibitor against the in vivo aggregation and toxicity of human islet amyloid polypeptide (IAPP), a hallmark of type 2 diabetes. GQDs initiated contact with IAPP through electrostatic and hydrophobic interactions as well as hydrogen bonding, which subsequently drove the peptide fibrillization off-pathway to eliminate the toxic intermediates. Such interactions, probed in vitro by a thioflavin T kinetic assay, fluorescence quenching, circular dichroism spectroscopy, a cell viability assay and in silico by discrete molecular dynamics simulations, translated to a significant recovery of embryonic zebrafish from the damage elicited by IAPP in vivo, as indicated by improved hatching as well as alleviated reactive oxygen species production, abnormality and mortality of the organism. This study points to the potential of using zero-dimensional nanomaterials for in vivo mitigation of a range of amyloidosis.

Understanding Effects of PAMAM Dendrimer Size and Surface Chemistry on Serum Protein Binding with Discrete Molecular Dynamics Simulations

Polyamidoamine (PAMAM) dendrimers, a class of polymeric nanoparticles (NPs) with highly-controllable sizes and surface chemistry, are promising candidates for many biomedical applications, including drug and gene delivery, imaging, and inhibition of amyloid aggregation. In circulation, binding of serum proteins with dendritic NPs renders the formation of protein corona and alters the biological identity of the NP core, which may subsequently elicit immunoresponse and cytotoxicity. Understanding the effects of PAMAM size and surface chemistry on serum protein binding is, therefore, crucial to enable their broad biomedical applications. Here, by applying atomistic discrete molecular dynamics (DMD) simulations, we first uncovered the binding of PAMAM with HSA and Ig and detailed the dependences of such binding on PAMAM size and surface modification. Compared to either anionic or cationic surfaces, modifications with neutral phosphorylcholine (PC), polyethylene glycol (PEG), and hydroxyls (OH) significantly reduced binding with proteins. The relatively strong binding between proteins and PAMAM dendrimers with charged surface groups was mainly driven by electrostatic interactions as well as hydrophobic interactions. Using steered DMD (SDMD) simulations, we conducted a force-pulling experiment in silico estimating the critical forces separating PAMAM-protein complexes and deriving the corresponding free energy barriers for dissociation. The SDMD-derived HSA-binding affinities were consistent with existing experimental measurements. Our results highlighted the association dynamics of protein-dendrimer interactions and binding affinities, whose implications range from fundamental nanobio interfacial phenomena to the development of stealth NPs.