Identification of a Novel Parallel β-Strand Conformation within Molecular Monolayer of Amyloid Peptide

Fabrication of Highly Sensitive and Selective Nitrite Colorimetric Sensor Based on the Enhanced Peroxidase Mimetic Activity of Using Acetic Acid Capped Zinc Oxide Nanosheets

Nitrite ions (NO2-), as one of the leading type-A inorganic-anion, showing significant-effects in the aquatic environment and also to humans health. Whereas, the higher uptake causes detrimental threat to human health leading to various chronic diseases, thus demanding efficient, reliable and convenient method for its monitoring. For this purpose, in the present research study we have fabricated the mimetic nonozyme like catalyst based colorimetric nitrite sensor. The acetic acid capped Zinc Oxide (ZnO) nanosheets (NSs) were introduce as per-oxidase mimetic like catalyst which shows high efficiency towards the oxidative catalysis of colorless tetramethylbenzidine (TMB) to oxidized-TMB (blue color) in the presence of Hydrogen-peroxide (H2O2). The present nitrite ions will stimulate the as formed oxidized-TMB (TMBox), and will caused diazotization reaction (diazotized-TMBox), which will not only decreases the peak intensity of UV-visible peak of TMBox at 652 nm but will also produces another peak at 446 nm called as diazotized-TMBox peak, proving the catalytic reaction between the nitrite ions and TMBox. Further, the prepared colorimetric sensor exhibits better sensitivity with a wider range of concentration (1 × 10-3-4.50 × 10-1 µM), lowest limit of detection (LOD) of 0.22 ± 0.05 nM and small limit of quantification (LOQ) 0.78 ± 0.05 nM having R2 value of 0.998. Further, the colorimetric sensor also manifest strong selectivity towards NO2- as compared to other interference in drinking water system. Resultantly, the prepared sensor with outstanding repeatability, stability, reproducibility, re-usability and its practicability in real water samples also exploit its diverse applications in food safety supervision and environmental monitoring.

Engineering of a Fluorescent Protein for a Sensing of an Intrinsically Disordered Protein through Transition in the Chromophore State

Intrinsically disordered proteins (IDPs) not only play important roles in biological processes but are also linked with the pathogenesis of various human diseases. Specific and reliable sensing of IDPs is crucial for exploring their roles but remains elusive due to structural plasticity. Here, we present the development of a new type of fluorescent protein for the ratiometric sensing and tracking of an IDP. A β-strand of green fluorescent protein (GFP) was truncated, and the resulting GFP was further engineered to undergo the transition in the absorption maximum upon binding of a target motif within amyloid-β (Aβ) as a model IDP through rational design and directed evolution. Spectroscopic and structural analyses of the engineered truncated GFP demonstrated that a shift in the absorption maximum is driven by the change in the chromophore state from an anionic (460 nm) state into a neutral (390 nm) state as the Aβ binds, allowing a ratiometric detection of Aβ. The utility of the developed GFP was shown by the efficient and specific detection of an Aβ and the tracking of its conformational change and localization in astrocytes.

Engineering of antimicrobial peptide fibrils with feedback degradation of bacterial-secreted enzymes

Proteins and peptides can assemble into functional amyloid fibrils with distinct architectures. These amyloid fibrils can fulfil various biological functions in living organisms, and then be degraded. By incorporating an amyloidogenic segment and enzyme-cleavage segment together, we designed a peptide (enzyme-cleavage amyloid peptides (EAP))-based functional fibril which could be degraded specifically by gelatinase. To gain molecular insights into the assembly and degradation of EAP fibrils, we determined the atomic structure of the EAP fibril using cryo-electron microscopy. The amyloidogenic segment of EAP adopted a β-strand conformation and mediated EAP-fibril formation mainly via steric zipper-like interactions. The enzyme-cleavage segment was partially involved in self-assembly, but also exhibited high flexibility in the fibril structure, with accessibility to gelatinase binding and degradation. Moreover, we applied the EAP fibril as a tunable scaffold for developing degradable self-assembled antimicrobial fibrils (SANs) by integrating melittin and EAP together. SANs exhibited superior activity for killing bacteria, and significantly improved the stability and biocompatibility of melittin. SANs were eliminated automatically by the gelatinase secreted from targeted bacteria. Our work provides a new strategy for rational design of functional fibrils with a feedback regulatory loop for optimizing the biocompatibility and biosafety of designed fibrils. Our work may aid further developments of "smart" peptide-based biomaterials for biomedical applications.

Single-molecule visualization determines conformational substate ensembles in β-sheet-rich peptide fibrils

An understanding of protein conformational ensembles is essential for revealing the underlying mechanisms of interpeptide recognition and association. However, experimentally resolving multiple simultaneously existing conformational substates remains challenging. Here, we report the use of scanning tunneling microscopy (STM) to analyze the conformational substate ensembles of β sheet peptides with a submolecular resolution (in-plane <2.6 Å). We observed ensembles of more than 10 conformational substates (with free energy fluctuations between several k_BTs) in peptide homoassemblies of keratin (KRT) and amyloidal peptides (-5Aβ42 and TDP-43 341-357). Furthermore, STM reveals a change in the conformational ensemble of peptide mutants, which is correlated with the macroscopic properties of peptide assemblies. Our results demonstrate that the STM-based single-molecule imaging can capture a thorough picture of the conformational substates with which to build an energetic landscape of interconformational interactions and can rapidly screen conformational ensembles, which can complement conventional characterization techniques.

Accurate Wide-Modulus-Range Nanomechanical Mapping of Ultrathin Interfaces with Bimodal Atomic Force Microscopy

The nanoscale determination of the mechanical properties of interfaces is of paramount relevance in materials science and cell biology. Bimodal atomic force microscopy (AFM) is arguably the most advanced nanoscale method for mapping the elastic modulus of interfaces. Simulations, theory, and experiments have validated bimodal AFM measurements on thick samples (from micrometer to millimeter). However, the bottom-effect artifact, this is, the influence of the rigid support on the determination of the Young's modulus, questions its accuracy for ultrathin materials and interfaces (1-15 nm). Here we develop a bottom-effect correction method that yields the intrinsic Young's modulus value of a material independent of its thickness. Experiments and numerical simulations validate the accuracy of the method for a wide range of materials (1 MPa to 100 GPa). Otherwise, the Young's modulus of an ultrathin material might be overestimated by a 10-fold factor.

Interfacial Interactions within Amyloid Protein Corona Based on 2D MoS2 Nanosheets

The interfacial interaction within the amyloid protein corona based on MoS₂ nanomaterial is crucial, both for understanding the biological effects of MoS₂ nanomaterial and the evolution of amyloid diseases. The specific nano-bio interface phenomenon of human islet amyloid peptide (hIAPP) and MoS₂ nanosheet was investigated by using theoretical and experimental methods. The MoS₂ nanosheet enables the attraction of hIAPP monomer, dimer, and oligomer on its surface through van der Waals forces. Especially, the means of interaction between two hIAPP peptides might be changed by MoS₂ nanosheet. In addition, it is interesting to find that the hIAPP oligomer can stably interact with the MoS₂ nanosheet in one unique "standing" binding mode with an entire exposed β-sheet surface. All the interaction modes on the surface of MoS₂ nanosheet can be the essence of amyloid protein corona that may provide the venue to facilitate the fibrillation of hIAPP proteins. Further, it was verified experimentally that MoS₂ nanosheets could accelerate the fibrillation of hIAPP at a certain concentration mainly based on the newly formed nano-bio interface. In general, our results provide insight into the molecular interaction mechanism of the nano-bio interface within the amyloid protein corona, and shed light on the pathway of amyloid protein aggregation that is related to the evolution of amyloid diseases.

Isomeric Effect of Nano-Inhibitors on Aβ40 Fibrillation at The Nano-Bio Interface

Chemical and physical properties of nanobio interface substantially affect the conformational transitions of adjacent biomolecules. Previous studies have reported the chiral effect and charge effect of nanobio interface on the misfolding, aggregation, and fibrillation of amyloid protein. However, the isomeric effect of nanobio interface on protein/peptides amyloidosis is still unclear. Here, three isomeric nanobio interfaces were designed and fabricated based on the same sized gold nanoclusters (AuNCs) modified with 4-mercaptobenzoic acid (p-MBA), 3-mercaptobenzoic acid (m-MBA), and 2-mercaptobenzoic acid (o-MBA). Then three isomeric AuNCs were employed as models to explore the isomeric effect on the misfolding, aggregation, and fibrillation of Aβ₄₀ at nanobio interfaces. Site-specific replacement experiments on the basis of theoretical analysis revealed the possible mechanism of Aβ₄₀ interacting with isomeric ligands of AuNCs at the nanobio interfaces. The distance and orientation of -COOH group from the surface of AuNCs can affect the electrostatic interaction between isomeric ligands and the positively charged residues (R5, K16, and K28) of Aβ₄₀, which may affect the inhibition efficiency of isomeric AuNCs on protein amyloidosis. Actually, the amyloid fibrillation kinetics results together with atomic force microscope (AFM) images, dynamic light scattering (DLS) results and circular dichroism (CD) spectra indeed proved that all the three isomeric AuNCs could inhibit the misfolding, aggregation and fibrillation of Aβ₄₀ in a dose-dependent manner, and the inhibition efficiency was definitely different from each other. The inhibition efficiency of o-MBA-AuNCs was higher than that of m-MBA-AuNCs and p-MBA-AuNCs at the same dosage. These results provide an insight for isomeric effect at nanobio interfaces, and open an avenue for structure-based nanodrug design target Alzheimer's disease (AD) and even other protein conformational diseases.

Identification and Nanomechanical Characterization of the HIV Tat-Amyloid β Peptide Multifibrillar Structures

HIV transactivator of transcription (Tat) protein could interact with amyloid β (Aβ) peptide which cause the growth of Aβ plaques in the brain and result in Alzheimer's disease in HIV-infected patients. Herein, we employ high-resolution atomic force microscopy and quantitative nanomechanical mapping to investigate the effects of Tat protein in Aβ peptide aggregation. Our results demonstrate that the Tat protein could bind to the Aβ fibril surfaces and result in the formation of Tat-Aβ multifibrillar structures. The resultant Tat-Aβ multifibrillar aggregates represent an increase in stiffness compared with Aβ fibrils due to the increase in β-sheet formation. The identification and characterization of the Tat-Aβ intermediate aggregates is important to understanding the interactions between Tat protein and Aβ peptide, and the development of novel therapeutic strategy for Alzheimer's disease-like disorder in HIV infected individuals.

Nanomechanical mapping of soft materials with the atomic force microscope: methods, theory and applications

Fast, high-resolution, non-destructive and quantitative characterization methods are needed to develop materials with tailored properties at the nanoscale or to understand the relationship between mechanical properties and cell physiology. This review introduces the state-of-the-art force microscope-based methods to map at high-spatial resolution the elastic and viscoelastic properties of soft materials. The experimental methods are explained in terms of the theories that enable the transformation of observables into material properties. Several applications in materials science, molecular biology and mechanobiology illustrate the scope, impact and potential of nanomechanical mapping methods.

Energy Landscapes of a Pair of Adsorbed Peptides

The wide relevance of peptide adsorption in natural and synthetic contexts means it has attracted much attention. Molecular dynamics (MD) simulation has been widely used in these endeavors. Much of this has focused on single peptides due to the computational effort required to capture the rare events that characterize their adsorption. This focus is, however, of limited practical relevance as in reality, most systems of interest operate in the nondilute regime where peptides will interact with other adsorbed peptides. As an alternative to MD simulation, we have used energy landscape mapping (ELM) to investigate two met-enkephalin molecules adsorbed at a gas/graphite interface. Major conformations of the adsorbed peptides and the connecting transition states are elucidated along with the associated energy barriers and rates of exchange. The last of these makes clear that MD simulations are currently of limited use in probing the co-adsorption of two peptides, let alone more. The constant volume heat capacity as a function of temperature is also presented. Overall, this study represents a significant step toward characterizing peptide adsorption beyond the dilute limit.

Modulation of Antimicrobial Peptide Conformation and Aggregation by Terminal Lipidation and Surfactants

The function and properties of peptide-based materials depend not only on the amino acid sequence but also on the molecular conformations. In this paper, we chose a series of peptides G_m(XXKK)_nX-NH₂ (m = 0, 3; n = 2, 3; X = I, L, and V) as the model molecules and studied the conformation regulation through N-terminus lipidation and their formulation with surfactants. The structural and morphological transition of peptide self-assemblies have also been investigated via transmission electron microscopy, atomic force microscopy, circular dichroism spectroscopy, and small-angle neutron scattering. With the terminal alkylation, the molecular conformation changed from random coil to β-sheet or α-helix. The antimicrobial activities of alkylated peptide were different. C₁₆-G₃(IIKK)₃I-NH₂ showed antimicrobial activity against Streptococcus mutans, while C₁₆-(IIKK)₂I-NH₂ and C₁₆-G₃(IIKK)₂I-NH₂ did not kill the bacteria. The surfactant sodium dodecyl sulfonate could rapidly induce the self-assemblies of alkylated peptides (C₁₆-(IIKK)₂I-NH₂, C₁₆-G₃(IIKK)₂I-NH₂, C₁₆-G₃(VVKK)₂V-NH₂) from nanofibers to micelles, along with the conformation changing from β-sheet to α-helix. The cationic surfactant hexadecyl trimethyl ammonium bromide made the lipopeptide nanofibers thinner, and nonionic surfactant polyoxyethylene (23) lauryl ether (C₁₂EO₂₃) induced the nanofibers much more intensively. Both the activity and the conformation of the α-helical peptide could be modulated by lipidation. Then, the self-assembled morphologies of alkylated peptides could also be further regulated with surfactants through hydrophobic, electrostatic, and hydrogen-bonding interactions. These results provided useful strategies to regulate the molecular conformations in peptide-based material functionalization.

Direct investigation of current transport in cells by conductive atomic force microscopy

Currents play critical roles in neurons. Direct observation of current flows in cells at nanometre dimensions and picoampere current resolution is still a daunting task. In this study, we investigated the current flows in hippocampal neurons, PC12 cells and astrocytes in response to voltages applied to the cell membranes using conductive atomic force microscopy (CAFM). The spines in the hippocampal neurons play crucial roles in nerve signal transfer. When the applied voltage was greater than 7.2 V, PC12 cells even show metallic nanowire-like characteristics. Both the cell body and glial filaments of astrocytes yielded CAFM test results that reflect different electrical conductance. To our best knowledge, the electrical characteristics and current transport through components of cells (especially neurons) in response to an applied external voltage have been revealed for the first time at nanometre dimensions and picoampere current levels. We believe that such studies will pave new ways to study and model the electrical characteristics and physiological behaviours in cells and other biological samples.

CLVFFA-Functionalized Gold Nanoclusters Inhibit Aβ40 Fibrillation, Fibrils' Prolongation, and Mature Fibrils' Disaggregation

The abnormal aggregation of amyloid beta (Aβ or A beta) from monomeric proteins into amyloid fibrils is an important pathological contact to Alzheimer's disease (AD). Amyloid beta 40 (Aβ40), the pivotal biomarker of AD, aggregates to form amyloid plaques. For this reason, inhibition of amyloid fibrillation had become a crucial prevention and therapeutic strategy. Usually, LVFFA is the central hydrophobic fragment of Aβ and can inhibit the aggregation of Aβ40. In this work, in order to improve the inhibitory ability of LVFFA, hexapeptide CLVFFA were conjugated at the surface of Au clusters (AuNCs) to manufacture a nanosized inhibitor, AuNCs-CLVFFA. Thioflavin T fluorescence and transmission electron microscope results showed that AuNCs-CLVFFA inhibited Aβ40 fibrillogenesis, fibrils' prolongation, and mature fibrils' disaggregation. Furthermore, AuNCs as the backbone of the inhibitor showed extraordinary inhibition ability for Aβ40 aggregation at a low AuNCs-CLVFFA concentration. Free hexapeptide CLVFFA, at the same concentration, showed almost no inhibition. Additionally, the inhibitor could maintain the optical properties of nanoclusters, and the cell viability demonstrated that the inhibitor had good biocompatibility and may potentially be applied into AD therapy or treatment.

Building two-dimensional materials one row at a time: Avoiding the nucleation barrier

Assembly of two-dimensional (2D) molecular arrays on surfaces produces a wide range of architectural motifs exhibiting unique properties, but little attention has been given to the mechanism by which they nucleate. Using peptides selected for their binding affinity to molybdenum disulfide, we investigated nucleation of 2D arrays by molecularly resolved in situ atomic force microscopy and compared our results to molecular dynamics simulations. The arrays assembled one row at a time, and the nuclei were ordered from the earliest stages and formed without a free energy barrier or a critical size. The results verify long-standing but unproven predictions of classical nucleation theory in one dimension while revealing key interactions underlying 2D assembly.

Determination of the viscoelastic properties of a single cell cultured on a rigid support by force microscopy

Understanding the relationship between the mechanical properties of living cells and physiology is a central issue in mechanobiology. Mechanical properties are used as fingerprints of the pathological state of a single cell. The force exerted on a cell is influenced by the stiffness of the solid support needed to culture it. This effect is a consequence of the cell's boundary conditions. It causes a cell to appear with mechanical properties different from their real values. Here we develop a bottom effect viscoelastic theory to determine the viscoelastic response of a cell. The theory transforms a force-distance curve into the cell's Young's modulus, loss modulus, relaxation time or viscosity coefficient with independence of the stiffness of the rigid support. The theory predicts that, for a given indentation, the force exerted on the cell's periphery will be larger than on a perinuclear region. Results based on the use of semi-infinite contact mechanics models introduce large numerical errors in the determination of the mechanical properties. Finite element simulations confirm the theory and define its range of applicability.

A swarm of slippery micropropellers penetrates the vitreous body of the eye

The intravitreal delivery of therapeutic agents promises major benefits in the field of ocular medicine. Traditional delivery methods rely on the random, passive diffusion of molecules, which do not allow for the rapid delivery of a concentrated cargo to a defined region at the posterior pole of the eye. The use of particles promises targeted delivery but faces the challenge that most tissues including the vitreous have a tight macromolecular matrix that acts as a barrier and prevents its penetration. Here, we demonstrate novel intravitreal delivery microvehicles-slippery micropropellers-that can be actively propelled through the vitreous humor to reach the retina. The propulsion is achieved by helical magnetic micropropellers that have a liquid layer coating to minimize adhesion to the surrounding biopolymeric network. The submicrometer diameter of the propellers enables the penetration of the biopolymeric network and the propulsion through the porcine vitreous body of the eye over centimeter distances. Clinical optical coherence tomography is used to monitor the movement of the propellers and confirm their arrival on the retina near the optic disc. Overcoming the adhesion forces and actively navigating a swarm of micropropellers in the dense vitreous humor promise practical applications in ophthalmology.

Free Energy Landscape for Alpha-Helix to Beta-Sheet Interconversion in Small Amyloid Forming Peptide under Nanoconfinement

Understanding the mechanism of fibrillization of amyloid forming peptides could be useful for the development of therapeutics for Alzheimer's disease (AD). Taking this standpoint, we have explored in this work the free energy profile for the interconversion of monomeric and dimeric forms of amyloid forming peptides into different secondary structures namely beta-sheet, helix, and random coil in aqueous solution using umbrella sampling simulations and density functional theory calculations. We show that the helical structures of amyloid peptides can form β sheet rich aggregates through random coil conformations in aqueous condition. Recent experiments ( Chem. Eur. J. 2018, 24, 3397-3402 and ACS Appl. Mater. Interfaces 2017, 9, 21116-21123) show that molybdenum disulfide nanosurface and nanoparticles can reduce the fibrillization process of amyloid beta peptides. We have unravelled the free energy profile for the interconversion of helical forms of amyloid forming peptides into beta-sheet and random coil in the presence of a two-dimensional nanosurface of MoS₂. Results indicate that the monomer and dimeric forms of the peptides adopt the random coil conformation in the presence of MoS₂ while the helical form is preferable for the monomeric form and that the beta-sheet and helix forms are the preferable forms for dimers in aqueous solution. This is due to strong interaction with MoS₂ and intramolecular hydrogen bonds of random coil conformation. The stabilization of random coil conformation does not lead to a β sheet like secondary structure for the aggregate. Thus, the confinement of MoS₂ promotes deaggregation of amyloid beta peptides rather than aggregation, something that could be useful for the development of therapeutics for AD.

CDtoolX, a downloadable software package for processing and analyses of circular dichroism spectroscopic data

Circular dichroism (CD) spectroscopy is a highly used method for the examination and characterization of proteins, including, amongst other features, their secondary and tertiary structures, thermal stability, comparisons of wildtype and mutant proteins, and monitoring the binding of small molecules, folding/unfolding pathways, and formation of macromolecular complexes. This article describes CDtoolX, a new, user-friendly, free-to-download-and-use software program that enables processing, displaying, archiving, calibrating, comparisons, and analyses of CD and synchrotron radiation circular dichroism spectroscopic data.

Mechanistic insights into the inhibition and size effects of graphene oxide nanosheets on the aggregation of an amyloid-β peptide fragment

The aggregation of amyloid-β (Aβ), which involves the formation of small oligomers and mature fibrils, has received considerable attention in the past few decades due to its close link with Alzheimer's disease (AD). The inhibition of β-sheet formation has been considered as the primary therapeutic strategy for AD. In this respect, graphene oxide (GO) has gained significant attention because of its high solubility, good biocompatibility and inhibitory effect on the aggregation of Aβ and the 33-42 fragment (Aβ33-42). However, the inhibitory mechanism at the atomic level remains elusive. Herein, we investigated the oligomerization of Aβ33-42 by performing replica exchange molecular dynamics simulations on four Aβ33-42 peptide chains in the absence and presence of two different sizes of GO. Our simulations show that isolated Aβ33-42 can form fibril-prone extended β-sheets and barrel-like structures, whereas they are suppressed in the presence of GO nanosheets. Our data reveal that GO inhibits Aβ33-42 oligomerization by making Aβ33-42 peptides separate from each other through strong interactions with M35. With the same total number of atoms, GO120 displays better inhibitory effect than GO60 by providing a larger effective contact surface area. This study provides the molecular mechanism of GO in inhibiting the aggregation of Aβ33-42, which might offer a theoretical insight into the design of drugs against AD at the atomic level.

Nano-assembly of amyloid β peptide: role of the hairpin fold

Structural investigations have revealed that β hairpin structures are common features in amyloid fibrils, suggesting that these motifs play an important role in amyloid assembly. To test this hypothesis, we characterized the effect of the hairpin fold on the aggregation process using a model β hairpin structure, consisting of two Aβ(14–23) monomers connected by a turn forming YNGK peptide. AFM studies of the assembled aggregates revealed that the hairpin forms spherical structures whereas linear Aβ(14–23) monomers form fibrils. Additionally, an equimolar mixture of the monomer and the hairpin assembles into non-fibrillar aggregates, demonstrating that the hairpin fold dramatically changes the morphology of assembled amyloid aggregates. To understand the molecular mechanism underlying the role of the hairpin fold on amyloid assembly, we performed single-molecule probing experiments to measure interactions between hairpin and monomer and two hairpin complexes. The studies reveal that the stability of hairpin-monomer complexes is much higher than hairpin-hairpin complexes. Molecular dynamics simulations revealed a novel intercalated complex for the hairpin and monomer and Monte Carlo modeling further demonstrated that such nano-assemblies have elevated stability compared with stability of the dimer formed by Aβ(14–23) hairpin. The role of such folding on the amyloid assembly is also discussed.

Nanoscale studies link amyloid maturity with polyglutamine diseases onset

The presence of expanded poly-glutamine (polyQ) repeats in proteins is directly linked to the pathogenesis of several neurodegenerative diseases, including Huntington’s disease. However, the molecular and structural basis underlying the increased toxicity of aggregates formed by proteins containing expanded polyQ repeats remain poorly understood, in part due to the size and morphological heterogeneity of the aggregates they form in vitro. To address this knowledge gap and technical limitations, we investigated the structural, mechanical and morphological properties of fibrillar aggregates at the single molecule and nanometer scale using the first exon of the Huntingtin protein as a model system (Exon1). Our findings demonstrate a direct correlation of the morphological and mechanical properties of Exon1 aggregates with their structural organization at the single aggregate and nanometric scale and provide novel insights into the molecular and structural basis of Huntingtin Exon1 aggregation and toxicity.