Surface Of Fibrils Research Articles

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.

Eye lens crystallin proteins inhibit the autocatalytic amyloid amplification nature of mature α-synuclein fibrils.

Parkinson´s disease is characterized by the accumulation of proteinaceous aggregates in Lewy bodies and Lewy Neurites. The main component found in such aggregates is α-synuclein. Here, we investigate how bovine eye lens crystallin proteins influence the aggregation kinetics of α-synuclein at mildly acidic pH (5.5) where the underlying aggregation mechanism of this protein is dominated by secondary nucleation of monomers on fibril surface providing an autocatalytic amyloid amplification process. Bovine α-, βH- and γB-crystallins were found to display chaperone-like activity inhibiting α-synuclein aggregation. This effect was shown to be time-dependent, with early additions of α-crystallin capable of retarding and even inhibiting aggregation during the time frame of the experiment. The inhibitory nature of crystallins was further investigated using trap and seed kinetic experiments. We propose crystallins interact with mature α-synuclein fibrils, possibly binding along the surfaces and at fibril free ends, inhibiting both elongation and monomer-dependent secondary nucleation processes in a mechanism that may be generic to some chaperones that prevent the onset of protein misfolding related pathologies.

Protofilament Structure and Supramolecular Polymorphism of Aggregated Mutant Huntingtin Exon 1

Huntington's disease is a progressive neurodegenerative disease caused by expansion of the polyglutamine domain in the first exon of huntingtin (HttEx1). The extent of expansion correlates with disease progression and formation of amyloid-like protein deposits within the brain. The latter display polymorphism at the microscopic level, both in cerebral tissue and in vitro. Such polymorphism can dramatically influence cytotoxicity, leading to much interest in the conditions and mechanisms that dictate the formation of polymorphs. We examine conditions that govern HttEx1 polymorphism in vitro, including concentration and the role of the non-polyglutamine flanking domains. Using electron microscopy, we observe polymorphs that differ in width and tendency for higher-order bundling. Strikingly, aggregation yields different polymorphs at low and high concentrations. Narrow filaments dominate at low concentrations that may be more relevant in vivo. We dissect the role of N- and C-terminal flanking domains using protein with the former (httNT or N17) largely removed. The truncated protein is generated by trypsin cleavage of soluble HttEx1 fusion protein, which we analyze in some detail. Dye binding and solid-state NMR studies reveal changes in fibril surface characteristics and flanking domain mobility. Higher-order interactions appear facilitated by the C-terminal tail, while the polyglutamine forms an amyloid core resembling those of other polyglutamine deposits. Fibril-surface-mediated branching, previously attributed to secondary nucleation, is reduced in absence of httNT. A new model for the architecture of the HttEx1 filaments is presented and discussed in context of the assembly mechanism and biological activity.

Water retention capabilities of collagen, gelatin and peptide as studied by IR/QCM/RH system.

In this study, water retention properties of triple helix collagen, gelatin (separated single chains) and peptide (broken peptide fragments) were studied by using IR micro-spectroscopy equipped with a relative humidity (RH) control system and quartz crystal microbalance (QCM). Adsorbed water ratios (wt%) are found to be in the order of collagen, gelatin and peptide (at about RH=60%, 22wt% for collagen, 14wt% for gelatin and 9wt% for peptide). Free water molecules with longer H bonds are the major adsorbed water species for collagen, gelatin and peptide. IR band shifts and changes in normalized band areas of functional groups are generally larger for collagen than gelatin and peptide, indicating larger interactions of water molecules with functional groups such as aliphatic CH2, CH3, amides, COO- and C-O for collagen. Relations between normalized band areas show that water molecules are interacting with aliphatic CH species and C-O bonds of collagen. Since the fibril structures of collagen triple helices are reported to be cross-linked by sugars, water molecules can be attracted to polar C-O bonds of sugars linking collagen triple helices in fibrils and they are interacting with adjacent aliphatic CH side chains on the surface of fibrils.

Effects of extraction method on dry pulp yield and morphological properties of pineapple leaf fibre

Pineapple leaves (PALs) are useful agro wastes which have the potentials to be used as an alternative source of non-wood natural fiber. In this study, different extraction methods had been investigated to identify the most feasible pineapple leaf fiber (PALF) extraction method, based on the dry pulp yield and the PALF morphology. The manual retting using a ceramic scrapper led to low yield of around 1.8 % (wt.), while water retting for 21 d led to about 6.0 % (wt.) yield of dark greenish dry pulp. Both methods resulted in PALFs which still contained with non-cellulosic residues, as verified by scanning electron microscopic (SEM) imaging. The chemical extraction of PALF using various NaOH solution concentrations (i.e. 1 to 20 % (wt.)) gave different yields. Based on the SEM images, clean and smooth surfaces of fibrils were observed when the NaOH solution concentrations applied at or higher than 6 % (wt.), implying that all impurities including lignin and wax had been completely removed. The mechanical-chemical extraction method produced significantly more dry pulp compared to the chemical extraction method at the same NaOH solution concentration. This is attributed to the fact that the crushed PAL has a larger surface area, thus providing more reaction possibilities with NaOH solution. Finally, it was found that the crushed PAL that cooked at 90 °C needed at least 90 min of cooking time to obtain satisfying whitish dry pulp.

Toward the Understanding of Small Protein-Mediated Collagen Intrafibrillar Mineralization.

The design of improved materials for orthopedic implants and bone tissue engineering scaffolds relies on materials mimicking the properties of bone. Calcium phosphate (Ca-PO4)-mineralized collagen fibrils arranged in a characteristic hierarchical structure constitute the building blocks of mineralized vertebrate tissues and control their biomechanical and biochemical properties. Large, flexible, acidic noncollagenous proteins (ANCPs) have been shown to influence collagen mineralization but little is known about mineralization mechanisms with the aid of small proteins. Osteocalcin (OCN) is a small, highly structured biomolecule known as a multifunctional hormone in its undercarboxylated form. Here, we examined the potential mechanism of collagen intrafibrillar mineralization in vitro mediated by OCN as a model protein. Rapid and random extrafibrillar mineralization of flakey Ca-PO4 particles was observed by transmission electron microscopy mainly on the outer surfaces of collagen fibrils of a preformed collagen scaffold in the absence of the protein. In contrast, the protein stabilized hydrated, spherical nanoclusters of Ca-PO4 on the outer surface of the fibrils, thereby retarding extrafibrillar mineralization. The nanoclusters then infiltrated the fibrils resulting in intrafibrillar mineralization with HAP crystals aligned with the fibrils. This mechanism is similar to that observed for unstructured ANCPs. Results of fibrillogenesis and immunogold labeling studies showed that OCN was associated primarily with the fibrils, consistent with ex vivo studies on mineralizing turkey tendon. The present findings contribute to expanding our understanding of collagen intrafibrillar mineralization and provide insight into design synthetic macromolecular matrices for orthopedic implants and bone regeneration.

Orientational order induced by a polymer network in the isotropic phase of liquid crystal.

We studied the paranematic ordering induced by a polymer network in the isotropic phase of a liquid crystal (LC) that occurs in polymer-stabilized cells with bend configuration of the LC director (π cells) fabricated via photopolymerization of photoreactive monomer RM 82 added in small concentrations (3-5 wt %) to a nematic LC [4-cyano-4'-pentylbiphenyl (5CB)] when low voltage was applied across the cell. The polymer network formed in the nematic phase of the LC consists of fine fibrils that are aligned along the LC director and thus mirror the bend deformation of the LC at the time of polymerization. When heated to temperatures above the nematic-to-isotropic (N-I) phase transition such highly ordered polymer network anchors LC molecules providing ordering of the LC around the fibrils which results in unusually high optical retardation of the cell, R_{cell}. We present a theoretical model that relates R_{cell} to the degree of order of the fibrils, the anchoring energy of the LC molecules on the surface of the polymer fibrils, and the fibril radius r_{0}. Fitting of the experimental R_{cell}(T) curves with the developed model reveals correlation of r_{0} with the nematic correlation length ξ_{0} which characterizes penetration of the nematic order in the isotropic phase of the LC. Accepting ξ_{0} as a material constant of about 1 nm leads to a very small radius of the fibrils, r_{0}∼1nm, which is also supported by other reported experimental data. High optical retardation and fast electro-optical response of the cells at the temperatures deep into the isotropic phase point toward the enhancement of the polymer-induced paranematic order by a well-oriented layer of LC molecules that are absorbed on the surface of fibrils. Application of high voltage at the isotropic phase temperatures results in high variations of the optical retardation of the cells. Characteristic on and off response times were about 10-100 μs, independent of the cell gap. Combination of large voltage-driven changes of the optical retardation occurring in the low-viscosity isotropic state with switching times that are at least two orders of magnitude shorter than the typical relaxation times of the cells operating in the nematic phase make such polymer-stabilized π cells very promising for application in fast electro-optical switches and light modulators.

Unique and outstanding quantum dots (QD)/tunicate cellulose nanofibrils (TCNF) nanohybrid platform material for use as 1D ink and 2D film

Quantum dots (QD)/polymer materials have wide applications in biological imaging, clinical diagnostics, anti-counterfeiting materials, light-emitting devices and solar cells. The development of QD/cellulose nanofibrils (CNF) hybrids with a more perfect structure and excellent properties is important for improving known applications. A unique tunicate CNF (TCNF) was homogeneously blended with outstanding CdSe/CdS core/shell QD to prepare a novel QD/TCNF hybrid. The QD were monodispersed on a single TCNF fibril surface as an evenly distributed monolayer with an extremely high packing density and no visible aggregation. The prepared hybrid is an excellent platform nanomaterial which was demonstrated by its good writing fidelity when applied as a 1D ink and by its good processability in the preparation of 2D films with acceptable transparency and flexibility. This one-step direct blending approach provides a facile shortcut to effectively fabricate cellulose-based high-performance functional QD nanomaterials at the single-fibril level.

Features of the Structural Organization and Sorption Properties of Cellulose

An improved model of the layered structure of cellulose microfibrils is proposed, taking into account the presence of slit-like pores between its structural elements. The scheme of the formation of donoracceptor intramolecular, intermolecular and interlayer hydrogen bonds of one glucopyranose unit in the cellulose crystallite is presented. The mechanism of specific adsorption interactions of water molecules in a monolayer with active centers located on the hydrophilic surfaces of elementary fibrils is described. The energy of dipole-dipole interactions was calculated depending on the distance between the active center and the adsorbate water molecule. The thermodynamic parameters characterizing the state of the adsorbate in the adsorption layers are determined by the proton magnetic relaxation method and sorption measurements. The possibility of determining the net heat of adsorption in a bilayer taking into account the Arrhenius nature of the correlation times of the thermal molecular motions of the adsorbate was established. An increase in the entropy of adsorbed water during the adsorption process was revealed. It was found that during adsorption, a part of the inner regions of crystallites transitions to their surface with the participation of cellulose hydroxyl groups, and during desorption, the reverse process is observed.

Stability of the Meat Protein Type I Collagen: Influence of pH, Ionic Strength, and Phenolic Antioxidant.

The water-holding capacity (WHC) is among the key factors in determining the quality of meat and its value, which is strongly influenced by the content and quality of the connective tissue proteins like collagen. Therefore, the factors that influence the proteins’ stability, e.g., pH, ionic strength, and the antioxidants which are used to increase the meat shelf-life, also affect the WHC. The interaction of collagen, whose structure is strongly influenced by the interaction with water molecules, can be studied following the behavior of water diffusion by low-resolution 1H NMR experiments. The present study is addressed to study the collagen stability as a function of pH, ionic strength, and phenolic antioxidants like catechin. The experimental study demonstrated how the 1H NMR time domain (TD) experiments are able to evaluate the hydration properties of collagen, not only as a function of ionic strength and pH, but also in determining the ability of catechin to interact both on the surface of the collagen fibrils and inside the fibrillar domain.

Changes to the Contour Length, Molecular Chain Length, and Solid-State Structures of Nanocellulose Resulting from Sonication in Water.

Sonication in water reduced the average contour lengths of nanocellulose prepared from wood cellulose fiber and microcrystalline cellulose. Most of the kinks in the wood cellulose nanofibrils were formed during the initial 10 min of sonication. Fragmentation occurred at the kinks and rigid segments associated with depolymerization during subsequent sonication for 10-120 min, resulting in the formation of cellulose nanocrystals with low aspect ratios. Solid-state cross-polarization magic angle sample spinning 13C-nuclear magnetic resonance revealed that the original crystalline regions of the cellulose were partly transformed to fibril surfaces or disordered regions by both pretreatment and the subsequent fragmentation of molecular chains during sonication. The nanocellulose prepared from microcrystalline cellulose had different fragmentation behavior with regard to molecular chain length following sonication. The results indicated that on average the hexagonal 36 cellulose chain structure formed the cross-section of each wood cellulose microfibril.

Structural changes in α-chitin through nanofibrillation by high-pressure homogenization in water

Chitin nanofiber was prepared from purified crab shell chitin by repeated high-pressure homogenization in water. The chitin nanofiber/water dispersion thus prepared was viscous and translucent, and maintained a stable dispersion at room temperature for several months. AFM images showed that the chitin nanofibers had heterogeneous network structures with widths ranging from several nanometers to several tens of nanometers. Some kinks and twisted structures were also observed in the AFM images. X-ray diffraction patterns showed that both the crystallinity index and crystal width of the original alpha-chitin decreased with nanofibrillation. Solid-state 13C-NMR spectra showed that the chemical shifts of all carbons were unchanged before and after nanofibrillation, and that all C6–OH groups had the gauche-gauche conformation irrespective of the crystalline fibril surfaces and insides. The degree of N-acetylation increased from 0.83 to 0.98, which was probably due to C2–NH2 groups present in the original chitin being partially removed during high-pressure homogenization in water. The original chitin and chitin nanofiber were dissolved in 8% LiCl/DMAc, and the solutions after dilution to 1% LiCl/DMAc were subjected to size-exclusion chromatography combined with multi-angle laser-light scattering to determine their molar masses and molar mass distributions. The weight-average molar mass (Mw) value of the original chitin was 271,200 (degree of polymerization [DP] ~1340). The Mw value of the chitin nanofiber was 165,500 (DP 820), showing that the DP of the original chitin decreased by 40% through the nanofibrillation in water to form the chitin nanofiber. Chitin nanofibers were prepared from purified crab-shell chitin particles by repeated high-pressure homogenization in water. AFM images showed that the chitin nanofibers had heterogeneous network structures. X-ray diffraction patterns showed that both the crystallinity index and crystal width of the original α-chitin decreased by nanofibrillation. Solid-state 13C-NMR spectra showed that all C6–OH groups had the gauche–gauche conformation. The degree of N-acetylation increased from 0.83 to 0.98 by nanofibrillation, while the weight-average molar masses of the original chitin and chitin nanofibers were 271,200 and 165,500, respectively.

Glycation changes molecular organization and charge distribution in type I collagen fibrils

Collagen fibrils are central to the molecular organization of the extracellular matrix (ECM) and to defining the cellular microenvironment. Glycation of collagen fibrils is known to impact on cell adhesion and migration in the context of cancer and in model studies, glycation of collagen molecules has been shown to affect the binding of other ECM components to collagen. Here we use TEM to show that ribose-5-phosphate (R5P) glycation of collagen fibrils – potentially important in the microenvironment of actively dividing cells, such as cancer cells – disrupts the longitudinal ordering of the molecules in collagen fibrils and, using KFM and FLiM, that R5P-glycated collagen fibrils have a more negative surface charge than unglycated fibrils. Altered molecular arrangement can be expected to impact on the accessibility of cell adhesion sites and altered fibril surface charge on the integrity of the extracellular matrix structure surrounding glycated collagen fibrils. Both effects are highly relevant for cell adhesion and migration within the tumour microenvironment.

Colloidal stability of chitin nanofibers in aqueous systems: Effect of pH, ionic strength, temperature & concentration

Chitin nanofibers are emerging as a very attractive bio-compatible material in number of advanced materials applications. In this work, the colloidal stability of the chitin nanofibers was investigated against pH, ionic strength, temperature and concentration. Aqueous solutions of chitin nanofibers were found to be stabilized due to the carboxylic acid moieties available in the fibril surface as evidenced by both 13C NMR and potentiometric titration methods. Amongst others, pH and ionic strength were the most influential factors which determine both hydrodynamic diameter and zeta potential. The chitin nanofiber dispersions were stabilized at pH values higher than 7, with an average zeta potential value of -22.5 mV. A monotonic increase of zeta potential was observed with respect to increase in ionic strength. Zeta potential got stabilized at -14.0 mV for ionic strengths over 20 mM of NaCl. Hydrodynamic particle size was also found to be a function of temperature and concentration.

Role of Cholesterol on Binding of Amyloid Fibrils with Lipid Bilayers

The aggregation of amyloid-beta proteins into soluble oligomers and fibril deposits is believed to trigger the molecular processes accounting for Alzheimer's disease. In addition, levels of cholesterol, which is an important component of the neuron plasma membrane, are elevated in the brain of Alzheimer's patients and they correlate with the development of the disease in mid-life individuals. A possible explanations for this correlation is that cholesterol affects binding of Abeta proteins to lipid bilayer as this process was shown to have a deleterious effect on neurons. Accordingly, experimental studies have shown that amyloid-beta fibrils bind more strongly to lipid bilayers containing higher cholesterol levels. The molecular mechanism of the process is, however, not well understood. Here, we perform extensive molecular dynamics simulations to investigate the role of cholesterol on fibril-bilayer binding. In particular, we compute the number of binding events as a function of cholesterol level. We find that binding events are driven by electrostatic interactions, they have a longer life-time and occur more frequently with increased cholesterol level. An explanation of these results at the molecular level is provided based on the distribution of residues on the fibril surface.

Recent Advances in the Pathophysiology of Musculocontractural Ehlers-Danlos Syndrome.

Musculocontractural Ehlers–Danlos Syndome (mcEDS) is a type of EDS caused by biallelic pathogenic variants in the gene for carbohydrate sulfotransferase 14/dermatan 4-O-sulfotransferase 1 (CHST14/D4ST1, mcEDS-CHST14), or in the gene for dermatan sulfate epimerase (DSE, mcEDS-DSE). Thus far, 41 patients from 28 families with mcEDS-CHST14 and five patients from four families with mcEDS-DSE have been described in the literature. Clinical features comprise multisystem congenital malformations and progressive connective tissue fragility-related manifestations. This review outlines recent advances in understanding the pathophysiology of mcEDS. Pathogenic variants in CHST14 or DSE lead to reduced activities of relevant enzymes, resulting in a negligible amount of dermatan sulfate (DS) and an excessive amount of chondroitin sulfate. Connective tissue fragility is presumably attributable to a compositional change in the glycosaminoglycan chains of decorin, a major DS-proteoglycan in the skin that contributes to collagen fibril assembly. Collagen fibrils in affected skin are dispersed in the papillary to reticular dermis, whereas those in normal skin are regularly and tightly assembled. Glycosaminoglycan chains are linear in affected skin, stretching from the outer surface of collagen fibrils to adjacent fibrils; glycosaminoglycan chains are curved in normal skin, maintaining close contact with attached collagen fibrils. Homozygous (Chst14−/−) mice have been shown perinatal lethality, shorter fetal length and vessel-related placental abnormalities. Milder phenotypes in mcEDS-DSE might be related to a smaller fraction of decorin DS, potentially through residual DSE activity or compensation by DSE2 activity. These findings suggest critical roles of DS and DS-proteoglycans in the multisystem development and maintenance of connective tissues, and provide fundamental evidence to support future etiology-based therapies.

Age-related changes of tendon fibril micro-morphology and gene expression.

Aging is hypothesized to be associated with changes in tendon matrix composition which may lead to alteration of tendon material properties and hence propensity to injury. Altered gene expression may offer insights into disease pathophysiology and thus open new perspectives toward designing pathophysiology‐driven therapeutics. Therefore, the current study aimed at identifying naturally occurring differences in tendon micro‐morphology and gene expression of newborn, young and old horses. Age‐related differences in the distribution pattern of tendon fibril thickness and in the expression of the tendon relevant genes collagen type 1 (Col1), Col3, Col5, tenascin‐C, decorin, tenomodulin, versican, scleraxis and cartilage oligomeric matrix protein were investigated. A qualitative and quantitative gene expression and collagen fibril diameter analysis was performed for the most frequently injured equine tendon, the superficial digital flexor tendon, in comparison with the deep digital flexor tendon. Most analyzed genes (Col1, Col3, Col5, tenascin‐C, tenomodulin, scleraxis) were expressed at a higher level in foals (age ≤ 6 months) than in horses of 2.75 years (age at which flexor tendons become mature in structure) and older, decorin expression increased with age. Decorin was previously reported to inhibit the lateral fusion of collagen fibrils, causing a thinner fibril diameter with increased decorin concentration. The results of this study suggested that reduction of tendon fibril diameters commonly seen in equine tendons with increasing age might be a natural age‐related phenomenon leading to greater fibril surface areas with increased fibrillar interaction and reduced sliding at the fascicular/fibrillar interface and hence a stiffer interfascicular/interfibrillar matrix. This may be a potential reason for the higher propensity to tendinopathies with increasing age.

Amyloidophilic Molecule Interactions on the Surface of Insulin Fibrils: Cooperative Binding and Fluorescence Quenching

Protein aggregation into insoluble fibrillar aggregates is linked to several neurodegenerative disorders, such as Alzheimer’s or Parkinson’s disease. Commonly used methods to study aggregation inhibition or fibril destabilization by potential drugs include spectroscopic measurements of amyloidophilic dye molecule fluorescence or absorbance changes. In this work we show the cross-interactions of five different dye molecules on the surface of insulin amyloid fibrils, resulting in cooperative binding and fluorescence quenching.

Distinct α-Synuclein:Lipid Co-Structure Complexes Affect Amyloid Nucleation through Fibril Mimetic Behavior.

A hallmark of Parkinson's disease is the presence of Lewy bodies consisting of lipids and proteins, mainly fibrillated α-synuclein (aSN). aSN is an intrinsically disordered protein exerting its physiological role in an ensemble of states, one of which coexists in large assemblies with lipids, recently termed co-structures. Here, we decipher the kinetics of aSN:lipid co-structure formation to decode its mechanism of formation, and we show that the co-structures form with a distinct stoichiometry. Through seeded fibrillation assays, we demonstrate that aSN:lipid co-structures accelerate aSN fibril nucleation compared to lipid vesicles alone. A small-angle X-ray scattering-based model is proposed in which aSN decorates the lipid vesicle surface, yielding properties similar to those of the fibril surface, enhancing fibril nucleation. The delicate balance of aSN structural states close to and on the membrane may under given conditions, e.g., increased local concentrations, be a crucial switching factor between functional and pathological behavior.

Targeting the Amyloid-β Fibril Surface with a Constrained Helical Peptide Inhibitor.

Amyloid-β (Aβ) oligomers are well-known toxic molecular species associated with Alzheimer's disease. Recent discoveries of the ability of amyloid fibril surfaces to convert soluble proteins into toxic oligomers suggested that these surfaces could serve as therapeutic targets for intervention. We have shown previously that a short helical peptide could be a key structural motif that can specifically recognize the K16-E22 region of the Aβ40 fibril surface with an affinity at the level of several micromolar. Here, we demonstrate that in-tether chiral center-induced helical stabilized peptides could also recognize the fibril surfaces, effectively inhibiting the surface-mediated oligomerization of Aβ40. Moreover, through extensive computational sampling, we observed two distinct ways in which the peptide inhibitors recognize the fibril surface. Apart from a binding mode that, in accord with the original design, involves hydrophobic side chains at the binding interface, we observed much more frequently another binding mode in which the hydrophobic staple interacts directly with the fibril surface. The affinity of the peptides for the fibril surface could be adjusted by tuning the hydrophobicity of the staple. The best candidate investigated here exhibits a submicromolar affinity (∼0.75 μM). Collectively, this work opens an avenue for the rational design of candidate drugs with stapled peptides for amyloid-related disease.