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Amyloid β peptide (Aβ) aggregation and deposition are considered the main causes of Alzheimer's disease. In a previous study, we demonstrated that anionic Zn-phthalocyanine (ZnPc) can interact with the Aβ peptide and inhibit the fibril-formation process. However, due to the inability of anionic ZnPc to cross the intact blood–brain barrier, we decided to explore the interaction of cationic methylated Zn-phthalocyanine (cZnPc) with the peptide. Using a ThT fluorescence assay, we observed that cZnPc dose-dependently and time-dependently inhibited Aβ1-42 fibril levels under in vitro fibril-formation conditions. Electron microscopy revealed that it caused Aβ1-42 peptides to form small aggregates. Western blotting and dot immunoblot oligomer experiments demonstrated that cZnPc increased rather than decreased the levels of oligomers from the very early stages of incubation. A binding assay confirmed that cZnPc could bind with the peptide. Docking simulations indicated that the oligomer species of Aβ1-42 had a higher ability to interact with cZnPc. ANS fluorescence assay results indicated that cZnPc did not affect the hydrophobicity of the peptide. However, cZnPc significantly increased intrinsic tyrosine fluorescence of the peptide after 8 h of incubation in fibril-formation conditions. Importantly, cell culture experiments demonstrated that cZnPc did not exhibit any toxicity up to a concentration of 10 µM. Instead, it protected a neuronal cell line from Aβ1-42-induced toxicity. Thus, our results suggest that cZnPc can affect the aggregation process of Aβ1-42, rendering it non-toxic, which could be crucial for the therapy of Alzheimer's disease. [ABSTRACT FROM AUTHOR]

Human amylin (hIAPP) is found in the form of amyloid deposits within the pancreatic cells of nearly all patients diagnosed with type 2 diabetes mellitus (T2DM). However, rat amylin (rIAPP) and pramlintide - hIAPP analogs - are both non-toxic and non-amyloidogenic. Their primary sequences exhibit only slight variations in a few amino acid residues, primarily concentrated in the central region, spanning residues 20 to 29. This inspired us to study this fragment and investigate the impact on the aggregation properties of substituting residues within the central region of amylin and its analogs. Six fragments derived from amylin have undergone comprehensive testing against various metal ions by implementing a range of analytical techniques, including Nuclear Magnetic Resonance (NMR) spectroscopy, Thioflavin T (ThT) assays, Atomic Force Microscopy (AFM), and cytotoxicity assays. These methodologies serve to provide a thorough understanding of how the substitutions and interactions with metal ions impact the aggregation behavior of amylin and its analogs. [ABSTRACT FROM AUTHOR]

Interfering with the aggregation of the protein alpha-synuclein (aSyn) has been a topic of research for > 25 years, as this protein is found in pathognomonic protein aggregates in the brain of patients with Parkinson's disease and related synucleinopathies. This study aimed to characterize the adsorption of aSyn and the inhibition of aSyn fibril formation by nanocellulose (NC) and NC coated with gold atoms (NCCGAs) using by both in silico and laboratory approaches. First, using the HDOCK server and Ascalaph designer software we assessed the possible molecular interaction of partial aSyn (36–55) and full length aSyn (1–140) when exposed to NC and NCCGAs. We then used acid hydrolysis to synthesize NC and then it reacted with HAuCl4 to generate NCCGAs. The adsorption of aSyn by NC and NCCGAs was analyzed at 280 nm and the inhibition of aSyn fibril formation was assessed using Thioflavin T. By comparing the docking results, we found that NCCGAs have more and better adsorption to partial/full length aSyn than NC. Also, molecular dynamics simulations showed that adsorbed partial/full length aSyn display stable interactions and that this increases over time. Experimentally, the adsorption of aSyn and the inhibition of aSyn fibril formation were observed upon exposure to NC or NCCGAs. Although both NC and NCCGAs adsorbed aSyn, NCCGAs had a higher capability (P > 0.05). The same pattern was observed for the inhibition of aSyn fibril formation. [ABSTRACT FROM AUTHOR]

Milk whey proteins, which are derived from skim milk through membrane filtration, exhibit valuable functional properties when transformed into a fibrillar form. This conversion enhances their suitability for various applications, including thickening, gelling, emulsification, and foaming. However, reported fibrillation methods have longer heating times, which may not be economical for the dairy industry. To address these challenges, the current study was undertaken with the objective of reducing the time required for fibril formation. In this study, 2% milk whey protein isolate (mWPI) solution at pH 2 was heated with static and stirring heating conditions at 80 °C for 20 h to convert milk whey proteins into fibrils. Fibrils were observed using the thioflavin T value, transmission electron microscopy, Tricine SDS-PAGE, rheology, and protein oxidation. Results suggest that stirring heating conditions with 14 h heating time produced fibrils with good morphology compared to static heating, showing a 6 h reduction compared to an earlier reported 80 °C for 20 h heating time. Also, stirring heating produced a uniform and homogeneous fibril solution compared to the static heating method. Gentle stirring during heating can also help to scale up fibril production in an industrial setup. The fibrillation method with processing intervention will help to produce fibrils with enhanced functionality at the pilot and industrial scales. [ABSTRACT FROM AUTHOR]

Collagen is an important material for biomedical research, but using mammalian tissue-derived collagen carries the risk of zoonotic disease transmission. Marine organisms, such as farmed tilapia, have emerged as a safe alternative source of collagen for biomedical research. However, the tilapia collagen products for biomedical research are rare, and their biological functions remain largely unexamined. In this study, we characterized a commercial tilapia skin collagen using SDS-PAGE and fibril formation assays and evaluated its effects on skin fibroblast adhesion, proliferation, and migration, comparing it with commercial collagen from rat tails, porcine skin, and bovine skin. The results showed that tilapia skin collagen is a type I collagen, similar to rat tail collagen, and has a faster fibril formation rate and better-promoting effects on cell migration than porcine and bovine skin collagen. We also confirmed its application in a 3D culture for kidney cells' spherical cyst formation, fibroblast-induced gel contraction, and tumor spheroid interfacial invasion. Furthermore, we demonstrated that the freeze-dried tilapia skin collagen scaffold improved wound closure in a mouse excisional wound model, similar to commercial porcine or bovine collagen wound dressings. In conclusion, tilapia skin collagen is an ideal biomaterial for biomedical research. [ABSTRACT FROM AUTHOR]

This paper proposes a new paradigm for the biophysical concept of measuring the affinity of molecular complexes, based on a matrix representation of biological interactions and subsequent numerical analysis of the stability of this matrix. Our numerical criterion of stability (lg(cond(W))) correlates well with experimental values such as K d and IC 5 0 as well as with experimental data of aggregation kinetics in studies of amyloid peptides. The main goal of this work is to reduce the cost of biochemical experiments by obtaining preliminary information on the interaction of chemical compounds. The paper also presents our numerical calculations in comparison with a large amount of experimental data on the examples of binding of small chemical molecules gefitinib, erlotinib, imatinib, naquatinib, and CO-1686 with proteins, protein–peptide interactions of the Bcl-2 protein family, antibody–antigen CD20–rituximab, and aggregation of amyloid peptides. The description of the software package that implements the presented algorithm is given on the website: https://binomlabs.com/. [ABSTRACT FROM AUTHOR]

Acid-solubilized (ASC) and pepsin-solubilized collagen (PSC) extracted at 4 °C (ASC-4 and PSC-4), 12 °C (ASC-12 and PSC-12), and 20 °C (ASC-20 and PSC-20) from the skin of farmed pufferfish (Takifugu obscurus) was characterized by SDS-polyacrylamide gel electrophoresis (SDS-PAGE), Fourier-transform infrared spectroscopy (FTIR), and fibril-forming tests. The results indicate that extraction at 12 °C can effectively improve the extraction efficiency of natural collagen compared with extraction at 4 °C. However, extraction at 20 °C results in a decrease in molecular integrity, thus, inducing the resultant collagen to degrade or even lose fibril-forming ability. Transmission electron microscope (TEM) images revealed that ASC-4, PSC-4, ASC-12, and PSC-12 can assemble into fibrils with D-periodicities, and ASC-20 associated into molecular aggregates alongside partial D-banded fibrils, while no well-defined fibrils were observed in PSC-20. Scanning electron microscope (SEM) analysis confirmed the well-defined fibril morphologies of ASC-4, PSC-4, ASC-12, and PSC-12 with imino acid contents between 190.0 and 197.8 residues/1000 residues. The denaturation temperature of ASC-4, PSC-4, ASC-12 and PSC-12 was 30.0, 27.6, 25.9 and 22.7 °C, respectively. This study indicates that ASC and PSC extracted at 4 °C and 12 °C could be alternatives to terrestrial collagens for industrial applications. [ABSTRACT FROM AUTHOR]

Many proteins can undergo pathological conformational changes that result in the formation of amyloidogenic fibril structures. Various neurodegenerative diseases are associated with such pathological fibril formation of specific proteins. Transthyretin (TTR) is a tetrameric globular transport protein in the blood plasma that can dissociate, unfold, and form long and stable fibrils. Many TTR mutations are known that promote (TTR) amyloidosis and cause severe diseases. TTR amyloidosis has been studied extensively using biochemical methods and structures of various mutations in the globular form have been characterized. Recently, also the structure of a TTR fibril has been determined. In an effort to better understand why some mutations increase or decrease the tendency of amyloid formation, we have applied a combined molecular dynamics and continuum solvent approach to calculate the energetic influence of residue changes in the globular versus fibril form. For 29 out of 36 tested TTR single residue mutations, the approach correctly predicts the increased or decreased tendency for amyloidosis allowing us also to elucidate the origins of the tendency. We find that indeed the destabilization of the globular monomer or changes in dimer and tetramer stability due to mutation has a dominant influence on the amyloidogenic tendency. The continuum solvent model predicts a significantly more favorable mean energy per residue of the fibril form compared to the globular form. This effect is only slightly modulated by single‐point mutations preserving the energetic preference for fibril formation upon protein unfolding. It explains why no correlation between experimental amyloidosis and calculated change in fibril stability was observed. [ABSTRACT FROM AUTHOR]

The study of protein aggregation, and amyloidosis in particular, has gained considerable interest in recent times. Several neurodegenerative diseases, such as Alzheimer's (AD) and Parkinson's (PD) show a characteristic buildup of proteinaceous aggregates in several organs, especially the brain. Despite the enormous upsurge in research articles in this arena, it would not be incorrect to say that we still lack a crystal-clear idea surrounding these notorious aggregates. In this review, we attempt to present a holistic picture on protein aggregation and amyloids in particular. Using a chronological order of discoveries, we present the case of amyloids right from the onset of their discovery, various biophysical techniques, including analysis of the structure, the mechanisms and kinetics of the formation of amyloids. We have discussed important questions on whether aggregation and amyloidosis are restricted to a subset of specific proteins or more broadly influenced by the biophysiochemical and cellular environment. The therapeutic strategies and the significant failure rate of drugs in clinical trials pertaining to these neurodegenerative diseases have been also discussed at length. At a time when the COVID-19 pandemic has hit the globe hard, the review also discusses the plausibility of the far-reaching consequences posed by the virus, such as triggering early onset of amyloidosis. Finally, the application(s) of amyloids as useful biomaterials has also been discussed briefly in this review. [ABSTRACT FROM AUTHOR]

Amyloid-β peptide (Aβ) aggregates are known to be correlated with pathological neurodegenerative diseases. The fibril formation process of such peptides in solution is influenced by several factors, such as the ionic strength of the buffer, concentration, pH, and presence of other molecules, just to mention a few. In this paper, we report a detailed analysis of in vitro Aβ42 fibril formation in the presence of cortisol at different relative concentrations. The thioflavin T fluorescence assay allowed us to monitor the fibril formation kinetics, while a morphological characterization of the aggregates was obtained by atomic force microscopy. Moreover, infrared absorption spectroscopy was exploited to investigate the secondary structure changes along the fibril formation path. Molecular dynamics calculations allowed us to understand the intermolecular interactions with cortisol. The combined results demonstrated the influence of cortisol on the fibril formation process: indeed, at cortisol-Aβ42 concentration ratio (ρ) close to 0.1 a faster organization of Aβ42 fragments into fibrils is promoted, while for ρ = 1 the formation of fibrils is completely inhibited. [ABSTRACT FROM AUTHOR]

Objectives: The heterogeneity of Amyloid‐beta (Aβ) plaque load in patients with Alzheimer's disease (AD) has puzzled neuropathology. Since brain Aβ plaque load does not correlate with cognitive decline, neurotoxic soluble Aβ oligomers have been championed as disease‐causing agents in early AD. So far, investigating molecular interactions between soluble oligomeric Aβ and insoluble Aβ in vivo has been difficult because of the abundance of Aβ oligomer species and the kinetic equilibrium in which they coexist. Here, we investigated whether Aβ plaque heterogeneity relates to interactions of different Aβ conformers. Materials and Methods: We took advantage of transgenic mice that generate exclusively Aβ dimers (tgDimer mice) but do not develop Aβ plaques or neuroinflammation during their lifetime, crossed them to the transgenic CRND8 mice that develop plaques after 90 days and measured Aβ plaque load using immunohistochemical and biochemical assays. Furthermore, we performed in vitro thioflavin T (ThT) aggregation assays titrating synthetic Aβ42‐S8C dimers into fibril‐forming synthetic Aβ42. Results: We observed a lower number of Aβ plaques in the brain of double transgenic mice compared to tgCRND8 mice alone while the average plaque size remained unaltered. Corroborating these in vivo findings, synthetic Aβ‐S8C dimers inhibited fibril formation of wild‐type Aβ also in vitro, seen by an increased half‐time in the ThT assay. Conclusions: Our study indicates that Aβ dimers directly interfere with Aβ fibril formation in vivo and in vitro. The variable interaction of Aβ dimers with insoluble Aβ seeds could thus contribute to the heterogeneity of Aβ plaque load in AD patients. [ABSTRACT FROM AUTHOR]

The nucleation of Alzheimer-associated Aβ peptide monomers can be catalyzed by preexisting Aβ fibrils. This leads to autocatalytic amplification of aggregate mass and underlies self-replication and generation of toxic oligomers associated with several neurodegenerative diseases. However, the nature of the interactions between the monomeric species and the fibrils during this key process, and indeed the ultrastructural localization of the interaction sites have remained elusive. Here we used NMR and optical spectroscopy to identify conditions that enable the capture of transient species during the aggregation and secondary nucleation of the Aβ42 peptide. Cryo-electron microscopy (cryo-EM) images show that new aggregates protrude from the entire length of the progenitor fibril. These protrusions are morphologically distinct from the wellordered fibrils dominating at the end of the aggregation process. The data provide direct evidence that self-replication through secondary nucleation occurs along the sides of fibrils, which become heavily decorated under the current solution conditions (14 μM Aβ42, 20 mM sodium phosphate, 200 μM EDTA, pH 6.8). [ABSTRACT FROM AUTHOR]

Abstract: The abnormal aggregation and deposition of human islet amyloid polypeptide (hIAPP) are implicated in the pathogeny of type 2 diabetes mellitus (T2DM). Many aromatic ring-containing Ru complexes inhibit the aggregation of hIAPP. A new Ru complex Ru(bipy)(met)2·3H2O (1), where bipy is 2,2ʹ-bipyridine and met is methionine, was synthesized and employed to resist the fibril formation of hIAPP and to promote the biocompatibility of metal complexes. Two polypyridyl Ru complexes, namely [Ru(bipy)3]Cl2(2) and Ru(bipy)2Cl2(3), were used for comparison. Results reveal that the three Ru complexes can inhibit hIAPP aggregation and depolymerize mature hIAPP fibrils. Interaction studies show that Ru complexes bind to hIAPP through metal coordination, hydrophobic interaction, and other intermolecular forces. The binding of the three compounds is spontaneous and exothermic. The compounds also rescue peptide-induced cytotoxicity to some extent. Similar to 3, the novel methionine-Ru complex 1 exhibits an enhanced inhibitory effect and binding affinity to hIAPP possibly because of the smaller steric hindrance and more profitable molecular configuration of 1 than those of 2. The newly designed amino acid-Ru complex may provide new insights into the treatment of T2DM and related amyloidosis diseases.Graphical abstract: Methionine-Ru complex effectively impedes the fibril formation of human islet amyloid polypeptide. [ABSTRACT FROM AUTHOR]

Hydrophobins are fungal proteins that can selfassemble into amphiphilic films at hydrophobic-hydrophilic interfaces. Class I hydrophobin aggregates resemble amyloid fibrils, sharing some features with them. Here, five site-directed mutants of Vmh2, a member of basidiomycota class I hydrophobins, were designed and characterized to elucidate the molecular determinants playing a key role in class I hydrophobin self-assembly. The mechanism of fibril formation proposed for Vmh2 foresees that the triggering event is the destabilization of a specific loop (L1), leading to the formation of a β-hairpin, which in turn generates the β-spine of the amyloid fibril. [ABSTRACT FROM AUTHOR]

Self-assembled environment of collagen is one of the important factors for improving and regulating the properties of collagen-based biomaterials. This study aimed to investigate the effect of ionic liquids (ILs) on the fibril-formation and gel properties of grass carp (Ctenopharyngodon idellus) skin collagen. Fibrillogenic kinetics analysis showed that the collagen self-assembly can be suppressed by the introduction of ILs, and the inhibitory effect is influenced by concentration and types of ILs. Scanning electron microscopy test indicated that the assembled collagen fibrils in the presence of ILs had bigger diameters than that in the conventional buffer. Differential scanning calorimetry analysis revealed that the thermal stability of collagen fibrils can be significantly increased when self-assembly is performed in the presence of ILs. Moreover, the introduction of ILs enhanced the mechanical strength of collagen gels. Finding from this work provides a new idea for improving the performance of fish-sourced collagen biomaterials. [ABSTRACT FROM AUTHOR]

Amyloidogenesis is associated with more than 30 diseases, but the molecular mechanisms involved in cell toxicity and fibril formation remain largely unknown. The inherent tendency of amyloid‐forming proteins to aggregate renders expression, purification, and experimental studies challenging. NT* is a solubility tag derived from a spider silk protein that was recently introduced for the production of several aggregation‐prone peptides and proteins at high yields. Herein, we investigate whether fusion to NT* can prevent amyloid fibril formation and enable controlled aggregation for experimental studies. As an example of an amyloidogenic protein, we chose the de novo‐designed polypeptide β17. The fusion protein NT*‐β17 was recombinantly expressed in Escherichia coli to produce high amounts of soluble and mostly monomeric protein. Structural analysis showed that β17 is kept in a largely unstructured conformation in fusion with NT*. After proteolytic release, β17 adopts a β‐sheet conformation in a pH‐ and salt‐dependent manner and assembles into amyloid‐like fibrils. The ability of NT* to prevent premature aggregation and to enable structural studies of prefibrillar states may facilitate investigation of proteins involved in amyloid diseases. [ABSTRACT FROM AUTHOR]

The effect of carboxymethylcellulose (CMC) on the fibril formation of collagen in vitro was studied by turbidity measurements and atomic force microscopy (AFM). The kinetics curves of fibril formation indicated that the rate of collagen fibrillogenesis was decreased with the addition of CMC, meanwhile the final turbidity was obviously increased as the CMC/collagen ratio reached 30%. The AFM images of collagen-CMC solutions showed that the number of nucleation sites of collagen fibrillogenesis was significantly increased with the presence of CMC, while the diameter of immature collagen fibrils was obviously decreased. Moreover, the thermal stability of collagen fibril hydrogels was obviously improved with the presence of CMC. In addition, the morphologies of collagen fibrils observed by AFM revealed that the adjacent fibril segments or fibrils were intertwisted and even tightly merged, probably due to the hydrogen bonding and molecular entanglement interactions between CMC and collagen molecules. [ABSTRACT FROM AUTHOR]

Acid-solubilized collagen (ASC) and pepsin-solubilized collagen (PSC) from golden pompano skins were extracted and characterized. The molecular weight of ASC was about 130 kDa for α1and 115 kDa for α2, which were slightly higher than those of PSC. Similar amino acid composition and Fourier transform infrared (FTIR) spectra were observed in both collagens, but slight differences were found in the peptide maps of collagen digested by V8 protease and trypsin. The denaturation temperatures (Tds) of ASC and PSC calculated from the reduced viscosity were 31.8 and 30.0°C, while the transition temperature (Tm) of ASC and PSC analyzed by DSC were 33.0 and 32.0°C, respectively. ASC has a lag phase, a growth phase, and a plateau phase in the turbidity–time curve, while PSC does not have similar phenomenon. It was found that the fibril gel of ASC could be formed at 25°C, leading to improved thermal stability. [ABSTRACT FROM PUBLISHER]

Purpose The purpose of this article is to discuss the tribological behavior of polytetrafluoroethylene (PTFE) and property changes imposed by wear tests.Design/methodology/approach Long-duration dry wear tests were carried out in a sliding bearing on shaft tribometer. Differential Scanning Calorimetry (DSC) and Fourier Transformed Infrared Spectroscopy (FTIR) analyses were performed in the PTFE in its original condition and after the tests.Findings The wear products merged in multilayer films and were expelled out of the test sequence. Through DSC and FTIR analyses in the polymeric material, before and after tests, it was possible to verify an increase of the crystallinity degree of PTFE, as well as absence of crystalline fusion of the material. The wear products presented changes in the infrared spectra, which suggests the occurrence of some bonds of hydrogen and oxygen.Originality/value It was verified on correlation that fibril mechanism, which occurred during PTFE wear, and its crystallinity degree increase. Also, analysis of PTFE wear products showed CO and CH bonds, which were imposed by wear test. [ABSTRACT FROM AUTHOR]

BACKGROUND The fish swim bladder is considered as a potential source of realistic collagen. Currently, processing of the Indian major carp rohu ( Labeo rohita) generates an enormous quantity of non-edible by-products, including swim bladders, which are discarded as waste with no commercial value. In the present study, collagen was prepared from rohu swim bladder and its physicochemical and fibril-forming capacities were assessed. RESULTS The collagen isolated from rohu swim bladder was characterised as type I, containing α1 and α2 chains with triple helical structure by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, fourier transform infrared spectroscopy and amino acid analysis. The extracted collagen denaturation temperature was found to be 42.16 °C by differential scanning calorimetry analysis and also exhibited a high solubility in the presence of low NaCl concentrations (0-0.6 mol L−1). The extracted collagen exhibited a high fibril-formation capacity at a NaCl concentration of 1.5 mol L−1. Examination of the microstructure of collagen by scanning electron microscopy ( SEM) showed a porous, sheet-like film and a multilayered structure. The fibril formation capacity of collagen was also confirmed using SEM analysis. CONCLUSION The rohu swim bladder type I collagen was successfully extracted using an enzymatic method with a yield of 465.2 g kg−1 (dry weight basis) and was characterised as a well maintained triple helical structure. The extracted collagen exhibited a high fibril-forming ability. The results of the present study confirm that utilisation of rohu swim bladder will open up a new avenue for the better disposal of by-products and also help to minimise environmental pollution issues. © 2016 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

We investigated the potential of collagen-genipin sols as biomaterials for treating artificial ulcers following endoscopic submucosal dissection. Collagen sol viscosity increased with condensation, allowing retention on tilted ulcers before gelation and resulting in collagen gel deposition on whole ulcers. The 1.44% collagen sols containing genipin as a crosslinker retained sol fluidity at 23°C for >20 min, facilitating endoscopic use. Collagen sols formed gel depositions on artificial ulcers in response to body temperature, and high temperature responsiveness of gelation because of increased neutral phosphate buffer concentration allowed for thick gel deposition on tilted ulcers. Finally, histological observations showed infiltration of gels into submucosal layers. Taken together, the present data show that genipin-induced crosslinking significantly improves the mechanical properties of collagen gels even at low genipin concentrations of 0.2-1 mM, warranting the use of in situ gelling collagen-genipin sols for endoscopic treatments of gastrointestinal ulcers. [ABSTRACT FROM AUTHOR]

In pigment cells, melanin synthesis takes place in specialized organelles, called melanosomes. The biogenesis and maturation of melanosomes is initiated by an unpigmented step that takes place prior to the initiation of melanin synthesis and leads to the formation of luminal fibrils deriving from the pigment cell-specific pre-melanosomal protein (PMEL). In the lumen of melanosomes, PMEL fibrils optimize sequestration and condensation of the pigment melanin. Interestingly, PMEL fibrils have been described to adopt a typical amyloid-like structure. In contrast to pathological amyloids often associated with neurodegenerative diseases, PMEL fibrils represent an emergent category of physiological amyloids due to their beneficial cellular functions. The formation of PMEL fibrils within melanosomes is tightly regulated by diverse mechanisms, such as PMEL traffic, cleavage and sorting. These mechanisms revealed increasing analogies between the formation of physiological PMEL fibrils and pathological amyloid fibrils. In this review we summarize the known mechanisms of PMEL fibrillation and discuss how the recent understanding of physiological PMEL amyloid formation may help to shed light on processes involved in pathological amyloid formation. [ABSTRACT FROM AUTHOR]

The effect of γ-poly(glutamic acid) (γ-PGA) on the self-assembly of collagen was studied. Under physiological conditions, the kinetic curves for fibril formation showed that the turbidity of collagen/γ-PGA blends at 313 nm was increased with the addition of γ-PGA. Furthermore, it was shown using both field-emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM) that fibrils with a larger diameter were obtained following the addition of γ-PGA, probably due to the electrostatic and hydrogen bond interactions between collagen and γ-PGA, which promoted the lateral association of collagen molecules. In addition, both the thermal stability and viscoelastic properties of the hybrid hydrogels, which were evaluated by differential scanning calorimetry and rheological measurements, respectively, were improved by the addition of γ-PGA. [ABSTRACT FROM PUBLISHER]

β-synuclein (βS) is a homologue of α-synuclein (αS), the major protein component of Lewy bodies in patients with Parkinson's disease. In contrast to αS, βS does not form fibrils, mitigates αS toxicity in vivo and inhibits αS fibril formation in vitro. Previously a missense mutation of βS, P123H, was identified in patients with Dementia with Lewy Body disease. The single P123H mutation at the C-terminus of βS is able to convert βS from a nontoxic to a toxic protein that is also able to accelerate formation of inclusions when it is in the presence of αS in vivo. To elucidate the molecular mechanisms of these processes, we compare the conformational properties of the monomer forms of αS, βS and P123H-βS, and the effects on fibril formation of coincubation of αS with βS, and with P123H-βS. NMR residual dipolar couplings and secondary structure propensities show that the P123H mutation of βS renders it more flexible C-terminal to the mutation site and more αS-like. In vitro Thioflavin T fluorescence experiments show that P123H-βS accelerates αS fibril formation upon coincubation, αS opposed to wild type βS that acts αS an inhibitor of αS aggregation. When P123H-βS becomes more αS-like it is unable to perform the protective function of βS, which suggests that the extended polyproline II motif of βS in the C-terminus is critical to its nontoxic nature and to inhibition of αS upon coincubation. These studies may provide a basis for understanding which regions to target for therapeutic intervention in Parkinson's disease. [ABSTRACT FROM AUTHOR]

The origins of formation of an intermediate state involved in amyloid formation and ways to prevent it are illustrated with the example of the Formin binding protein 28 (FBP28) WW domain, which folds with biphasic kinetics. Molecular dynamics of protein folding trajectories are used to examine local and global motions and the time depenadence of formation of contacts between Cαs and Cßs of selected pairs of residues. Focus is placed on the WT FBP28 WW domain and its six mutants (L26D, L26E, L26W, E27Y, T29D, and T29Y), which have structures that are determined by high-resolution NMR spectroscopy. The origins of formation of an intermediate state are elucidated, viz. as formation of hairpin 1 by a hydrophobic collapse mechanism causing significant delay of formation of both hairpins, especially hairpin 2, which facilitates the emergence of an intermediate state. It seems that three-state folding is a major folding scenario for all six mutants and WT. Additionally, two-state and downhill folding scenarios were identified in ~15% of the folding trajectories for L26D and L26W, in which both hairpins are formed by the Matheson-Scheraga mechanism much faster than in three-state folding. These results indicate that formation of hairpins connecting two antiparallel ß-strands determines overall folding. The correlations between the local and global motions identified for all folding trajectories lead to the identification of the residues making the main contributions in the formation of the intermediate state. The presented findings may provide an understanding of protein folding intermediates in general and lead to a procedure for their prevention. [ABSTRACT FROM AUTHOR]

The disease oculopharyngeal muscular dystrophy is caused by alanine codon trinucleotide expansions in the N-terminal segment of the nuclear poly(A) binding protein PABPN1. As histochemical features of the disease, intranuclear inclusions of PABPN1 have been reported. Whereas the purified N-terminal domain of PABPN1 forms fibrils in an alanine-dependent way, fibril formation of the full-length protein occurs also in the absence of alanines. Here, we addressed the question whether the stability of the RNP domain or domain swapping within the RNP domain may add to fibril formation. A variant of full-length PABPN1 with a stabilizing disulfide bond at position 185/201 in the RNP domain fibrillized in a redox-sensitive manner suggesting that the integrity of the RNP domain may contribute to fibril formation. Thermodynamic analysis of the isolated wild-type and the disulfide-linked RNP domain showed two state unfolding/refolding characteristics without detectable intermediates. Quantification of the thermodynamic stability of the mutant RNP domain pointed to an inverse correlation between fibril formation of full-length PABPN1 and the stability of the RNP domain. [ABSTRACT FROM AUTHOR]

We studied the effect of fibril formation of fish scale collagen on the osteoblastic differentiation of human mesenchymal stem cells (hMSCs). We found that hMSCs adhered easily to tilapia scale collagen, which remarkably accelerated the early stage of osteoblastic differentiation in hMSCs during in vitro cell culture. Osteoblastic markers such as ALP activity, osteopontin, and bone morphogenetic protein 2 were markedly upregulated when the hMSCs were cultured on a tilapia collagen surface, especially in the early osteoblastic differentiation stage. We hypothesized that this phenomenon occurs due to specific fibril formation of tilapia collagen. Thus, we examined the time course of collagen fibril formation using high-speed atomic force microscopy. Moreover, to elucidate the effect of the orientation of fibril formation on the differentiation of hMSCs, we measured ALP activity of hMSCs cultured on two types of tilapia scale collagen membranes with different degrees of fibril formation. The ALP activity in hMSCs cultured on a fibrous collagen membrane was significantly higher than on a non-fibrous collagen membrane even before adding osteoblastic differentiation medium. These results showed that the degree of the fibril formation of tilapia collagen was essential for the osteoblastic differentiation of hMSCs. © 2014 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 103A: 2531-2539, 2015. [ABSTRACT FROM AUTHOR]

Amyloid β (Aβ), a 39-42 amino acid peptide derived from amyloid precursor protein, is deposited as fibrils in Alzheimer's disease brains, and is considered to play a major role in the pathogenesis of the disease. We have investigated the effects of a water-soluble Zn-phthalocyanine, ZnPc( COONa)8, a macrocyclic compound with near-infrared optical properties, on Aβ fibril formation in vitro. A thioflavin T fluorescence assay showed that ZnPc( COONa)8 significantly inhibited Aβ fibril formation, increasing the lag time and dose-dependently decreasing the plateau level of fibril formation. Moreover, it destabilized pre-formed Aβ fibrils, resulting in an increase in low-molecular-weight species. After fibril formation in the presence of ZnPc( COONa)8, immunoprecipitation of Aβ1-42 using Aβ-specific antibody followed by near-infrared scanning demonstrated binding of ZnPc( COONa)8 to Aβ1-42. A study using the hydrophobic fluorescent probe 8-anilino-1-naphthalenesulfonic acid showed that ZnPc( COONa)8 decreased the hydrophobicity during Aβ1-42 fibril formation. CD spectroscopy showed an increase in the α helix structure and a decrease in the β sheet structure of Aβ1-40 in fibril-forming buffer containing ZnPc( COONa)8. SDS/PAGE and a dot-blot immunoassay showed that ZnPc( COONa)8 delayed the disappearance of low-molecular-weight species and the appearance of higher-molecular-weight oligomeric species of Aβ1-42. A cell viability assay showed that ZnPc( COONa)8 was not toxic to a neuronal cell line (A1), but instead protected A1 cells against Aβ1-42-induced toxicity. Overall, our results indicate that ZnPc( COONa)8 binds to Aβ and decreases the hydrophobicity, and this change is unfavorable for Aβ oligomerization and fibril formation. [ABSTRACT FROM AUTHOR]

Tufted astrocytes ( TAs) in progressive supranuclear palsy ( PSP) and astrocytic plaques ( APs) in corticobasal degeneration ( CBD) have been regarded as the pathological hallmarks of major sporadic 4-repeat tauopathies. To better define the astrocytic inclusions in PSP and CBD and to outline the pathological features of each disease, we reviewed 95 PSP cases and 30 CBD cases that were confirmed at autopsy. TAs exhibit a radial arrangement of thin, long, branching accumulated tau protein from the cytoplasm to the proximal processes of astrocytes. APs show a corona-like arrangement of tau aggregates in the distal portions of astrocytic processes and are composed of fuzzy, short processes. Immunoelectron microscopic examination using quantum dot nanocrystals revealed filamentous tau accumulation of APs located in the immediate vicinity of the synaptic structures, which suggested synaptic dysfunction by APs. The pathological subtypes of PSP and CBD have been proposed to ensure that the clinical phenotypes are in accordance with the pathological distribution and degenerative changes. The pathological features of PSP are divided into 3 representative subtypes: typical PSP type, pallido-nigro-luysian type ( PNL type), and CBD-like type. CBD is divided into three pathological subtypes: typical CBD type, basal ganglia- predominant type, and PSP-like type. TAs are found exclusively in PSP, while APs are exclusive to CBD, regardless of the pathological subtypes, although some morphological variations exist, especially with regard to TAs. The overlap of the pathological distribution of PSP and CBD makes their clinical diagnosis complicated, although the presence of TAs and APs differentiate these two diseases. The characteristics of tau accumulation in both neurons and glia suggest a different underlying mechanism with regard to the sites of tau aggregation and fibril formation between PSP and CBD: proximal-dominant aggregation of TAs and formation of filamentous NFTs in PSP in contrast to the distal-dominant aggregation of APs and formation of less filamentous pretangles in CBD. [ABSTRACT FROM AUTHOR]

Several disease-linked mutations of apolipoprotein A-I, the major protein in high-density lipoprotein (HDL), are known to be amyloidogenic, and the fibrils often contain N-terminal fragments of the protein. Here, we present a combined computational and experimental study of the fibril-associated disordered 1-93 fragment of this protein, in wild-type and mutated (G26R, S36A, K40L, W50R) forms. In atomic-level Monte Carlo simulations of the free monomer, validated by circular dichroism spectroscopy, we observe changes in the position-dependent β-strand probability induced by mutations. We find that these conformational shifts match well with the effects of these mutations in thioflavin T fluorescence and transmission electron microscopy experiments. Together, our results point to molecular mechanisms that may have a key role in disease-linked aggregation of apolipoprotein A-I. [ABSTRACT FROM AUTHOR]

Amyloid peptides have great potential as building blocks in the creation of functional nanowires due to their natural ability to self-assemble into nanofibrillar structures and because they can be easily modified with various functional groups. However, significant modifications of an amyloid peptide generally alter its self-assembly property, making it difficult to construct functionalized fibrils with a desired structure and function. In this study, a very effective method to overcome this problem is demonstrated by using our structure-controllable amyloid peptides (SCAPs) terminated with a three-amino-acid-residue cap. The method consists on mixing two or more structurally related amyloid peptides with a fraction of modified SCAPs which co-assemble into a fibril. This SCAP-mixing method provides remarkable control over the self-assembly process both on the small oligomers level and the macroscopic fibrils level. Furthermore, it is shown that the modified peptides imbedded in the resulting fibril can subsequently be functionalized to generate nanowires with the desired properties, highlighting the importance of this SCAP method for nanotechnology applications. [ABSTRACT FROM AUTHOR]

The formation of amyloid-like fibrils, which polymerize from various soluble proteins under physiological and acidic conditions, causes a wide range of protein-folding diseases, such as Alzheimer’s disease and Parkinson’s disease. Fibril assembly in in vitro solutions containing nitric oxide, a free radical that functions as an important signalling molecule involved in numerous physiological and pathological processes, has not been reported. Here, we investigated the protein assembly that occur in thyroglobulin under mildly acidic conditions in the presence of nitric oxide. Solution studies, size exclusion chromatography, dynamic light scattering and analytical ultracentrifugation, demonstrated the size changes of thyroglobulin oligomers after nitric oxide treatment. Following electron microscopic analysis visualized their structural changes and revealed that the molecules can morphologically form polymerized fibril assemblies with a length of 2–5 μm and width 10–100 nm. Taken together, these results provide suggestive evidence for the propensity of forming polymerized thyroglobulin fibrils implying their presence in thyroid cells, which may be related to the onset or progression of thyroid diseases. [ABSTRACT FROM AUTHOR]

Islet amyloid polypeptide (IAPP) fibrillation has been commonly associated with the exacerbation of type 2 diabetes prognosis. Consequently, inhibition of IAPP fibrillation to minimize β-cell cytotoxicity is an important approach towards β-cell preservation and type 2 diabetes management. In this study, we identified three tetrapeptides, TNGQ, MANT, and YMSV, that inhibited IAPP fibrillation. Using thioflavin T (ThT) fluorescence assay, circular dichroism (CD) spectroscopy, dynamic light scattering (DLS), and molecular docking, we evaluated the potential anti-fibrillation mechanism of the tetrapeptides. ThT fluorescence kinetics and microscopy as well as transmission electron microscopy showed that TNGQ was the most effective inhibitor based on the absence of normal IAPP fibrillar morphology. CD spectroscopy showed that TNGQ maintained the α-helical conformation of monomeric IAPP, while DLS confirmed the presence of varying fibrillation species. Molecular docking showed that TNGQ and MANT interact with monomeric IAPP mainly by hydrogen bonding and electrostatic interaction, with TNGQ binding at IAPP surface compared to YMSV, which had the highest docking score, but interact mainly through hydrophobic interaction in IAPP core. The highly polar TNGQ was the most active and appeared to inhibit IAPP fibrillation by disaggregation of preformed IAPP fibrils. These findings indicate the potential of TNGQ in the development of peptide-based anti-fibrillation and antidiabetic nutraceuticals. [ABSTRACT FROM AUTHOR]

In vitro amyloid formation has been suggested to be a common property of any polypeptide chain depending on particular environmental conditions although in vivo amyloid fibril formation can be promoted by point mutations or triplet expansions. Here, we explored the influence of agitation on fibril formation of amyloidogenic alanine segments fused to Cold Shock Protein B (CspB) of Bacillus subtilis. While without agitation fibril formation was clearly dependent on the presence of an amyloidogenic alanine segment, fibril formation was independent of the amyloidogenic segment under agitation. Agitation even led to fibrillation of native CspB lacking the amyloidogenic segment. Furthermore, agitation not only influenced the kinetics of fibril formation, but also resulted in completely different fibril morphologies. These results indicate that experimental conditions can alter the region that undergoes a conformational change during in vitro fibrillation. Moreover, the data show that deductions from in vitro assays on in vivo fibril formation mechanisms are afflicted with a certain degree of uncertainty and therefore need to be cautiously discussed. [ABSTRACT FROM AUTHOR]

Fibril formation by collagen from piglet skin was studied at temperatures of 28-39°C. Collagen fibrils obtained in this temperature range differ in the degree of ordering. Electron microscopy shows that fibrils of minimal diameter are formed at physiological pH, ionic strength (PBS), and temperature. The greater diameter of fibrils formed at 34.5°C is due to enhanced collagen hydration. Fibril diameter at 38.5°C is increased because of cooperative unfolding of the triple helix and weaker binding between collagen molecules. The optimal temperature for fibrillogenesis appears to be 36.5°C, and such fibrils are most similar to those observed in vivo. [ABSTRACT FROM AUTHOR]

The protein NA14 is a key adaptor protein mediating the intermolecular interactions of microtubules and Spastin. To gain insight into its structure and function, we have expressed, purified and characterized human NA14 and some variants. NA14 is rather insoluble and tends to oligomerize and form fibrils. Successive mutation of the three Cys and two potentially exposed Leu residues (83 and 93) yielded a water-soluble quintuple variant, named 3CS-2LR. NA14 and its variants have a high helical content as determined by circular dichroism (CD). Based on nuclear magnetic resonance data of the quintuple mutant and the wild-type (wt) protein in the presence of dodecylphosphocholine micelles, the N-(M1-N13) and C-termini (K105-S119) were found to lack preferred structure. The remaining residues (14–104) participate in NA14 self-association, probably by forming a parallel coiled-coil structure. We hypothesize that Leu 83 and Leu 93 mediate interactions among NA14, Spastin and microtubules. We have also examined urea and thermal denaturation of the quintuple and other NA14 variants at different pH values by CD. The pH dependence of the conformational stability and the elevated native-state pKa determined for the two conserved Tyr allow us to propose that the NA14 structure may be stabilized by two Glu-COO− ||| HO-Tyr H-bonds, highly conserved in NA14-like proteins in other species. [ABSTRACT FROM AUTHOR]

The (1-42) β-amyloid peptide is a main component of the plaques found in the brain of patients suffering from the Alzheimer's disease. As the single substitution of Glu for Gln at position 22 of this peptide seems to be responsible for the manifestation of the more severe amyloidosis (Dutch-type), we decided to evaluate the aggregation characteristics of peptide analogs interchanging Glu and Gln residues at positions 22 and also 15 in the minor (12-24) (VHHQKLVFFAEDV) fragment. The Q15Q22, E15E22, E15Q22 and the native Q15E22 were compared to the (1-42) β-amyloid peptide in terms of fibril or structured aggregates formation propensity. In contrast to a rather similar solubility data measured of all analogs, fluorescence and light scattering methods indicated that only Q15E22 and Q15Q22 displayed relevant fibril formation capacity. Conversely, E15E22 and E15Q22 were not capable of the formation of this type of structure thus suggesting a key role for the Q residue in the unique aggregation characteristic of the β-amyloid peptide. [ABSTRACT FROM AUTHOR]

A familial form of Alzheimer disease recently was described in a kindred in Osaka, Japan. This kindred possesses an amyloid β-protein (Aβ) precursor mutation within the Aβ coding region that results in the deletion of Glu22 (ΔE22). We report here results of studies of [[ΔE22]]Aβ40 and [[ΔE22]]Aβ42 that sought to elucidate the conformational dynamics, oligomerization behavior, fibril formation kinetics, fibril morphology, and fibril stability of these mutant peptides. Both [[ΔE22]]Aβ peptides had extraordinary β-sheet formation propensities. The [[ΔE22]]Aβ40 mutant formed β-sheet secondary structure elements ≈≈400-fold faster. Studies of β-sheet stability in the presence of fluorinated alcohol cosolvents or high pH revealed that the ΔE22 mutation substantially increased stability, producing a rank order of [[ΔE22]]Aβ42 ≫≫ Aβ42 > [[ΔE22]]Aβ40 > Aβ40. The mutation facilitated formation of oligomers by [[ΔE22]]Aβ42 (dodecamers and octadecamers) that were not observed with Aβ42. Both Aβ40 and Aβ42 peptides formed nebulous globular and small string-like structures immediately upon solvation from lyophilizates, whereas short protofibrillar and fibrillar structures were evident immediately in the ΔE22 samples. Determination of the critical concentration for fibril formation for the [[ΔE22]]Aβ peptides showed it to be ≈≈1/2 that of the wild type homologues, demonstrating that the mutations causes a modest increase in fibril stability. The magnitude of this increase, when considered in the context of the extraordinary increase in β-sheet propensity for the ΔE22 peptides, suggests that the primary biophysical effect of the mutation is to accelerate conformational changes in the peptide monomer that facilitate oligomerization and higher-order assembly. [ABSTRACT FROM AUTHOR]

Abstract: Several natural polyphenols with potent inhibitory effects on amyloid fibril formation have been reported. Herein, we studied modulation of transthyretin (TTR) fibrillogenesis by selected polyphenols. We demonstrate that both curcumin and nordihydroguaiaretic acid (NDGA) bind to TTR and stabilize the TTR tetramer. However, while NDGA slightly reduced TTR aggregation, curcumin strongly suppressed TTR amyloid fibril formation by generating small “off-pathway” oligomers and EGCG maintained most of the protein in a non-aggregated soluble form. This indicates alternative mechanisms of action supported by the occurrence of different non-toxic intermediates. Moreover, EGCG and curcumin efficiently disaggregated pre-formed TTR amyloid fibrils. Our studies, together with the safe toxicological profile of these phytochemicals may guide a novel pharmacotherapy for TTR-related amyloidosis targeting different steps in fibrillogenesis. Structured summary of protein interactions: TTR binds to TTR by comigration in gel electrophoresis (View interaction) TTR binds to TTR by dynamic light scattering (View interaction) TTR binds to TTR by electron microscopy (View interaction) [Copyright &y& Elsevier]

The effect of additives like curcumin and surfactants on the self-assembly of collagen from a simple 2-dimensional system of Langmuir films of the protein at air/solution interface has been attempted in this study using quartz crystal microbalance (QCM) and dynamic surface tensiometer. Though pure curcumin is not surface active, a synergistic effect of collagen with curcumin seems to lead to enhanced surface activity in the protein. In general, the presence of additives, increases the surface activity of collagen even for the lowest concentration and the largest change in surface activity is seen for collagen with sodium dodecyl sulfate (SDS). The results suggest interplay between the unexposed hydrophobic groups, and the opening out and solvation of the more charged or polar groups at the surface leading to aggregation followed by self-assembly. Modulation of aggregation at interface in collagen due to these additives may be an approach that could be explored for possible applications in bio-materials and for delivery of protein-drug complexes. [ABSTRACT FROM AUTHOR]

We report here the detailed characterisation of a non-naturally occurring variant of human lysozyme, I59T, which possesses a destabilising point mutation at the interface of the α- and β-domains. Although more stable in its native structure than the naturally occurring variants that give rise to a familial form of systemic amyloidosis, I59T possesses many attributes that are similar to these disease-associated species. In particular, under physiologically relevant conditions, I59T populates transiently an intermediate in which a region of the structure unfolds cooperatively; this loss of global cooperativity has been suggested to be a critical feature underlying the amyloidogenic nature of the disease-associated lysozyme variants. In the present study, we have utilised this variant to provide direct evidence for the generic nature of the conformational transition that precedes the ready formation of the fibrils responsible for lysozyme-associated amyloid disease. This non-natural variant can be expressed at higher levels than the natural amyloidogenic variants, enabling, for example, singly isotopically labelled protein to be generated much more easily for detailed structural studies by multidimensional NMR spectroscopy. Moreover, we demonstrate that the I59T variant can readily form fibrils in vitro, similar in nature to those of the amyloidogenic I56T variant, under significantly milder conditions than are needed for the wild-type protein. [ABSTRACT FROM PUBLISHER]

Abstract: Small heat shock proteins (sHsps) associate with aggregated proteins, changing their physical properties in such a way that chaperone mediated disaggregation becomes much more efficient. In Escherichia coli two small Hsps, IbpA and IbpB, exist. They are 48% identical at the amino acid level, yet their roles in stabilisation of protein aggregates are quite distinct. Here we analysed the biochemical properties of IbpA. We found that IbpA assembles into protofilaments which in turn form mature fibrils. Such fibrils are atypical for sHsps. Interaction of IbpA with either its cochaperone IbpB or an aggregated substrate blocks IbpA fibril formation. Structured summary: MINT-7876715: ibpA (uniprotkb:P0C054) and ibpA (uniprotkb:P0C054) bind (MI:0407) by molecular sieving (MI:0071) MINT-7888427: ibpB (uniprotkb:P0C058) and ibpB (uniprotkb:P0C058) bind (MI:0407) by molecular sieving (MI:0071) MINT-7888448: ibpA (uniprotkb:P0C054) and ibpA (uniprotkb:P0C054) bind (MI:0407) by electron microscopy (MI:0040) MINT-7888434: ibpB (uniprotkb:P0C058) and ibpB (uniprotkb:P0C058) bind (MI:0407) by electron microscopy (MI:0040) MINT-7888459: ibpA (uniprotkb:P0C054) and ibpA (uniprotkb:P0C054) bind (MI:0407) by fluorescence microscopy (MI:0416) [Copyright &y& Elsevier]

A translucent collagen gel was formed from a transparent acidic solution of red stingray collagen by adjusting to physiological ionic strength and pH in phosphate buffer and then incubating at 25–37°C. During fibril formation from red stingray collagen, the turbidity increased when the NaCl concentration was increased at constant pH and the rate of fibril formation was accelerated by higher pH or lower NaCl concentration. The Tm of red stingray collagen fibrillar gel was estimated as 44.3 ± 3.5°C, which was higher than that of the collagen solution, 33.2°C. In addition, red stingray collagen gel maintained its shape without melting and was suitable for culture of mouse stromal cells at 37°C. [ABSTRACT FROM AUTHOR]

Collagen is composed of fibrils that are formed by self-assembly of smaller units, monomers which are triple-helical polypeptide. However, the mechanism of fibril formation at the level of individual molecules has remained to be clarified. We found that the fluorescence of thioflavin T, which has been widely used as a specific dye for amyloid fibrils, also increased by binding with fibrils of atelocollagen prepared from yellowfin tuna skin. There was a linear correlation between the fluorescence increase and the amount of atelocollagen within a collagen concentration range of 0–0.15 mg/ml at pH 6.5 with 50 µM thioflavin T. In contrast, neither actinidain-processed collagen that keeps monomeric nature nor heat-denatured collagen could cause the fluorescence increase of thioflavin T at all. The relationship between the fluorescence increase and thioflavin T concentration was fit to a theoretical binary binding curve. An apparent dissociation constant, Kd, and a maximal fluorescence increase, ΔFmax, were calculated at various pHs. The values of Kd and ΔFmax were dependent on pH (Kd was 9.4 µM at pH 6.5). The present finding demonstrates that thioflavin T specifically binds to collagen fibrils and may be used as a sensitive tool for the study of collagen structure. [ABSTRACT FROM PUBLISHER]

Human transthyretin (hTTR) is one of several proteins known to cause amyloid disease. Conformational changes in its native structure result in aggregation of the protein, leading to insoluble amyloid fibrils. The transthyretin (TTR)-related proteins comprise a protein family of 5-hydroxyisourate hydrolases with structural similarity to TTR. In this study, we tested the amyloidogenic properties, if any, of sea bream TTR (sbTTR) and Escherichia coli transthyretin-related protein (ecTRP), which share 52% and 30% sequence identity, respectively, with hTTR. We obtained filamentous structures from all three proteins under various conditions, but, interestingly, different structures displayed different tinctorial properties. hTTR and sbTTR formed thin, curved fibrils at low pH (pH 2–3) that bound thioflavin-T (thioflavin-T-positive) but did not stain with Congo Red (CR) (CR-negative). Aggregates formed at the slightly higher pH of 4.0–5.5 had different morphology, displaying predominantly amorphous structures. CR-positive material of hTTR was found in this material, in agreement with previous results. ecTRP remained soluble at pH 2–12 at ambient temperatures. By raising of the temperature, fibril formation could be induced at neutral pH in all three proteins. Most of these temperature-induced fibrils were thicker and straighter than the in vitro fibrils seen at low pH. In other words, the temperature-induced fibrils were more similar to fibrils seen in vivo. The melting temperature of ecTRP was 66.7 °C. This is approximately 30 °C lower than the melting temperatures of sbTTR and hTTR. Information from the crystal structures was used to identify possible explanations for the reduced thermostability of ecTRP. [ABSTRACT FROM AUTHOR]

The effect of the polypeptide environment on polyalanine-induced fibril formation was investigated with amyloidogenic fragments from PAPBN1, a nuclear protein controlling polyadenylation. Mutation-caused extensions of the natural 10 alanine sequence up to maximally 17 alanines result in fibril formation of PABPN1 and the development of the disease oculopharyngeal muscular dystrophy (OPMD). We explored the influence of fibril formation on the structure and function of a one-domain protein linked to the fibril-forming part of PABPN1. The well-characterized, stably folded, one-domain protein, cold-shock protein CspB from Bacillus subtilis, was fused either to the C terminus of the entire N-terminal domain of PABPN1 or directly to peptides consisting of 10 or 17 alanine residues. The fusion protein between the N-terminal domain of PABPN1 and CspB formed fibrils in which the structure and activity of CspB were retained. In the fibrils formed by fusions in which the polyalanine sequence was directly linked to CspB, CspB was unfolded. These results indicate that the folded conformation and the function of a protein domain can be maintained in amyloid-like fibrils, and that the distance between this domain and the fibril plays an important role. [ABSTRACT FROM AUTHOR]

Abstract: Intranuclear fibrils due to poly-alanine expansions in the N-terminal domain of the poly(A) binding protein PABPN1 correlate with the disease oculopharyngeal muscular dystrophy (OPMD). For monitoring fibril formation by fluorescence and real-time NMR spectroscopy, tryptophans were introduced either into the middle or C-terminal of the poly-alanine segment. The kinetics of fibril formation which were monitored by fluorescence spectroscopy were matched by real-time NMR kinetics. Our results show that fibril formation is concomitant with the burial of the tryptophans in the fibrillar core. Since no soluble pre-fibrillar intermediate(s) was detected, fibril formation of this domain may be regarded as a two state conversion from an unfolded soluble into folded insoluble species. [Copyright &y& Elsevier]

The monomeric Alzheimer's β amyloid peptide, Aβ, is known to adopt a disordered state in water at room temperature, and a circular dichroism (CD) spectroscopy experiment has provided the secondary-structure contents for the disordered state: 70% random, 25% β-structural, and 5% helical. We performed an enhanced conformational sampling (multicanonical molecular dynamics simulation) of a 25-residue segment (residues 12-36) of Aβ in explicit water and obtained the conformational ensemble over a wide temperature range. The secondary-structure contents calculated from the conformational ensemble at 300°K reproduced the experimental secondary-structure contents. The constructed free-energy landscape at 300°K was not plain but rugged with five clearly distinguishable clusters, and each cluster had its own characteristic tertiary structure: a helix-structural cluster, two β-structural clusters, and two random-structural clusters. This indicates that the contribution from the five individual clusters determines the secondary-structure contents experimentally measured. The helical cluster had a similarity with a stable helical structure for monomeric Aβ in 2,2,2-trifluoroethanol (TFE)/water determined by an NMR experiment: The positions of helices in the helical cluster were the same as those in the NMR structure, and the residue-residue contact patterns were also similar with those of the NMR structure. The cluster-cluster separation in the conformational space indicates that free-energy barriers separate the clusters at 300°K. The two β-structural clusters were characterized by different strand-strand hydrogen-bond (H-bond) patterns, suggesting that the free-energy barrier between the two clusters is due to the H-bond rearrangements. [ABSTRACT FROM AUTHOR]

The review discusses the molecular origins of the forces and free energies that determine several things about proteins, and how experiment and theory reveal this information. The first subject is the stability of the folded, native structures. The second is the range of molecular mechanisms by which proteins find their way to those folded structures in laboratory environments. The third is the much more complex problem of how folding occurs in the cellular environment. This topic includes a discussion of crowding and of the roles of chaperone molecules. The review concludes with a discussion of protein aggregation and fibril formation and of misfolding and therapies associated with it. [ABSTRACT FROM AUTHOR]