Relevant bibliographies by topics / Protein amyloid fibril

Academic literature on the topic 'Protein amyloid fibril'

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Published: 9 March 2023
Last updated: 10 March 2023

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Journal articles on the topic "Protein amyloid fibril"

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Dean, Dexter N., and Jennifer C. Lee. "Modulating functional amyloid formation via alternative splicing of the premelanosomal protein PMEL17." Journal of Biological Chemistry 295, no. 21 (April 10, 2020): 7544–53. http://dx.doi.org/10.1074/jbc.ra120.013012.

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The premelanosomal protein (PMEL17) forms functional amyloid fibrils involved in melanin biosynthesis. Multiple PMEL17 isoforms are produced, two of which arise from excision of a cryptic intron within the amyloid-forming repeat (RPT) domain, leading to long (lRPT) and short (sRPT) isoforms with 10 and 7 imperfect repeats, respectively. Both lRPT and sRPT isoforms undergo similar pH-dependent mechanisms of amyloid formation and fibril dissolution. Here, using human PMEL17, we tested the hypothesis that the minor, but more aggregation-prone, sRPT facilitates amyloid formation of lRPT. We observed that cross-seeding by sRPT fibrils accelerates the rate of lRPT aggregation, resulting in propagation of an sRPT-like twisted fibril morphology, unlike the rodlike structure that lRPT normally adopts. This templating was specific, as the reversed reaction inhibited sRPT fibril formation. Despite displaying ultrastructural differences, self- and cross-seeded lRPT fibrils had a similar β-sheet structured core, revealed by Raman spectroscopy, limited-proteolysis, and fibril disaggregation experiments, suggesting the fibril twist is modulated by N-terminal residues outside the amyloid core. Interestingly, bioinformatics analysis of PMEL17 homologs from other mammals uncovered that long and short RPT isoforms are conserved among members of this phylogenetic group. Collectively, our results indicate that the short isoform of RPT serves as a “nucleator” of PMEL17 functional amyloid formation, mirroring how bacterial functional amyloids assemble during biofilm formation. Whereas bacteria regulate amyloid assembly by using individual genes within the same operon, we propose that the modulation of functional amyloid formation in higher organisms can be accomplished through alternative splicing.
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Šneideris, Tomas, Lina Baranauskienė, Jonathan G. Cannon, Rasa Rutkienė, Rolandas Meškys, and Vytautas Smirnovas. "Looking for a generic inhibitor of amyloid-like fibril formation among flavone derivatives." PeerJ 3 (September 24, 2015): e1271. http://dx.doi.org/10.7717/peerj.1271.

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A range of diseases is associated with amyloid fibril formation. Despite different proteins being responsible for each disease, all of them share similar features including beta-sheet-rich secondary structure and fibril-like protein aggregates. A number of proteins can form amyloid-like fibrilsin vitro, resembling structural features of disease-related amyloids. Given these generic structural properties of amyloid and amyloid-like fibrils, generic inhibitors of fibril formation would be of interest for treatment of amyloid diseases. Recently, we identified five outstanding inhibitors of insulin amyloid-like fibril formation among the pool of 265 commercially available flavone derivatives. Here we report testing of these five compounds and of epi-gallocatechine-3-gallate (EGCG) on aggregation of alpha-synuclein and beta-amyloid. We used a Thioflavin T (ThT) fluorescence assay, relying on halftimes of aggregation as the measure of inhibition. This method avoids large numbers of false positive results. Our data indicate that four of the five flavones and EGCG inhibit alpha-synuclein aggregation in a concentration-dependent manner. However none of these derivatives were able to increase halftimes of aggregation of beta-amyloid.
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Buell, Alexander K. "The growth of amyloid fibrils: rates and mechanisms." Biochemical Journal 476, no. 19 (October 11, 2019): 2677–703. http://dx.doi.org/10.1042/bcj20160868.

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Abstract Amyloid fibrils are β-sheet-rich linear protein polymers that can be formed by a large variety of different proteins. These assemblies have received much interest in recent decades, due to their role in a range of human disorders. However, amyloid fibrils are also found in a functional context, whereby their structural, mechanical and thermodynamic properties are exploited by biological systems. Amyloid fibrils form through a nucleated polymerisation mechanism with secondary processes acting in many cases to amplify the number of fibrils. The filamentous nature of amyloid fibrils implies that the fibril growth rate is, by several orders of magnitude, the fastest step of the overall aggregation reaction. This article focusses specifically on in vitro experimental studies of the process of amyloid fibril growth, or elongation, and summarises the state of knowledge of its kinetics and mechanisms. This work attempts to provide the most comprehensive summary, to date, of the available experimental data on amyloid fibril elongation rate constants and the temperature and concentration dependence of amyloid fibril elongation rates. These data are compared with those from other types of protein polymers. This comparison with data from other polymerising proteins is interesting and relevant because many of the basic ideas and concepts discussed here were first introduced for non-amyloid protein polymers, most notably by the Japanese school of Oosawa and co-workers for cytoskeletal filaments.
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Waterhouse, Sarah H., and Juliet A. Gerrard. "Amyloid Fibrils in Bionanotechnology." Australian Journal of Chemistry 57, no. 6 (2004): 519. http://dx.doi.org/10.1071/ch04070.

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An amyloid fibril is a highly ordered, insoluble form of protein that results when a normally soluble protein aggregates via a self-association process to form a structured nanotube. Such fibrils can now be routinely generated from purified proteins in the laboratory, and have attracted burgeoning interest due to their role in a variety of disease states. This article focusses on a new alternative direction in amyloid research, exploring the potential application of the amyloid fibril as a form of nanotubular scaffolding in bionanotechnology.
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Stepanenko, Olga V., Maksim I. Sulatsky, Ekaterina V. Mikhailova, Olesya V. Stepanenko, Irina M. Kuznetsova, Konstantin K. Turoverov, and Anna I. Sulatskaya. "Trypsin Induced Degradation of Amyloid Fibrils." International Journal of Molecular Sciences 22, no. 9 (May 2, 2021): 4828. http://dx.doi.org/10.3390/ijms22094828.

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Proteolytic enzymes are known to be involved in the formation and degradation of various monomeric proteins, but the effect of proteases on the ordered protein aggregates, amyloid fibrils, which are considered to be extremely stable, remains poorly understood. In this work we study resistance to proteolytic degradation of lysozyme amyloid fibrils with two different types of morphology and beta-2-microglobulun amyloids. We showed that the proteolytic enzyme of the pancreas, trypsin, induced degradation of amyloid fibrils, and the mechanism of this process was qualitatively the same for all investigated amyloids. At the same time, we found a dependence of efficiency and rate of fibril degradation on the structure of the amyloid-forming protein as well as on the morphology and clustering of amyloid fibrils. It was assumed that the discovered relationship between fibrils structure and the efficiency of their degradation by trypsin can become the basis of a new express method for the analysis of amyloids polymorphism. Unexpectedly lower resistance of both types of lysozyme amyloids to trypsin exposure compared to the native monomeric protein (which is not susceptible to hydrolysis) was attributed to the higher availability of cleavage sites in studied fibrils. Another intriguing result of the work is that the cytotoxicity of amyloids treated with trypsin was not only failing to decline, but even increasing in the case of beta-2-microglobulin fibrils.
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Lempart, Justine, Eric Tse, James A. Lauer, Magdalena I. Ivanova, Alexandra Sutter, Nicholas Yoo, Philipp Huettemann, Daniel Southworth, and Ursula Jakob. "Mechanistic insights into the protective roles of polyphosphate against amyloid cytotoxicity." Life Science Alliance 2, no. 5 (September 18, 2019): e201900486. http://dx.doi.org/10.26508/lsa.201900486.

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The universally abundant polyphosphate (polyP) accelerates fibril formation of disease-related amyloids and protects against amyloid cytotoxicity. To gain insights into the mechanism(s) by which polyP exerts these effects, we focused on α-synuclein, a well-studied amyloid protein, which constitutes the major component of Lewy bodies found in Parkinson’s disease. Here, we demonstrate that polyP is unable to accelerate the rate-limiting step of α-synuclein fibril formation but effectively nucleates fibril assembly once α-synuclein oligomers are formed. Binding of polyP to α-synuclein either during fibril formation or upon fibril maturation substantially alters fibril morphology and effectively reduces the ability of α-synuclein fibrils to interact with cell membranes. The effect of polyP appears to be α-synuclein fibril specific and successfully prevents the uptake of fibrils into neuronal cells. These results suggest that altering the polyP levels in the extracellular space might be a potential therapeutic strategy to prevent the spreading of the disease.
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Bondarev, Stanislav, Kirill Antonets, Andrey Kajava, Anton Nizhnikov, and Galina Zhouravleva. "Protein Co-Aggregation Related to Amyloids: Methods of Investigation, Diversity, and Classification." International Journal of Molecular Sciences 19, no. 8 (August 4, 2018): 2292. http://dx.doi.org/10.3390/ijms19082292.

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Amyloids are unbranched protein fibrils with a characteristic spatial structure. Although the amyloids were first described as protein deposits that are associated with the diseases, today it is becoming clear that these protein fibrils play multiple biological roles that are essential for different organisms, from archaea and bacteria to humans. The appearance of amyloid, first of all, causes changes in the intracellular quantity of the corresponding soluble protein(s), and at the same time the aggregate can include other proteins due to different molecular mechanisms. The co-aggregation may have different consequences even though usually this process leads to the depletion of a functional protein that may be associated with different diseases. The protein co-aggregation that is related to functional amyloids may mediate important biological processes and change of protein functions. In this review, we survey the known examples of the amyloid-related co-aggregation of proteins, discuss their pathogenic and functional roles, and analyze methods of their studies from bacteria and yeast to mammals. Such analysis allow for us to propose the following co-aggregation classes: (i) titration: deposition of soluble proteins on the amyloids formed by their functional partners, with such interactions mediated by a specific binding site; (ii) sequestration: interaction of amyloids with certain proteins lacking a specific binding site; (iii) axial co-aggregation of different proteins within the same amyloid fibril; and, (iv) lateral co-aggregation of amyloid fibrils, each formed by different proteins.
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Xu, Sherry C. S., Josephine G. LoRicco, Anthony C. Bishop, Nathan A. James, Welby H. Huynh, Scott A. McCallum, Nadia R. Roan, and George I. Makhatadze. "Sequence-independent recognition of the amyloid structural motif by GFP protein family." Proceedings of the National Academy of Sciences 117, no. 36 (August 24, 2020): 22122–27. http://dx.doi.org/10.1073/pnas.2001457117.

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Cnidarian fluorescent protein (FP) derivatives such as GFP, mCherry, and mEOS2 have been widely used to monitor gene expression and protein localization through biological imaging because they are considered functionally inert. We demonstrate that FPs specifically bind amyloid fibrils formed from many natural peptides and proteins. FPs do not bind other nonamyloid fibrillar structures such as microtubules or actin filaments and do not bind to amorphous aggregates. FPs can also bind small aggregates formed during the lag phase and early elongation phase of fibril formation and can inhibit amyloid fibril formation in a dose-dependent manner. These findings suggest caution should be taken in interpreting FP-fusion protein localization data when amyloid structures may be present. Given the pathological significance of amyloid-related species in some diseases, detection and inhibition of amyloid fibril formation using FPs can provide insights on developing diagnostic tools.
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Pepys, M. B. "Pathogenesis, diagnosis and treatment of systemic amyloidosis." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 356, no. 1406 (February 28, 2001): 203–11. http://dx.doi.org/10.1098/rstb.2000.0766.

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Amyloidosis is a disorder of protein folding in which normally soluble proteins are deposited as abnormal, insoluble fibrils that disrupt tissue structure and cause disease. Although about 20 different unrelated proteins can form amyloid fibrils in vivo , all such fibrils share a common cross–β core structure. Some natural wild–type proteins are inherently amyloidogenic, form fibrils and cause amyloidosis in old age or if present for long periods at abnormally high concentration. Other amyloidogenic proteins are acquired or inherited variants, containing amino–acid substitutions that render them unstable so that they populate partly unfolded states under physiological conditions, and these intermediates then aggregate in the stable amyloid fold. In addition to the fibrils, amyloid deposits always contain the non–fibrillar pentraxin plasma protein, serum amyloid P component (SAP), because it undergoes specific calcium–dependent binding to amyloid fibrils. SAP contributes to amyloidogenesis, probably by stabilizing amyloid fibrils and retarding their clearance. Radiolabelled SAP is an extremely useful, safe, specific, non–invasive, quantitative tracer for scintigraphic imaging of systemic amyloid deposits. Its use has demonstrated that elimination of the supply of amyloid fibril precursor proteins leads to regression of amyloid deposits with clinical benefit. Current treatment of amyloidosis comprises careful maintenance of impaired organ function, replacement of end–stage organ failure by dialysis or transplantation, and vigorous efforts to control underlying conditions responsible for production of fibril precursors. New approaches under development include drugs for stabilization of the native fold of precursor proteins, inhibition of fibrillogenesis, reversion of the amyloid to the native fold, and dissociation of SAP to accelerate amyloid fibril clearance in vivo .
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Trusova, Valeriya, Olga Zhytniakivska, Uliana Tarabara, Kateryna Vus, and Galyna Gorbenko. "Interactions of Fibrillar Insulin with Proteins: A Molecular Docking Study." 2, no. 2 (June 2, 2022): 133–40. http://dx.doi.org/10.26565/2312-4334-2022-2-17.

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During the last decades growing attention has been paid to ascertaining the factors responsible for the toxic potential of particular protein aggregates, amyloid fibrils, whose formation is associated with a range of human pathologies, including the neurodegenerative diseases, systemic amyloidosis, type II diabetes, etc. Despite significant progress in elucidating the mechanisms of cytotoxic action of amyloid fibrils, the role of fibril-protein interactions in determining the amyloid toxicity remains poorly understood. In view of this, in the present study the molecular docking techniques has been employed to investigate the interactions between the insulin amyloid fibrils (InsF) and three biologically important multifunctional proteins, viz. serum albumin, lysozyme and insulin in their native globular state. Using the ClusPro, HDOCK, PatchDock and COCOMAPS web servers, along with BIOVIA Discovery Studio software, the structural characteristics of fibril-protein complexes such as the number of interacting amino acid residues, the amount of residues at fibril and protein interfaces, the contributions of various kinds of interactions, buried area upon the complex formation, etc. It was found that i) hydrophilic-hydrophilic and hydrophilic-hydrophobic interactions play dominating role in the formation of fibril-protein complexes; ii) there is no significant differences between the investigated proteins in the number of fibrillar interacting residues; iii) the dominating hydrogen bond forming residues are represented by glutamine and asparagine in fibrillar insulin, lysine in serum albumin and arginine in lysozyme; iv) polar buried area exceeds the nonpolar one upon the protein complexation with the insulin fibrils. The molecular docking evidence for the localization of phosphonium fluorescent dye TDV at the fibril-protein interface was obtained.
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Dissertations / Theses on the topic "Protein amyloid fibril"

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Hosia, Waltteri. "Molecular mechanisms in amyloid fibril formation /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-976-5.

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Faendrich, Marcus. "Protein folding aspects of amyloid fibril formation." Thesis, University of Oxford, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.393572.

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Binger, Katrina Jean. "The reversibility of amyloid fibril formation." Connect to thesis, 2009. http://repository.unimelb.edu.au/10187/4912.

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The aggregation of misfolded proteins into amyloid fibrils is implicated in the pathogenesis of several human degenerative diseases, including Alzheimer’s, Parkinson’s and Type II diabetes. Links between the deposition of amyloid fibrils and the progression of these diseases are poorly understood, with much of the current research focused on monomer misfolding and subsequent assembly of oligomers and mature fibrils. This project examines the formation of human apolipoprotein (apo) C-II amyloid fibrils, with a focus on the stability and reversibility of amyloid fibril assembly.
The initial stages of the project were to develop a model for apoC-II amyloid fibril formation. This was achieved by analysis of the concentration dependent kinetics of apoC-II amyloid fibril formation, and correlation of these data with the final size distribution of the fibrils, determined by sedimentation velocity experiments. On the basis of these studies, a new reversible model for apoC-II amyloid fibril formation is proposed that includes fibril breaking and re-joining as integral parts of the assembly mechanism. The model was tested by rigorous experimentation, with antibody-labelling transmission electron microscopy providing direct evidence for spontaneous fibril breaking and re-joining.
The development of this model for apoC-II fibril assembly provided the foundation for experiments to investigate factors that promote, inhibit or reverse amyloid fibril formation. Factors that were considered include a molecular chaperone protein, αB-crystallin, and a chemical modification, methionine oxidation. Investigations on the effect of αB-crystallin revealed that the inhibition of apoC-II fibril formation occurs by two distinct mechanisms: transient interaction with monomer preventing oligomerisation, and binding to mature fibrils, which inhibits fibril elongation. Studies on the effect of methionine oxidation on apoC-II fibril formation showed that both the assembly and stability of the fibrils was affected by this modification. ApoC-II contains two methionine residues (Met-9 and Met-60), and upon oxidation of these residues fibril formation was inhibited. In addition, the treatment of pre-formed fibrils with hydrogen peroxide caused dissociation of the fibrils via the oxidation of Met-60, located with the fibril core structural region. The final chapter details the development of antibodies that specifically recognise the conformation of apoC-II amyloid fibrils, which provide the foundation for future studies to examine the role that apoC-II amyloid fibrils play in disease.
Overall, this thesis reveals the dynamic and reversible nature of amyloid fibril formation. New insight is also obtained of the general stability of amyloid fibrils and the processes that may regulate their formation, persistence and disease pathogenesis in vivo.
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Vernaglia, Brian Anthony. "The effects of partial denaturation on in vitro fibril formation /." Thesis, Connect to Dissertations & Theses @ Tufts University, 2004.

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Thesis (Ph.D.)--Tufts University, 2004.
Adviser: Eliana De Bernardez Clark. Submitted to the Dept. of Chemical Engineering. Includes bibliographical references (leaves 173-181). Access restricted to members of the Tufts University community. Also available via the World Wide Web;
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Gustafsson, Magnus. "Palmitoylation and amyloid fibril formation of lung surfactant protein C /." Stockholm, 2000. http://diss.kib.ki.se/2000/91-628-4386-9/.

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Pothier, Laura J. "Effects of amino acid substitutions on the conformation and stability of A[beta]₁₆₋₂₂ aggregates /." Connect to online version, 2007. http://ada.mtholyoke.edu/setr/websrc/pdfs/www/2007/213.pdf.

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Beugelsdijk, Alex. "Understanding amyloid fibril growth through theory and simulation." Thesis, Kansas State University, 2014. http://hdl.handle.net/2097/18117.

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Master of Science
Biochemistry and Molecular Biophysics
Jianhan Chen
Proteins are fundamental building blocks of life in an organism, and to function properly, they must adopt an appropriate three-dimensional conformation or conformational ensemble. In protein aggregation diseases, proteins misfold to incorrect structures that allow them to join together and form aggregates. A wide variety of proteins are involved in these aggregation diseases and there are multiple theories of their disease mechanism. However, a common theme is that they aggregate into filamentous structures. Therapies that target the process by which the aggregating proteins assemble into these similar fibril-like structures may by effective at countering aggregation diseases. This requires models that can accurately describe the assembly process of the fibrils. An analytical theory was recently described where fibrils grow by the templating of peptides onto an existing amyloid core and the kinetics of the templating process is modeled as a random walk in the backbone hydrogen bonding space. In this thesis, I present my work integrating molecular simulation with this analytical model to investigate the dependence of fibril growth kinetics on peptide sequence and other molecular details. Using the Aβ16-22 peptide as a model system, we first calculate the rate matrix of transitions among all possible hydrogen bonding microscopic states using numerous short-time simulations. These rates were then used to construct a kinetic Monte Carlo model for simulations of long-timescale fibril growth. The results demonstrate the feasibility of using such a theory/simulation framework for bridging the significant gap between fibril growth and simulation timescales. At the same time, the study also reveals some limits of describing the fibril growth as a templating process in the backbone hydrogen bonding space alone. In particular, we found that dynamics in nonspecifically bound states must also be considered. Possible solutions to this deficiency are discussed at the end.
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Eden-Jones, Kym Denys. "Kinetic Monte Carlo simulations of autocatalytic protein aggregation." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/9365.

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The self-assembly of proteins into filamentous structures underpins many aspects of biology, from dynamic cell scaffolding proteins such as actin, to the amyloid plaques responsible for a number of degenerative diseases. Typically, these self-assembly processes have been treated as nucleated, reversible polymerisation reactions, where dynamic fluctuations in a population of monomers eventually overcome an energy barrier, forming a stable aggregate that can then grow and shrink by the addition and loss of more protein from its ends. The nucleated, reversible polymerisation framework is very successful in describing a variety of protein systems such as the cell scaffolds actin and tubulin, and the aggregation of haemoglobin. Historically, amyloid fibrils were also thought to be described by this model, but measurements of their aggregation kinetics failed to match the model's predictions. Instead, recent work indicates that autocatalytic polymerisation - a process by which the number of growth competent species is increased through secondary nucleation, in proportion to the amount already present - is better at describing their formation. In this thesis, I will extend the predictions made in this mean-field, autocatalytic polymerisation model through use of kinetic Monte Carlo simulations. The ubiquitous sigmoid-like growth curve of amyloid fibril formation often possesses a notable quiescent lag phase which has been variously attributed to primary and secondary nucleation processes. Substantial variability in the length of this lag phase is often seen in replicate experimental growth curves, and naively may be attributed to fluctuations in one or both of these nucleation processes. By comparing analytic waiting-time distributions, to those produced by kinetic Monte Carlo simulation of the processes thought to be involved, I will demonstrate that this cannot be the case in sample volumes comparable with typical laboratory experiments. Experimentally, the length of the lag phase, or "lag time", is often found to scale with the total protein concentration, according to a power law with exponent γ. The models of nucleated polymerisation and autocatalytic polymerisation predict different values for this scaling exponent, and these are sometimes used to identify which of the models best describes a given protein system. I show that this approach is likely to result in a misidentification of the dominant mechanisms under conditions where the lag phase is dominated by a different process to the rest of the growth curve. Furthermore, I demonstrate that a change of the dominant mechanism associated with total protein concentration will produce "kinks" in the scaling of lag time with total protein concentration, and that these may be used to greater effect in identifying the dominant mechanisms from experimental kinetic data. Experimental data for bovine insulin aggregation, which is well described by the autocatalytic polymerisation model for low total protein concentrations, displays an intriguing departure from the predicted behaviour at higher protein concentrations. Additionally, the protein concentration at which the transition occurs, appears to be affected by the presence of salt. Coincident with this, an apparent change in the fibril structure indicates that different aggregation mechanisms may operate at different total protein concentrations. I demonstrate that a transition whereby the self-assembly mechanisms change once a critical concentration of fibrils or fibrillar protein is reached, can explain the observed behaviour and that this predicts a substantially higher abundance of shorter laments - which are thought to be pathogenic - at lower total protein concentrations than if self-assembly were consistently autocatalytic at all protein concentration. Amyloid-like loops have been observed in electron and atomic-force microscographs, together with non-looped fibrils, for a number of different proteins including ovalbumin. This implies that fibrils formed of these proteins are able to grow by fibrillar end-joining, and not only monomer addition as is more commonly assumed. I develop a simple analytic expression for polymerisation by monomer addition and fibrillar end-joining, (without autocatalysis) and show that this is not sufficient to explain the growth curves obtained experimentally for ovalbumin. I then demonstrate that the same data can be explained by combining fibrillar end-joining and fragmentation. Through the use of an analytic expression, I estimate the kinetic rates from the experimental growth curves and, via simulation, investigate the distribution of lament and loop lengths. Together, my findings demonstrate the relative importance of different molecular mechanisms in amyloid fibril formation, how these might be affected by various environmental parameters, and characteristic behaviour by which their involvement might be detected experimentally.
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Ridgley, Devin Michael. "Self-Assembly of Large Amyloid Fibers." Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/48186.

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Functional amyloids found throughout nature have demonstrated that amyloid fibers are potential industrial biomaterials. This work introduces a new 'template plus adder' cooperative mechanism for the spontaneous self-assembly of micrometer sized amyloid fibers. A short hydrophobic template peptide induces a conformation change within a highly α-helical adder protein to form β-sheets that continue to assemble into micrometer sized amyloid fibers. This study utilizes a variety of proteins that have template or adder characteristics which suggests that this mechanism may be employed throughout nature. Depending on the amino acid composition of the proteins used the mixtures form amyloid fibers of a cylindrical (~10 μm diameter, ~2 GPa Young's modulus) or tape (5-10 μm height, 10-20 μm width and 100-200 MPa Young's modulus) morphology. Processing conditions are altered to manipulate the morphology and structural characteristics of the fibers. Spectroscopy is utilized to identify certain amino acid groups that contribute to the self-assembly process. Aliphatic amino acids (A, I, V and L) are responsible for initiating conformation change of the adder proteins to assemble into amyloid tapes. Additional polyglutamine segments (Q-blocks) within the protein mixtures will form Q hydrogen bonds to reinforce the amyloid structure and form a cylindrical fiber of higher modulus. Atomic force microscopy is utilized to delineate the self-assembly of amyloid tapes and cylindrical fibers from protofibrils (15-30 nm width) to fibers (10-20 μm width) spanning three orders of magnitude. The aliphatic amino acid content of the adder proteins' α-helices is a good predictor of high density β-sheet formation within the protein mixture. Thus, it is possible to predict the propensity of a protein to undergo conformation change into amyloid structures. Finally, Escherichia coli is genetically engineered to express a template protein which self-assembles into large amyloid fibers when combined with extracellular myoglobin, an adder protein. The goal of this thesis is to produce, manipulate and characterize the self-assembly of large amyloid fibers for their potential industrial biomaterial applications. The techniques used throughout this study outline various methods to design and engineer amyloid fibers of a tailored modulus and morphology. Furthermore, the mechanisms described here may offer some insight into naturally occurring amyloid forming systems.
Ph. D.
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Iwakawa, Naoto. "Dynamic Structural Changes of Proteins Revealed by NMR Spectroscopy Under Physicochemical Perturbations." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263679.

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Books on the topic "Protein amyloid fibril"

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Thomas, Scheibel, ed. Fibrous proteins. Austin, Tex: Landes Bioscience, 2008.

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Lachmann, Helen J., and Giampaolo Merlini. The patient with amyloidosis. Edited by Giuseppe Remuzzi. Oxford University Press, 2015. http://dx.doi.org/10.1093/med/9780199592548.003.0152.

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Amyloidosis is a disorder of protein folding in which normally soluble plasma proteins are deposited in the extracellular space in an abnormal insoluble fibrillar form. The process of amyloid formation and deposition causes cytotoxicity and progressive organ dysfunction. Amyloid is remarkably diverse and can be hereditary or acquired, localized or systemic, and lethal or merely an incidental finding. The most important numerically are AL amyloidosis, in which the fibrils are composed of monoclonal immunoglobulin light chains, and AA amyloidosis, in which the acute phase reactant Serum Amyloid A component forms the fibrils.The kidney is involved in 75% of patients with systemic amyloidosis. Heavy proteinuria or nephrotic syndrome is characteristic of most amyloid variants.Without treatment, systemic disease is usually fatal but measures that reduce the supply of amyloid fibril precursor proteins can result in regression of amyloid deposits, prevention of organ failure, and improved quality of life and survival. Early diagnosis, before irreversible organ damage has occurred, is the key to effective treatment. Recent advances in diagnosis and therapy have much improved the outlook of patients with AL amyloidosis, but agents with broader promise are under investigation.
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Alzheimers Disease Insights Into Low Molecular Weight And Cytotoxic Aggregates From In Vitro And Computer Experiments Molecular Basis Of Amyloidbeta Protein Aggregation And Fibril Formation. Imperial College Press, 2011.

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The nature and origin of amyloid fibrils. Chichester: Wiley, 1996.

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The Nature and Origin of Amyloid Fibrils. John Wiley & Sons, 1996.

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Mittal, Sajjan. Amyloidosis. Edited by Patrick Davey and David Sprigings. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780199568741.003.0181.

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Amyloidosis is a multisystem disease caused by the extracellular deposition of insoluble abnormal fibrils that injure tissues and organs. The fibrils are formed by the aggregation of misfolded, normally soluble proteins. Systemic amyloid light-chain (AL) amyloidosis (primary amyloidosis) is the commonest type of amyloidosis in the developed world, accounting for 80% of cases. The remainder are due to AA amyloidosis (secondary or reactive amyloidosis), familial amyloidosis, or other rare types of amyloidosis. The most common clinical features at diagnosis are nephrotic syndrome, heart failure (typically with predominant right heart failure), sensorimotor and/or autonomic peripheral neuropathy, and hepatosplenomegaly.
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Wetzel, Ronald, and Rakesh Mishra. Structural Biology. Oxford University Press, 2014. http://dx.doi.org/10.1093/med/9780199929146.003.0012.

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The 3,144–amino acid huntingtin protein (HTT) folds in water into a structure consisting of compact, organized domains interspersed with intrinsically disordered protein (IDP) elements. The IDPs function as sites of post-translational modifications and proteolysis as well as in targeting, binding, and aggregation. Although the dominant structural motif of HTT is the α‎-helix–rich HEAT repeat, the expanded polyglutamine (polyQ) toxicity responsible for Huntington’s disease is most likely played out within intrinsically disordered HTT exon 1–like fragments consisting of the 16– to 17–amino acid N-terminal HTTNT segment, the polyQ segment, and a proline-rich segment. The physical behavior of HTT exon 1 fragments is dominated by interactive, polyQ repeat length–dependent structural transitions responsible for membrane and protein–protein interactions and the formation of tetramers, higher oligomers, amyloid fibrils, and inclusions. Understanding the basis of this solution behavior may be the key to disease mechanisms and molecular therapeutic strategies.
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Book chapters on the topic "Protein amyloid fibril"

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Roode, Lianne W. Y., Ulyana Shimanovich, Si Wu, Sarah Perrett, and Tuomas P. J. Knowles. "Protein Microgels from Amyloid Fibril Networks." In Advances in Experimental Medicine and Biology, 223–63. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-9791-2_7.

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Smith, Andrew. "Fibril Formation by Short Synthetic Peptides." In Protein Aggregation and Fibrillogenesis in Cerebral and Systemic Amyloid Disease, 29–51. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5416-4_2.

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Rossevatn, K., P. K. Andresen, K. Sletten, G. Husby, K. Nordstoga, K. H. Johnson, and P. Westermark. "The Complete Primary Structure of Bovine Serum Amyloid Protein a (SAA) and of Tissue Amyloid Fibril Protein a (AA) Subspecies." In Amyloid and Amyloidosis 1990, 103–6. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-3284-8_26.

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Ban, Tadato, and Yuji Goto. "Real-Time Observation of Amyloid-β Fibril Growth by Total Internal Reflection Fluorescence Microscopy." In Protein Misfolding Diseases, 699–709. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2010. http://dx.doi.org/10.1002/9780470572702.ch33.

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Gertz, Morie A., Martha Skinner, Alan S. Cohen, Lawreen Heller Conners, and Robert A. Kyle. "Structural and Immunologic Studies of a Kappa Amyloid Fibril Protein." In Amyloidosis, 517–24. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4613-2199-6_66.

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Klafki, H. W., H. D. Kratzin, A. I. Pick, K. Eckart, and N. Hilschmann. "Complete Amino-Acid Sequence of a Lambda Amyloid Fibril Protein Isolated from the Liver of Amyloidosis Patient DIA." In Amyloid and Amyloidosis 1990, 185–88. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-3284-8_46.

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Ban, Tadato, and Yuji Goto. "Direct Observation of Amyloid Fibril Growth Monitored by Total Internal Reflection Fluorescence Microscopy." In Protein Misfolding, Aggregation, and Conformational Diseases, 335–43. Boston, MA: Springer US, 2006. http://dx.doi.org/10.1007/0-387-25919-8_17.

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Isobe, Takashi, Takanori Miki, Fuyuki Kametani, and Tomotaka Shinoda. "Amyloid Associated with Calcifying Epithelial Odontogenic Tumor — A New Type of Amyloid Fibril Protein CEOT." In Amyloidosis, 805–11. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4613-2199-6_100.

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Powers, James M. "Senile Cerebral Amyloid — Evidence for a Neuronal Origin of the Fibril Protein." In Amyloidosis, 743–49. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4613-2199-6_94.

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Eulitz, M., and R. P. Linke. "Complete Primary Structure of an Immunoglobulin λII-Chain Derived Amyloid Fibril Protein (HAR)." In Amyloidosis, 491–96. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4613-2199-6_62.

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Conference papers on the topic "Protein amyloid fibril"

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Dee, Derek, Fan Bu, Lanfang Shi, and Sara Zamani. "Comparing the structure and functionality of amyloid fibrils assembled from peanut, pea, lentil, and mung bean proteins." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/kkyn7687.

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Protein structure dictates functionality, and one way to dramatically alter protein structure is to induce proteins to self-assemble into amyloid fibrils. Amyloid fibrils, or nanofibrils, are long (100–1000’s nm), narrow (10’s nm), highly-organized protein aggregates that hold promise for various applications in biotechnology and food. Converting plant proteins into fibrils may improve their functionality and create sustainable materials, yet most nanofibril research has focused on animal-derived proteins, so there is a need to learn more about fibrils derived from plant proteins. This project compared fibrils assembled from crude protein extracts from peanut, pea, lentils and mung bean, comparing their fibril assembly kinetics, fibril structure, emulsification and viscosity properties. Peanut and mung bean fibrils assembled much faster (kPeanut = 0.90 ± 0.40 h-1, kMungbean = 0.95 ± 0.40 h-1) compared to pea and lentil fibrils (kPea = 0.19 ± 0.03 h-1, kLentil = 0.24 ± 0.01 h-1), at 80 °C, pH 2 with stirring. Fibrils from the different legume proteins displayed markedly different structures that could be generally classified as either long and straight (1000’s nm) or short and curly (100’s nm). The former are more similar to fibrils typically generated from animal proteins (e.g., whey, egg white proteins) while the latter are typical of legume protein fibrils presented in the literature. The longer/straighter or shorter/curly fibrils displayed unique functionalities (emulsion particle size and viscosity profiles) that did not directly correlate with fibril morphology, although several confounding factors limit the establishment of direct structure-function associations. This work indicates several approaches to optimize the assembly of legume protein fibrils that may find use in new plant-based materials and foods.
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Lomakin, Aleksey, David B. Teplow, Daniel A. Kirschner, and George B. Benedek. "Nucleation and Growth of Amyloid β-Protein Fibrils: Detection of Nuclei and Quantitation of Rate Constants." In Photon Correlation and Scattering. Washington, D.C.: Optica Publishing Group, 1996. http://dx.doi.org/10.1364/pcs.1996.sab.3.

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Alzheimer's disease is a progressive, neurodegenerative disorder characterized by amyloid deposition in senile plaques in the cerebral parenchyma and vasculature.(1) These plaques are composed primarily of fibers of the amyloid β-protein, Aβ. A number of studies have provided information on the structure of fibrils formed both in vivo and in vitro, and on factors affecting fiber formation. Synthetic Aβ peptides also form fibers which are ultrastructurally indistinguishable from those isolated from the brain. These peptides have been utilized to examine how a variety of parameters, including temperature, pH, solvent composition, peptide concentration, and peptide sequence, influence the final structure of Aβ aggregates. What is substantially less understood, however, is the kinetics of Aβ fibril growth.
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Trusova, Valeriya M. "Amyloid fibrils: Dark side of protein aggregation." In 2015 International Young Scientists Forum on Applied Physics (YSF). IEEE, 2015. http://dx.doi.org/10.1109/ysf.2015.7333123.

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Park, Jiyong, Byungnam Kahng, and Wonmuk Hwang. "Supramolecular Structure and Stability of the GNNQQNY β-Sheet Bilayer Filament: A Computational Study." In ASME 2007 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2007. http://dx.doi.org/10.1115/sbc2007-175588.

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Self-assembly of β-sheet forming peptides into filaments has drawn great interests in biomedical applications [1,2]; Hydrogels formed by filaments self-assembled from de novo designed peptides possess potential applications for cell culture scaffolds [3]. On the other hand, peptides derived from amyloidogenic proteins in neurodegenerative diseases such as Alzheimer’s and Parkinson’s also form similar β-sheet filaments in vitro. They share little sequence homology, yet filaments formed by these self-assembling peptides commonly have the cross-β structure, the key signature of the amyloid fibril. Detailed structural information of the self-assembled β-sheet filaments has been limited partly due to the difficulty in preparing ordered filament samples, and it has been only recently that solid-state nuclear magnetic resonance and x-ray techniques have revealed their molecular structure at the atomic level [4,5]. Although molecular structures of amyloid fibrils are becoming available, physical principles governing their self-assembly and the properties of the filaments are not well-understood, for which computational as well as theoretical approaches are desirable [6].
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Nizhnikov, A. A. "Amyloid proteins of plants and microorganisms: biological functions and participation in the formation of supra-organismal systems." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.184.

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Here we will review the latest advances in the study of functional amyloids of plants and symbiotic bacteria demonstrating the involvement of these protein fibrils in protein storage in plant seeds and formation of supra-organismal interactions.
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Jiang, Jun, and Shaul Mukamel. "TWO DIMENSIONAL ULTRAVIOLET SPECTROSCOPY OF PROTEINS AND AMYLOID FIBRILS." In Laser Science. Washington, D.C.: OSA, 2010. http://dx.doi.org/10.1364/ls.2010.ltha1.

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Athamneh, Ahmad, and Justin Barone. "Enzyme-Mediated Self-Assembly of Highly Ordered Structures From Disordered Proteins." In ASME 2008 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. ASMEDC, 2008. http://dx.doi.org/10.1115/smasis2008-540.

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Trypsin hydrolysis of wheat gluten produced glutamine-rich short peptides with a tendency to self-assemble into supermolecular structures extrinsic to native wheat gluten. Fourier transform infrared and X-ray diffraction data suggested that the new structures formed resembled that of cross-β amyloid fibrils found in some insect silk and implicated in prion diseases. The superstructures were about 10 μm in diameter with clear right-handed helical configuration and appeared to be bundles of smaller fibrils of about 63 nm in diameter. Results demonstrate the potential for utilizing cheap protein sources and natural mechanisms of protein self-assembly to design advanced nanomaterials that can provide a wide range of structural and chemical functionality.
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ALEXANDRESCU, ANDREI T. "AN NMR-BASED QUENCHED HYDROGEN EXCHANGE INVESTIGATION OF MODEL AMYLOID FIBRILS FORMED BY COLD SHOCK PROTEIN A." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2000. http://dx.doi.org/10.1142/9789814447362_0008.

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Soares, Izadora Fonseca Zaiden, João Nicoli Ferreira dos Santos, and Lis Gomes Silva. "Dramatic cognitive improvement with acetylcholinesterase inhibitor in cerebral amyloid angiopathyrelated inflammation." In XIII Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2021. http://dx.doi.org/10.5327/1516-3180.578.

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Context: Cerebral amyloid angiopathy (CAA) is characterized by progressive deposition of amyloid-ß fibrils in the walls of small arterioles and capillaries of the leptomeninges and cerebral cortex. A rare subtype of CAA is CAA-related inflammation (CAA-RI), which exhibits marked perivascular or transmural inflammatory infiltration in brain tissue. The major clinical features of CAA-RI are rapidly progressive dementia, behavioral changes, headache, seizures, or stroke-like signs. Conclusive diagnosis requires histopathological confirmation, but validated clinicoradiological criteria for the diagnosis of probable CAA-RI have good sensitivity (82%) and specificity (97%). Treatment with high dose corticosteroids with or without other immunosuppressive therapy is recommended. We report a case of probable CAA-RI that did not respond to corticosteroid therapy but had a surprising improvement with acetylcholinesterase inhibitor. Case report: A 77-year-old illiterate woman presented with a history of subacute onset of seizures and behavioral changes. Her medical history was positive for a hearing loss due to a toxic exposure in childhood, and a cured breast cancer. The neurological examination showed attention impairment, disorientation, and incoherent speech. CSF showed a mildly elevated protein count. Brain MRI met criteria for probable CAA-RI. She had a poor response with high doses of corticosteroids, but after a trial with Donepezil she showed important cognitive and functional improvement. Conclusion: This result attracts attention to the importance of the cholinergic pathway in the etiology and pathological mechanisms of CAA. Randomized Controlled Trials would be required to confirm our hypothesis and to find new therapeutic options for CAA.
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