scholarly journals Inhibition of peptide aggregation by means of enzymatic phosphorylation

2016 ◽  
Vol 12 ◽  
pp. 2462-2470 ◽  
Author(s):  
Kristin Folmert ◽  
Malgorzata Broncel ◽  
Hans v. Berlepsch ◽  
Christopher Hans Ullrich ◽  
Mary-Ann Siegert ◽  
...  
Keyword(s):  
Amyloid Fibrils ◽  
Conformational Transition ◽  
Structural Characteristics ◽  
Random Coil ◽  
Amyloid Formation ◽  
Initial Growth ◽  
Amyloid Fibril Formation ◽  
Dependent Protein ◽  
Enzymatic Phosphorylation ◽  
Β Sheet

As is the case in numerous natural processes, enzymatic phosphorylation can be used in the laboratory to influence the conformational populations of proteins. In nature, this information is used for signal transduction or energy transfer, but has also been shown to play an important role in many diseases like tauopathies or diabetes. With the goal of determining the effect of phosphorylation on amyloid fibril formation, we designed a model peptide which combines structural characteristics of α-helical coiled-coils and β-sheets in one sequence. This peptide undergoes a conformational transition from soluble structures into insoluble amyloid fibrils over time and under physiological conditions and contains a recognition motif for PKA (cAMP-dependent protein kinase) that enables enzymatic phosphorylation. We have analyzed the pathway of amyloid formation and the influence of enzymatic phosphorylation on the different states along the conformational transition from random-coil to β-sheet-rich oligomers to protofilaments and on to insoluble amyloid fibrils, and we found a remarkable directing effect from β-sheet-rich structures to unfolded structures in the initial growth phase, in which small oligomers and protofilaments prevail if the peptide is phosphorylated.

scholarly journals Cysteine oxidation triggers amyloid fibril formation of the tumor suppressor p16INK4A

2019 ◽  
Author(s):  
Christoph Göbl ◽  
Vanessa K Morris ◽  
Loes van Dam ◽  
Marieke Visscher ◽  
Paulien E. Polderman ◽  
...  
Keyword(s):  
Redox State ◽  
Amyloid Fibrils ◽  
Structural Rearrangement ◽  
Amyloid Formation ◽  
Cysteine Oxidation ◽  
Cellular Redox ◽  
Cycle Arrest ◽  
Amyloid Fibril Formation ◽  
Helical Protein ◽  
Β Sheet

AbstractAccumulation of the CDK4/6 inhibitor p16INK4A in response to oncogenic transformation leads to cell cycle arrest and senescence and is therefore frequently lost in cancer. p16INK4A is also known to accumulate under conditions of oxidative stress and thus could potentially be regulated by the reversible oxidation of cysteines (redox signaling). Indeed, oxidation of the single cysteine in p16INK4A in human cells occurs under relatively mild oxidizing conditions and leads to disulfide-dependent dimerization. p16INK4A is an all alpha-helical protein, but here we report that upon cysteine-dependent dimerization, p16INK4A undergoes a dramatic structural rearrangement and forms aggregates that have the typical features of amyloid fibrils, including binding of diagnostic dyes, presence of cross-β sheet structure, and typical dimensions found in electron microscopy. p16INK4A amyloid formation abolishes its function as a CDK4/6 inhibitor. Collectively, these observations mechanistically link the cellular redox state to the inactivation of p16INK4A through the formation of amyloid fibrils.

scholarly journals Modulating functional amyloid formation via alternative splicing of the premelanosomal protein PMEL17

2020 ◽  
Vol 295 (21) ◽  
pp. 7544-7553 ◽  
Author(s):  
Dexter N. Dean ◽  
Jennifer C. Lee
Keyword(s):  
Alternative Splicing ◽  
Amyloid Fibrils ◽  
Limited Proteolysis ◽  
Amyloid Formation ◽  
Functional Amyloid ◽  
Melanin Biosynthesis ◽  
Functional Amyloids ◽  
Fibril Morphology ◽  
Amyloid Assembly ◽  
Β Sheet

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.

scholarly journals Structure and Aggregation Mechanisms in Amyloids

Molecules ◽  
2020 ◽  
Vol 25 (5) ◽  
pp. 1195 ◽  
Author(s):  
Zaida L. Almeida ◽  
Rui M. M. Brito
Keyword(s):  
Molecular Species ◽  
Molecular Mechanisms ◽  
Amyloid Fibrils ◽  
Current Knowledge ◽  
Point Of View ◽  
Resonance Spectroscopy ◽  
Amyloid Formation ◽  
Amyloid Fibril Formation ◽  
Misfolding Diseases ◽  
Amyloid Cascade

The aggregation of a polypeptide chain into amyloid fibrils and their accumulation and deposition into insoluble plaques and intracellular inclusions is the hallmark of several misfolding diseases known as amyloidoses. Alzheimer′s, Parkinson′s and Huntington’s diseases are some of the approximately 50 amyloid diseases described to date. The identification and characterization of the molecular species critical for amyloid formation and disease development have been the focus of intense scrutiny. Methods such as X-ray and electron diffraction, solid-state nuclear magnetic resonance spectroscopy (ssNMR) and cryo-electron microscopy (cryo-EM) have been extensively used and they have contributed to shed a new light onto the structure of amyloid, revealing a multiplicity of polymorphic structures that generally fit the cross-β amyloid motif. The development of rational therapeutic approaches against these debilitating and increasingly frequent misfolding diseases requires a thorough understanding of the molecular mechanisms underlying the amyloid cascade. Here, we review the current knowledge on amyloid fibril formation for several proteins and peptides from a kinetic and thermodynamic point of view, the structure of the molecular species involved in the amyloidogenic process, and the origin of their cytotoxicity.

scholarly journals Monomeric amyloid β-peptide (1-42) significantly populates compact fibril-like conformations

2020 ◽  
Author(s):  
Bogdan Barz ◽  
Alexander K. Buell ◽  
Soumav Nath
Keyword(s):  
Amyloid Fibrils ◽  
Amyloid Β ◽  
Random Coil ◽  
Amyloid Β Peptide ◽  
Secondary Nucleation ◽  
Fibril Structure ◽  
Amyloid Fibril Formation ◽  
Dynamics Simulations ◽  
The Individual ◽  
Structural Ensemble

AbstractThe aggregation of the amyloid β (Aβ) peptide is a major hallmark of Alzheimer’s disease. This peptide can aggregate into oligomers, proto-fibrils, and mature fibrils, which eventually assemble into amyloid plaques. The peptide monomers are the smallest assembly units, and play an important role in most of the individual processes involved in amyloid fibril formation, such as primary and secondary nucleation and elongation. The structure of the Aβ monomer has been shown to be very dynamic and mostly disordered, both in experimental and in computational studies, similar to a random coil. This structural state of the monomer contrasts with the very stable and well defined structural core of the amyloid fibrils. An important question is whether the monomer can adopt transient fibril-like conformations in solution and what role such conformations might play in the aggregation process. Here we use enhanced and extensive molecular dynamics simulations to study the Aβ42 monomer structural flexibility with different force fields, water models and salt concentrations. We show that the monomer behaves as a random coil under different simulation conditions. Importantly, we find a conformation with the N-terminal region structured very similarly to that of recent experimentally determined fibril models. This is to the best of our knowledge the first monomeric structural ensemble to show such a similarity with the fibril structure.

scholarly journals Effect of pH on the Conformational Transition of Silk Fibroin in Aqueous Solution Monitored by Thioflavin-T Fluorescence

2021 ◽  
Author(s):  
Ben Jia ◽  
Lan Jia ◽  
Jingxin Zhu
Keyword(s):  
Aqueous Solution ◽  
Secondary Structure ◽  
Silk Fibroin ◽  
Conformational Transition ◽  
Thioflavin T ◽  
Random Coil ◽  
Fluorescence Dye ◽  
Assembly Behavior ◽  
Β Sheet

Abstract In this work, the potential application of the fluorescence dye Thioflavin-T (ThT), which can specifically bind to amyloid, as a powerful tool for monitoring secondary structure transitions of silk fibroin (SF) induced by pH was examined. Results showed that ThT emission intensities substantially increased when pH decreased from 6.8 to 4.8. This increase may be due to conformational transitions from random coil to β-sheet. The morphology and secondary structure of SF were also investigated via TEM, AFM and circular dichroism spectroscopy. The information obtained herein can be utilized not only for the development of convenient and efficient noninvasive method for monitoring the assembly behavior of SF in aqueous solution but also for in vitro fluorescence imaging.

scholarly journals Identification of Novel 1,3,5-Triphenylbenzene Derivative Compounds as Inhibitors of Hen Lysozyme Amyloid Fibril Formation

2019 ◽  
Vol 20 (22) ◽  
pp. 5558
Author(s):  
Hassan Ramshini ◽  
Reza Tayebee ◽  
Alessandra Bigi ◽  
Francesco Bemporad ◽  
Cristina Cecchi ◽  
...  
Keyword(s):  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Inhibitory Effect ◽  
Fibril Formation ◽  
Amyloid Formation ◽  
Binding Assays ◽  
Egg White Lysozyme ◽  
Amyloid Fibril Formation ◽  
Activity Measurements ◽  
Model Protein

Deposition of soluble proteins as insoluble amyloid fibrils is associated with a number of pathological states. There is a growing interest in the identification of small molecules that can prevent proteins from undergoing amyloid fibril formation. In the present study, a series of small aromatic compounds with different substitutions of 1,3,5-triphenylbenzene have been synthesized and their possible effects on amyloid fibril formation by hen egg white lysozyme (HEWL), a model protein for amyloid formation, and of their resulting toxicity were examined. The inhibitory effect of the compounds against HEWL amyloid formation was analyzed using thioflavin T and Congo red binding assays, atomic force microscopy, Fourier-transform infrared spectroscopy, and cytotoxicity assays, such as the 3-(4,5-Dimethylthiazol)-2,5-Diphenyltetrazolium Bromide (MTT) reduction assay and caspase-3 activity measurements. We found that all compounds in our screen were efficient inhibitors of HEWL fibril formation and their associated toxicity. We showed that electron-withdrawing substituents such as –F and –NO2 potentiated the inhibitory potential of 1,3,5-triphenylbenzene, whereas electron-donating groups such as –OH, –OCH3, and –CH3 lowered it. These results may ultimately find applications in the development of potential inhibitors against amyloid fibril formation and its biologically adverse effects.

Raman Spectroscopic Investigation of the Denaturation Process of Silk Fibroin

1989 ◽  
Vol 43 (7) ◽  
pp. 1269-1272 ◽  
Author(s):  
Siding Zheng ◽  
Guanxian Li ◽  
Wenhuo Yao ◽  
Tongyin Yu
Keyword(s):  
Raman Spectroscopy ◽  
Silk Fibroin ◽  
Conformational Transition ◽  
Transition Process ◽  
Random Coil ◽  
Helical Conformation ◽  
Extension Rate ◽  
Α Helix ◽  
Β Sheet ◽  
Denaturation Process

The mechanical denaturation process of silk fibroin is examined by Raman spectroscopy. The fresh silk fibroins from the middle gland of mature silkworms are drawn to various ratios on a tensile tester ( R = ldrawn/ linitial, where l is length) and their conformations are measured with Raman spectroscopy. Undrawn silk fibroin is mainly in the random coil structure with some α-helical conformation, the characteristic bands appearing at 1252 and 1660 (random coil) and at 942, 1106, and 1270 cm−1 (α-helix). When the samples are drawn up to R = 4 at an extension rate of 500 mm/min, two peaks at 1233 cm−1 (the amide III band) and 1085 cm−1 appear; it is shown that the β-sheet conformation is then formed. With an increase in drawing ratios, the intensities of these β-sheet bands increase and those of the random coil and α-helical bands decrease gradually. These changes indicate that, under the action of stress, the conformation of fibroin is altered from random coil and α-helix to β-sheet structures. This result is quite similar to the results achieved by the spinning of the silkworm. The effect of the water content in liquid silk on this conformational transition process is revealed and discussed.

Sensing and modulation of amyloid fibrils by photo-switchable organic dots

Nanoscale ◽  
2020 ◽  
Vol 12 (32) ◽  
pp. 16805-16818
Author(s):  
Aslam Uddin ◽  
Bibhisan Roy ◽  
Gregor P. Jose ◽  
Sk Saddam Hossain ◽  
Partha Hazra
Keyword(s):  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Early Stage ◽  
Fibril Formation ◽  
Amyloid Formation ◽  
Amyloid Fibril Formation

Our study demonstrates that organic dots can be used for the imaging and early stage detection of amyloid fibril formation and the modulation of amyloid formation pathways.

scholarly journals Barriers to Small Molecule Drug Discovery for Systemic Amyloidosis

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3571
Author(s):  
Gareth J. Morgan
Keyword(s):  
Small Molecules ◽  
Light Chain ◽  
Amyloid Fibrils ◽  
Systemic Amyloidosis ◽  
Light Chains ◽  
Al Amyloidosis ◽  
Amyloid Formation ◽  
Amyloid Fibril Formation ◽  
Amyloid Light Chain

Inhibition of amyloid fibril formation could benefit patients with systemic amyloidosis. In this group of diseases, deposition of amyloid fibrils derived from normally soluble proteins leads to progressive tissue damage and organ failure. Amyloid formation is a complex process, where several individual steps could be targeted. Several small molecules have been proposed as inhibitors of amyloid formation. However, the exact mechanism of action for a molecule is often not known, which impedes medicinal chemistry efforts to develop more potent molecules. Furthermore, commonly used assays are prone to artifacts that must be controlled for. Here, potential mechanisms by which small molecules could inhibit aggregation of immunoglobulin light-chain dimers, the precursor proteins for amyloid light-chain (AL) amyloidosis, are studied in assays that recapitulate different aspects of amyloidogenesis in vitro. One molecule reduced unfolding-coupled proteolysis of light chains, but no molecules inhibited aggregation of light chains or disrupted pre-formed amyloid fibrils. This work demonstrates the challenges associated with drug development for amyloidosis, but also highlights the potential to combine therapies that target different aspects of amyloidosis.

Conformational Preferences of Aβ25-35 and Aβ35-25 in Membrane Mimicking Environments

2019 ◽  
Vol 26 (5) ◽  
pp. 386-390
Author(s):  
Dhandayuthapani Sambasivam ◽  
Senthilkumar Sivanesan ◽  
Sayeeda Sultana ◽  
Jayakumar Rajadas
Keyword(s):  
Structural Transition ◽  
Conformational Transition ◽  
The Other ◽  
Random Coil ◽  
Structural Modifications ◽  
Sds Micelles ◽  
Conformational Preferences ◽  
Helix Conformation ◽  
Α Helix ◽  
Β Sheet

Background: The structural transition of aggregating Abeta peptides is the key event in the progression of Alzheimer’s Disease (AD). Objective: In the present work, the structural modifications of toxic Aβ25-35 and the scrambled Aβ35-25 were studied in Trifluoroethanol (TFE) and in aqueous SDS micelles. Methods: Using CD spectroscopic investigations, the conformational transition of Aβ25-35 and Aβ35-25 peptides were determined in different membrane mimicking environments such as TFE and SDS. An interval scan CD of the peptides on evaporation of TFE was performed. TFE titrations were carried out to investigate the intrinsic ability of the structural conformations of peptides. Results: We show by spectroscopic evidence that Aβ25-35 prefers beta sheet structures upon increasing TFE concentrations. On the other hand, the non-toxic scrambled Aβ35-25 peptide only undergoes a transition from random coil to α-helix conformation with increasing TFE. In the interval scan studies, Aβ25-35 did not show any structural transitions, whereas Aβ35-25 showed transition from α-helix to β-sheet conformation. In membrane simulating aqueous SDS micelles, Aβ25-35 showed a transition from random coil to α-helix while Aβ35-25 underwent transition from random coil to β-sheet conformation. Conclusion: Overall, the current results seek new insights into the structural properties of amyloidogenic and the truncated sequence in membrane mimicking solvents.

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