The physical chemistry of the amyloid phenomenon: thermodynamics and kinetics of filamentous protein aggregation

2014 ◽  
Vol 56 ◽  
pp. 11-39 ◽  
Author(s):  
Alexander K. Buell ◽  
Christopher M. Dobson ◽  
Tuomas P.J. Knowles
Keyword(s):  
Protein Aggregation ◽  
Molecular Chaperones ◽  
Amyloid Fibrils ◽  
Theoretical Modelling ◽  
Amyloid Formation ◽  
Recent Developments ◽  
The Individual ◽  
Kinetics Of ◽  
Soluble State ◽  
Insight Into

In this chapter, we present an overview of the kinetics and thermodynamics of protein aggregation into amyloid fibrils. The perspective we adopt is largely experimental, but we also discuss recent developments in data analysis and we show that only a combination of well-designed experiments with appropriate theoretical modelling is able to provide detailed mechanistic insight into the complex pathways of amyloid formation. In the first part of the chapter, we describe measurements of the thermodynamic stability of the amyloid state with respect to the soluble state of proteins, as well as the magnitude and origin of this stability. In the second part, we discuss in detail the kinetics of the individual molecular steps in the overall mechanism of the conversion of soluble protein into amyloid fibrils. Finally, we highlight the effects of external factors, such as salt type and concentration, chemical denaturants and molecular chaperones on the kinetics of aggregation.

scholarly journals Suppression of aggregate and amyloid formation by a novel intrinsically disordered region in metazoan Hsp110 chaperones

2021 ◽  
Author(s):  
Unekwu M. Yakubu ◽  
Kevin A. Morano
Keyword(s):  
Protein Aggregation ◽  
Molecular Chaperones ◽  
Citrate Synthase ◽  
Neuronal Cell ◽  
Amyloid Formation ◽  
Nucleotide Exchange ◽  
Aggregation Assay ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Region

AbstractMolecular chaperones maintain protein homeostasis (proteostasis) by ensuring the proper folding of polypeptides. Loss of proteostasis has been linked to the onset of numerous neurodegenerative disorders including Alzheimer’s, Parkinson’s, and Huntington’s disease. Hsp110 is related to the canonical Hsp70 class of protein folding molecular chaperones and interacts with Hsp70 as a nucleotide exchange factor (NEF), promoting rapid cycling of ADP for ATP. In addition to its NEF activity, Hsp110 possesses an Hsp70-like substrate binding domain (SBD) whose biological roles remain undefined. Previous work in Drosophila melanogaster has shown that loss of the sole Hsp110 gene (Hsc70cb) accelerates the aggregation of polyglutamine (polyQ)-expanded human Huntingtin, while its overexpression protects against polyQ-mediated neuronal cell death. We hypothesize that in addition to its role as an Hsp70 NEF, Drosophila Hsp110 may function in the fly as a protective protein “holdase”, preventing the aggregation of unfolded polypeptides via the SBD-β subdomain. Using an in vitro protein aggregation assay we demonstrate for the first time that Drosophila Hsp110 effectively prevents aggregation of the model substrate citrate synthase. We also report the discovery of a redundant and heretofore unknown potent holdase capacity in a 138 amino-acid region of Hsp110 carboxyl-terminal to both SBD-β and SBD-α (henceforth called the C-terminal extension). This sequence is highly conserved in metazoan Hsp110 genes, completely absent from fungal representatives, including Saccharomyces cerevisiae SSE1, and is computationally predicted to contain an intrinsically disordered region (IDR). We demonstrate that this IDR sequence within the human Hsp110s, Apg-1 and Hsp105α, inhibits the formation of amyloid Aβ-42 and α-synuclein fibrils in vitro but cannot mediate fibril disassembly. Together these findings demonstrate the existence of a second independent, passive holdase property of metazoan Hsp110 chaperones capable of suppressing both general protein aggregation and amyloidogenesis and raise the possibility of exploitation of this IDR for therapeutic benefit in combating neurodegenerative disease.

scholarly journals Codon 129 polymorphism of the human prion protein influences the kinetics of amyloid formation

2006 ◽  
Vol 87 (8) ◽  
pp. 2443-2449 ◽  
Author(s):  
Patrick A. Lewis ◽  
M. Howard Tattum ◽  
Samantha Jones ◽  
Daljit Bhelt ◽  
Mark Batchelor ◽  
...  
Keyword(s):  
Prion Protein ◽  
Amyloid Fibrils ◽  
Prion Diseases ◽  
Amyloid Formation ◽  
Native Structure ◽  
Prion Strain ◽  
Profound Influence ◽  
Human Prion Protein ◽  
Kinetics Of ◽  
Codon 129

The human prion protein (PrP) has a common polymorphism at residue 129, which can be valine or methionine. This polymorphism has a strong influence on susceptibility to prion diseases and on prion-strain properties. Previous work has shown that this amino acid variation has no measurable effect on the native structure of cellular PrP (PrPC). Here, it is shown that the polymorphism does not change the efficiency of conversion to the β-PrP conformation or affect the binding of copper(II) ions. However, in a partially denatured conformation, the polymorphic variation has a profound influence on the ability of the protein to form amyloid fibrils spontaneously.

scholarly journals The Enigma of Amyloid Forming Proteins: Insights From Molecular Simulations

2019 ◽  
Vol 72 (8) ◽  
pp. 574 ◽  
Author(s):  
Nevena Todorova ◽  
Irene Yarovsky
Keyword(s):  
Amyloid Fibrils ◽  
Conformational Dynamics ◽  
Computational Modelling ◽  
Amyloid Β ◽  
Local Environment ◽  
Theoretical Modelling ◽  
Apolipoprotein C ◽  
Amyloidogenic Peptides ◽  
Insight Into ◽  
Aggregation Phenomena

Molecular level insight into the interplay between protein sequence, structure, and conformational dynamics is crucial for the comprehensive understanding of protein folding, misfolding, and aggregation phenomena that are pertinent to the formation of amyloid fibrils implicated in several degenerative diseases. Computational modelling provides insight into protein behaviour at spatial and temporal resolution still largely outside the reach of experiments. Herein we present an account of our theoretical modelling research conducted in collaboration with several experimental groups where we explored the effects of local environment on the structure and aggregation propensity of several types of amyloidogenic peptides and proteins, including apolipoprotein C-II, insulin, amylin, and amyloid-β using a variety of computational approaches.

scholarly journals The Kinetics of Amyloid Fibril Formation by de Novo Protein Albebetin and Its Mutant Variants

Biomolecules ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 241
Author(s):  
Vitalii Balobanov ◽  
Rita Chertkova ◽  
Anna Egorova ◽  
Dmitry Dolgikh ◽  
Valentina Bychkova ◽  
...  
Keyword(s):  
Amyloid Fibrils ◽  
De Novo ◽  
Point Mutations ◽  
Inhibitory Effect ◽  
Structural Basis ◽  
Amyloid Formation ◽  
Amyloid Fibril Formation ◽  
External Conditions ◽  
New Perspective ◽  
Kinetics Of

Engineering of amyloid structures is one of the new perspective areas of protein engineering. Studying the process of amyloid formation can help find ways to manage it in the interests of medicine and biotechnology. One of the promising candidates for the structural basis of artificial functional amyloid fibrils is albebetin (ABB), an artificial protein engineered under the leadership of O.B. Ptitsyn. Various aspects of the amyloid formation of this protein and some methods for controlling this process are investigated in this paper. Four stages of amyloid fibrils formation by this protein from the first non-fibrillar aggregates to mature fibrils and large micron-sized complexes have been described in detail. Dependence of albebetin amyloids formation on external conditions and some mutations also have been described. The introduction of similar point mutations in the two structurally identical α-β-β motifs of ABB lead to different amiloidogenesis kinetics. The inhibitory effect of a disulfide bond and high pH on amyloid fibrils formation, that can be used to control this process, was shown. The results of this work are a good basis for the further design and use of ABB-based amyloid constructs.

scholarly journals The Hsc70 disaggregation machinery removes monomer units directly from α-synuclein fibril ends

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Matthias M. Schneider ◽  
Saurabh Gautam ◽  
Therese W. Herling ◽  
Ewa Andrzejewska ◽  
Georg Krainer ◽  
...  
Keyword(s):  
Molecular Chaperones ◽  
De Novo ◽  
Cellular Protein ◽  
Amyloid Formation ◽  
First Order ◽  
Hsp70 Family ◽  
First Order Kinetics ◽  
Reaction Proceeds ◽  
Kinetics Of

AbstractMolecular chaperones contribute to the maintenance of cellular protein homoeostasis through assisting de novo protein folding and preventing amyloid formation. Chaperones of the Hsp70 family can further disaggregate otherwise irreversible aggregate species such as α-synuclein fibrils, which accumulate in Parkinson’s disease. However, the mechanisms and kinetics of this key functionality are only partially understood. Here, we combine microfluidic measurements with chemical kinetics to study α-synuclein disaggregation. We show that Hsc70 together with its co-chaperones DnaJB1 and Apg2 can completely reverse α-synuclein aggregation back to its soluble monomeric state. This reaction proceeds through first-order kinetics where monomer units are removed directly from the fibril ends with little contribution from intermediate fibril fragmentation steps. These findings extend our mechanistic understanding of the role of chaperones in the suppression of amyloid proliferation and in aggregate clearance, and inform on possibilities and limitations of this strategy in the development of therapeutics against synucleinopathies.

scholarly journals Hsp40s display class-specific binding profiles, serving complementary roles in the prevention of tau amyloid formation

2021 ◽  
Author(s):  
Rose Irwin ◽  
Ofrah Faust ◽  
Ivana Petrovic ◽  
Sharion Grayer Wolf ◽  
Hagen Hofmann ◽  
...  
Keyword(s):  
Molecular Chaperones ◽  
Specific Binding ◽  
Small Heat Shock Protein ◽  
Fiber Formation ◽  
Amyloid Formation ◽  
Protein Homeostasis ◽  
Protein Tau ◽  
Amyloid Fiber Formation ◽  
Tau Aggregation ◽  
Insight Into

The microtubule-associated protein, tau, is the major subunit of neurofibrillary tangles, forming insoluble, amyloid-type aggregates associated with neurodegenerative conditions, such as Alzheimer's disease. Tau aggregation, however, can be prevented in the cell by a class of proteins known as molecular chaperones, which play important roles in maintaining protein homeostasis. While numerous chaperones are known to interact with tau, though, little is known about the detailed mechanisms by which these prevent tau aggregation. Here, we describe the effects of the ATP-independent Hsp40 chaperones, DNAJA2 and DNAJB1, on tau amyloid fiber formation and compare these to the well-studied small heat shock protein HSPB1. We find that each chaperone prevents tau aggregation differently, by interacting with distinct sets of tau species along the aggregation pathway and thereby affecting their incorporation into fibers. Whereas HSPB1 only binds tau monomers, DNAJB1 and DNAJA2 recognize aggregation-prone tau conformers and even mature fibers, thus efficiently preventing formation of tau amyloids. In addition, we find that both Hsp40s bind tau seeds and fibers via their C-terminal domain II (CTDII), with DNAJA2 being further capable of recognizing tau monomers by a second, different site in CTDI. These results provide important insight into the molecular mechanism by which the different members of the Hsp40 chaperone family counteract the formation, propagation, and toxicity of tau aggregates. Furthermore, our findings highlight the fact that chaperones from different families and different classes play distinct, but complementary roles in preventing pathological protein aggregation.

scholarly journals Effect of spin labelling on the aggregation kinetics of yeast prion protein Ure2

2021 ◽  
Vol 8 (3) ◽  
Author(s):  
Emilie N. Liu ◽  
Giovanna Park ◽  
Junsuke Nohara ◽  
Zhefeng Guo
Keyword(s):  
Protein Aggregation ◽  
Amyloid Fibrils ◽  
Prion Diseases ◽  
Aggregation Kinetics ◽  
Amyloid Formation ◽  
Yeast Prion ◽  
Aggregation Rate ◽  
Rate Limiting Step ◽  
Wide Range ◽  
Spin Labelling

Amyloid formation is involved in a wide range of neurodegenerative diseases including Alzheimer's and prion diseases. Structural understanding of the amyloid is critical to delineate the mechanism of aggregation and its pathological spreading. Site-directed spin labelling has emerged as a powerful structural tool in the studies of amyloid structures and provided structural evidence for the parallel in-register β-sheet structure for a wide range of amyloid proteins. It is generally accepted that spin labelling does not disrupt the structure of the amyloid fibrils, the end product of protein aggregation. The effect on the rate of protein aggregation, however, has not been well characterized. Here, we employed a scanning mutagenesis approach to study the effect of spin labelling on the aggregation rate of 79 spin-labelled variants of the Ure2 prion domain. The aggregation of Ure2 protein is the basis of yeast prion [URE3]. We found that all spin-labelled Ure2 mutants aggregated within the experimental timeframe of 15 to 40 h. Among the 79 spin-labelled positions, only five residue sites (N23, N27, S33, I35 and G42) showed a dramatic delay in the aggregation rate as a result of spin labelling. These positions may be important for fibril nucleation, a rate-limiting step in aggregation. Importantly, spin labelling at most of the sites had a muted effect on Ure2 aggregation kinetics, showing a general tolerance of spin labelling in protein aggregation studies.

scholarly journals A Biocompatible Fluorescent Probe for the Selective Detection of Amyloid Fibrils

2020 ◽  
Author(s):  
Anirban Das ◽  
Tanoy Dutta ◽  
Laxmikant Gadhe ◽  
Apurba Koner ◽  
Ishu Saraogi
Keyword(s):  
Amyloid Fibrils ◽  
Intramolecular Charge Transfer ◽  
Aggregation Kinetics ◽  
Amyloid Formation ◽  
Cellular Internalization ◽  
Protein Fibrils ◽  
Model Protein ◽  
Low Toxicity ◽  
Kinetics Of ◽  
Biological Milieu

The misfolding and aggregation of proteins leading to amyloid formation has been linked to numerous diseases, necessitating the development of tools to monitor the fibrillation process. Here we report an intramolecular charge transfer (ICT) dye, DMNDC, as an alternative to Thioflavin-T (ThT), most commonly used for monitoring amyloid fibrils. Using insulin as a model protein, we show that DMNDC efficiently detects all stages of fibril formation, namely, nucleation, elongation, and saturation. An approximately 70 nm hypsochromic shift along with a large increase in emission intensity was observed upon binding of DMNDC to protein fibrils. The aggregation kinetics of insulin remained unaffected at excess DMNDC concentration, suggesting that DMNDC does not inhibit insulin aggregation. Additionally, the efficient cellular internalization and low toxicity of DMNDC make it highly suited for sensing and imaging of amyloid fibrils in the complex biological milieu.<br>

Events and festivals in Asia and the Middle East/North Africa (MENA) region

2012 ◽  
Vol 3 (1) ◽  
pp. 4-8 ◽  
Author(s):  
Karin Weber ◽  
Jane Ali‐Knight
Keyword(s):  
Mena Region ◽  
Content Type ◽  
Qualitative Approaches ◽  
Recent Developments ◽  
Individual Contributions ◽  
Key Issues ◽  
The Subject ◽  
The Individual ◽  
Insight Into ◽  
Selection Of

PurposeThis editorial aims to provide a brief overview of recent developments in the events industry in general, and in Asia and the MENA region in particular. The discussion forms a prelude for the individual contributions of this special issue.Design/methodology/approachThe papers cover a variety of different research methods and methodologies including both quantitative and qualitative approaches.FindingsSetting the stage for the selection of papers is a thought‐provoking introduction, followed by six papers that aim to provide insights into key issues by examining pertinent literature, addressing relevant research questions, and providing applied and theoretical outcomes relevant to both academics and practitioners in the event and festival fields. These papers cover the variety, scope and diversity of events in Asia and MENA region, with a mixture of papers that examine event‐specific aspects and those that approach the subject from a broader destination/policy perspective.Originality/valueThe selection of papers are unique as they provide a thorough and extensive insight into the opportunities and challenges facing emergent festival and event destinations in Asia and the MENA region.

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