Hierarchical Assembly of β2-Microglobulin Amyloid In Vitro Revealed by Atomic Force Microscopy

Kad, Neil M.; Myers, Sarah L.; Smith, David P.; Smith, D. A.; Radford, Sheena E.; Thomson, Neil H.

doi:10.1016/s0022-2836(03)00583-7

Cited by 214 publications

(185 citation statements)

References 65 publications

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“…The lag period of these curves is well accepted as being a nucleation stage during which nonfluorescent oligomeric species are formed prior to the fibrillar structures that will grow under a subsequent rapid, cooperative regime. This behavior is that which has most frequently been observed among the many amyloidogenic proteins studied to date [3,[17][18][19].…”

Section: Ans and Tht Fluorescence Experiments Reveal A Lag-phase Durimentioning

confidence: 59%

A comparative analysis of the folding and misfolding pathways of the third PDZ domain of PSD95 investigated under different pH conditions

Murciano-Calles

Cobos

Mateo

et al. 2011

Biophysical Chemistry

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comparative analysis of the folding and misfolding pathways of the third PDZ domain of PSD95 investigated under different pH conditions. Biophysical Chemistry, Elsevier, 2011, 158 (2-3) This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT AbstractEquilibrium unfolding at neutral pH of the third PDZ domain of PSD95 is well described by the presence of a partly unfolded intermediate that presents association phenomena. After some days' incubation annular and fibrillar structures form from the oligomers. At pH values below 3, however, differential scanning calorimetry shows that PDZ3 seems to unfold under a two-state scheme. Kinetic measurements followed by dynamic light scattering, ThT and ANS fluorescence reveal that the misfolding pathway still exists despite the absence of any populated intermediates and shows an irreversible assembling of the supramacromolecular structures as well as an appreciable lag-phase, contrary to what is found in similar experiments at neutral pH. Moreover, as shown by transmission-electronmicroscopy images, the annular structures seen at neutral pH completely disappear from incubated solutions. According to the structural information, this titration behavior appears to be the consequence of a conformational equilibrium that depends on the protonation of some Glu residues located at the C-terminal α3 helix and at the hairpin formed by strands β2 and β3. Our calculations suggest that the enthalpic contribution of these interactions may well be as much as 40 kJ·mol -1 . The possible regulatory role of this equilibrium upon PDZ3 functionality and amyloid formation is briefly discussed. A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT IntroductionProtein aggregation is considered today to be a generic property of polypeptides and is thus a considerable problem for living organisms, which must develop response strategies to avoid its harmful effects. These effects span from arthritis to serious neurodegenerative diseases. At the molecular and energetic level, the self-organization mechanism of proteins relies on many properties related to both the protein system (hydrophobicity, β-sheet propensities etc.) and the solvent conditions (pH, ionic strength, organic reagents etc.). These properties can modulate the misfolding pathway in ways ranging from downhill to nucleationcooperative aggregation mechanisms.In spite of extensive reports in the literature, our knowledge of the basic processes by which polypeptide chains can give rise to well ordered supramacromolecular structures is still poorly understood [1]. It has been sug...

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Section: Ans and Tht Fluorescence Experiments Reveal A Lag-phase Durimentioning

confidence: 59%

A comparative analysis of the folding and misfolding pathways of the third PDZ domain of PSD95 investigated under different pH conditions

Murciano-Calles

Cobos

Mateo

et al. 2011

Biophysical Chemistry

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“…Additionally, as Wu and coworkers have demonstrated, the use of scattering-based techniques [73], including X-ray / neutron scattering and light scattering, combined with theory and simulation should be very useful in the study of aggregation-prone IDPs. Several groups in the amyloid field are already pursuing these types of multi-faceted approaches [5,84,[94][95][96][97][98][99][100][101][102][103][104][105][106][107]. However, we remain blind to interactions and conformational fluctuations that occur at low concentrations.…”

Section: Tests Of the Predictions Made By Raos And Allegramentioning

confidence: 99%

A polymer physics perspective on driving forces and mechanisms for protein aggregation

Pappu

Wang

Vitalis

et al. 2008

Archives of Biochemistry and Biophysics

159

172

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Protein aggregation is a commonly occurring problem in biology. Cells have evolved stress-response mechanisms to cope with problems posed by protein aggregation. Yet, these quality control mechanisms are overwhelmed by chronic aggregation-related stress and the resultant consequences of aggregation become toxic to cells. As a result, a variety of systemic and neurodegenerative diseases are associated with various aspects of protein aggregation and rational approaches to either inhibit aggregation or manipulate the pathways to aggregation might lead to an alleviation of disease phenotypes. To develop such approaches, one needs a rigorous and quantitative understanding of protein aggregation. Much work has been done in this area. However, several unanswered questions linger, and these pertain primarily to the actual mechanism of aggregation as well as to the types of intermolecular associations and intramolecular fluctuations realized at low protein concentrations. It has been suggested that the concepts underlying protein aggregation are similar to those used to describe the aggregation of synthetic polymers. Following this suggestion, the relevant concepts of polymer aggregation are introduced. The focus is on explaining the driving forces for polymer aggregation and how these driving forces vary with chain length and solution conditions. It is widely accepted that protein aggregation is a nucleation-dependent process. This view is based mainly on the presence of long times for the accumulation of aggregates and the elimination of these lag times with "seeds". In this sense, protein aggregation is viewed as being analogous to the aggregation of colloidal particles. The theories for polymer aggregation reviewed in this work suggest an alternative mechanism for the origin of long lag times in protein aggregation. The proposed mechanism derives from the recognition that polymers have unique dynamics that distinguish them from other aggregation-prone systems such as colloidal particles.

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“…The determination of detailed structures of the mature fibrils is also challenging due to their intractable and frequently heterogeneous nature, which again seriously limits the application of the traditional methods of structural biology such as solution NMR spectroscopy and X-ray diffraction techniques. Structural information concerning amyloid fibrils has, however, been obtained from atomic force microscopy (AFM) [30,31], FTIR [32,33], X-ray fibre diffraction studies [17], cryoelectron microscopy [34,35], hydrogen/deuterium exchange analysed by mass spectrometry and NMR [36][37][38][39] and solid state NMR [40,41]. Important information about both the structures of the aggregates and the mechanism of their formation has also been obtained by using methods such as limited proteolysis [42,43], systematic site-directed mutagenesis [44][45][46], and the analysis of the effects of interactions with specific antibodies.…”

Section: The Generic Nature Of the Amyloid Structurementioning

confidence: 99%

Probing the origins, diagnosis and treatment of amyloid diseases using antibodies

Dumoulin

Dobson

2004

Biochimie

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The deposition of proteins in the form of amyloid fibrils is the characteristic feature of more than 20 medical conditions affecting the central nervous system or a variety of peripheral tissues. These disorders, which include Alzheimer's disease, the prion diseases and type II diabetes, are of enormous importance in the context of present-day human health and welfare. Extensive research is therefore being carried out to define the molecular details of the mechanism of the pathological conversion of amyloidogenic proteins from their soluble forms into fibrillar structures. This review focuses on recent studies that demonstrate the power of using antibodies or antibody fragments to probe the process of fibril formation, and discusses the emerging potential of these species as diagnostic and therapeutic agents.

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Hierarchical Assembly of β2-Microglobulin Amyloid In Vitro Revealed by Atomic Force Microscopy

Cited by 214 publications

References 65 publications

A comparative analysis of the folding and misfolding pathways of the third PDZ domain of PSD95 investigated under different pH conditions

A comparative analysis of the folding and misfolding pathways of the third PDZ domain of PSD95 investigated under different pH conditions

A polymer physics perspective on driving forces and mechanisms for protein aggregation

Probing the origins, diagnosis and treatment of amyloid diseases using antibodies

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