Determination of Polypeptide Conformation with Nanoscale Resolution in Water

Ramer, Georg; Ruggeri, Francesco Simone; Levin, Aviad; Knowles, Tuomas P. J.; Centrone, Andrea

doi:10.1021/acsnano.8b01425

Cited by 110 publications

(153 citation statements)

References 57 publications

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“…In addition, this approach has enabled the direct measurement and correlation of the morphological, chemical and secondary/quaternary structural properties of protein and for characterizing a wide range of systems in life science at the nanoscale [ 25 , 28 ]. More specifically, the method has excelled in studying the properties of heterogeneous samples, such as protein micro-droplets for drug delivery [ 31 ], the process of protein aggregation and amyloid formation [ 25 , 32 , 33 , 34 , 35 ], localization of glycogen structure with specific IR signature inside Candida albicans fungi cells [ 36 ], viruses inside infected bacteria [ 37 ], polymers inside Rhodobacter capsulatus cells [ 38 ], distribution of protein-rich material in E. Coli and human HeLa cells [ 39 ], presence of exogenous elements such as metal-carbonyl compounds in human cells, hair composition [ 40 ] and variations in the primate osteonal bone composition [ 41 , 42 ].…”

Section: Introductionmentioning

confidence: 99%

Identification of Oxidative Stress in Red Blood Cells with Nanoscale Chemical Resolution by Infrared Nanospectroscopy

Ruggeri

Marcott

Dinarelli

et al. 2018

IJMS

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During their lifespan, Red blood cells (RBC), due to their inability to self-replicate, undergo an ageing degradation phenomenon. This pathway, both in vitro and in vivo, consists of a series of chemical and morphological modifications, which include deviation from the biconcave cellular shape, oxidative stress, membrane peroxidation, lipid content decrease and uncoupling of the membrane-skeleton from the lipid bilayer. Here, we use the capabilities of atomic force microscopy based infrared nanospectroscopy (AFM-IR) to study and correlate, with nanoscale resolution, the morphological and chemical modifications that occur during the natural degradation of RBCs at the subcellular level. By using the tip of an AFM to detect the photothermal expansion of RBCs, it is possible to obtain nearly two orders of magnitude higher spatial resolution IR spectra, and absorbance images than can be obtained on diffraction-limited commercial Fourier-transform Infrared (FT-IR) microscopes. Using this approach, we demonstrate that we can identify localized sites of oxidative stress and membrane peroxidation on individual RBC, before the occurrence of neat morphological changes in the cellular shape.

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Section: Introductionmentioning

confidence: 99%

Identification of Oxidative Stress in Red Blood Cells with Nanoscale Chemical Resolution by Infrared Nanospectroscopy

Ruggeri

Marcott

Dinarelli

et al. 2018

IJMS

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“…The spectra were acquired by using measuring off-resonance, on the left of the IR amplitude maximum resonant frequency. 35,44,45 Spectra analysis Spectra were analysed using the microscope's built-in Analysis Studio (Anasys) and OriginPRO. The spectra where despiked, an adjacent averaging filter (5pts) and a Savitzky-Golay filter (15 pts, 2 nd order) were applied in series and then the spectra were normalised to one respect to the maximum of intensity.…”

Section: Afm-ir Measurements Maps Treatment and Analysismentioning

confidence: 99%

“…[24][25][26][27][28][29][30][31][32][33][34] AFM-IR is becoming widely applicable in biology since is capable of acquiring simultaneously morphological, nanomechanical and nanoscale-resolved chemical IR maps and absorption spectra from protein aggregates, liquid-liquid phase separated condensates, chromosomes, and single cells. 29,31,[34][35][36] As fundamental achievement, we have recently demonstrated that AFM-IR enables to acquire infrared absorption spectra for secondary structure determination from single protein molecules. 37 In the present work, we exploit the powerful combination of single molecule imaging and vibrational spectroscopy offered by AFM-IR to characterise at the single aggregate scale the morphological, chemical and structural properties of the aggregate species of A42 in the absence and the presence of bexarotene.…”

mentioning

confidence: 99%

Infrared Nanospectroscopy Reveals the Molecular Interaction Fingerprint of an Aggregation Inhibitor with Single Aβ42 Oligomers

Ruggeri

Habchi

Chia

et al. 2020

Preprint

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Very significant efforts have been devoted in the last twenty years to developing compounds that can interfere with the aggregation pathways of proteins related to misfolding disorders, including Alzheimer's and Parkinson's diseases. However, no disease-modifying drug has become available for clinical use to date for these conditions. One of the main reasons for this failure is the incomplete knowledge of the molecular mechanisms underlying the process by which small molecules interact with protein aggregates and interfere with their aggregation pathways. Here, we leverage the single molecule level morphological and chemical sensitivity of infrared nanospectroscopy to provide the first direct measurement of the interaction between single A42 oligomeric and fibrillar species and an aggregation inhibitor, bexarotene, originally an anticancer drug capable recently shown to be able to inhibit A42 aggregation in animal models of Alzheimer's disease.Our results demonstrate that the carbonyl group of this compound interacts with A42 aggregates through a single hydrogen bond. These results establish infrared nanospectroscopy as powerful tool in structure-based drug discovery for protein misfolding diseases.Alzheimer's disease (AD) is characterised by memory loss and cognitive impairment. AD is the primary cause of dementia, which affects currently over 50 million people worldwide, a number expected to exceed 150 million by 2050. 1-3 The self-assembly of the 42-residue isoform of the amyloid- (A) peptide into intractable aggregates is considered to be at the core of the molecular pathways leading to AD. [3][4][5] It is therefore important to understand at the molecular level the aggregation process of A42 in order to develop effective therapeutic strategies that aim at inhibiting its self-assembly.Great efforts have been devoted in the last twenty years to understand the molecular basis of this devastating disorder and to develop small molecules that could interfere with the aggregation pathway of A42. 6-12 Indeed, disease-modifying small molecules represent c.a. one third of the registered trials, in which anti-A therapies dominate. 13 However, despite these efforts, no compound has entered the clinical use to date. 13,14 These repeated failures are in part related to an incomplete understanding of the molecular mechanisms underlying the process by which small molecules interact with protein aggregates and how they interfere with the pathways of aggregation. It is increasingly recognised that inhibiting A aggregation per se could have unexpected consequences on the toxicity, as it could not only decrease it, but also leave it unaffected, or even increase it. 15 This complexity is due to the non-linear nature of the aggregation network, in which neurotoxic small oligomeric intermediates [16][17][18][19][20] , can be formed in a variety of ways, some of which highly sensitive to small perturbation. Therefore, promising effective therapeutic strategies must be aimed at targeting precise species in a controlled inte...

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“…AFM‐IR offers a unique opportunity to solve this problem without a substantial sacrifice of sensitivity and spatial resolution . AFM‐IR measures thermal expansions of the sample that are induced by pulsed infrared (IR) radiation .…”

Section: Introductionmentioning

confidence: 99%

Nanoscale Structural Organization of Insulin Fibril Polymorphs Revealed by Atomic Force Microscopy–Infrared Spectroscopy (AFM‐IR)

Rizevsky

Kurouski

2019

ChemBioChem

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Spontaneous aggregation of misfolded proteins typically results in the formation of morphologically and structurally different amyloid fibrils, protein aggregates that are strongly associated with various neurodegenerative disorders. Elucidation of the structural organization of amyloid aggregates is crucial to understanding their role in the onset and progression of these diseases. Using atomic force microscopy–infrared spectroscopy (AFM‐IR), we investigated the structural organization of insulin fibrils. We found that insulin aggregation results in the formation of two structurally different fibril polymorphs. One polymorph has a β‐sheet core surrounded by primarily unordered protein secondary structure. This polymorph has β‐sheet‐rich surface, whereas the surface of the other fibril polymorph is primarily composed of unordered protein. Using AFM‐IR, we also revealed the structural organization of the insulin oligomers. Finally, we discovered a new pathway for amyloid fibril formation that is based on a fusion of several oligomers into a single fibril structure.

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Determination of Polypeptide Conformation with Nanoscale Resolution in Water

Cited by 110 publications

References 57 publications

Identification of Oxidative Stress in Red Blood Cells with Nanoscale Chemical Resolution by Infrared Nanospectroscopy

Identification of Oxidative Stress in Red Blood Cells with Nanoscale Chemical Resolution by Infrared Nanospectroscopy

Infrared Nanospectroscopy Reveals the Molecular Interaction Fingerprint of an Aggregation Inhibitor with Single Aβ42 Oligomers

Nanoscale Structural Organization of Insulin Fibril Polymorphs Revealed by Atomic Force Microscopy–Infrared Spectroscopy (AFM‐IR)

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