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Article ; Online: Unraveling the Physicochemical Determinants of Protein Liquid-liquid Phase Separation by Nanoscale Infrared Vibrational Spectroscopy.

Ruggeri, Francesco S / Miller, Alyssa M / Vendruscolo, Michele / Knowles, Tuomas P J

2021 Volume 11, Issue 16, Page(s) e4122

Abstract: The phenomenon of reversible liquid-liquid phase separation of proteins underlies the formation of membraneless organelles, which are crucial for cellular processes such as signalling and transport. In addition, it is also of great interest to uncover ... ...

Abstract	The phenomenon of reversible liquid-liquid phase separation of proteins underlies the formation of membraneless organelles, which are crucial for cellular processes such as signalling and transport. In addition, it is also of great interest to uncover the mechanisms of further irreversible maturation of the functional dense liquid phase into aberrant insoluble assemblies due to its implication in human disease. Recent advances in methods based on atomic force microscopy (AFM) have made it possible to study protein condensates at the nanometer level, providing unprecedented information on the nature of the intermolecular interactions governing phase separation. Here, we provide an in-depth description of a protocol for the characterisation of the morphology, stiffness, and chemical properties of protein condensates using infrared nanospectroscopy (AFM-IR).
Language	English
Publishing date	2021-08-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	2833269-6
ISSN	2331-8325 ; 2331-8325
ISSN (online)	2331-8325
ISSN	2331-8325
DOI	10.21769/BioProtoc.4122
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Article ; Online: Unraveling the physicochemical determinants of protein liquid-liquid phase separation by nanoscale infrared vibrational spectroscopy

Ruggeri, Francesco S. / Miller, Alyssa M. / Vendruscolo, Michele / Knowles, Tuomas P.J.

Bio-protocol

2021 Volume 11, Issue 16

Abstract	The phenomenon of reversible liquid-liquid phase separation of proteins underlies the formation of membraneless organelles, which are crucial for cellular processes such as signalling and transport. In addition, it is also of great interest to uncover the mechanisms of further irreversible maturation of the functional dense liquid phase into aberrant insoluble assemblies due to its implication in human disease. Recent advances in methods based on atomic force microscopy (AFM) have made it possible to study protein condensates at the nanometer level, providing unprecedented information on the nature of the intermolecular interactions governing phase separation. Here, we provide an in-depth description of a protocol for the characterisation of the morphology, stiffness, and chemical properties of protein condensates using infrared nanospectroscopy (AFM-IR).
Keywords	Atomic force microscopy ; Infrared nanospectroscopy ; Liquid-liquid phase separation ; Single-molecule biophysics
Subject code	612
Language	English
Publishing country	nl
Document type	Article ; Online
ZDB-ID	2833269-6
ISSN	2331-8325
ISSN	2331-8325
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Thermoresponsive, Pyrrolidone-Based Antifouling Polymer Brushes

Teunissen, Lucas W. / Kuzmyn, Andriy R. / Ruggeri, Francesco S. / Smulders, Maarten M.J. / Zuilhof, Han

Advanced Materials Interfaces

2022 Volume 9, Issue 6

Abstract: Commonly, modification of surfaces with thermoresponsive polymers is performed using poly(N-isopropylacrylamide) (poly(NIPAM)). However, integration of poly(NIPAM) with a second polymer to obtain more complex copolymer structures has proven challenging ... ...

Abstract	Commonly, modification of surfaces with thermoresponsive polymers is performed using poly(N-isopropylacrylamide) (poly(NIPAM)). However, integration of poly(NIPAM) with a second polymer to obtain more complex copolymer structures has proven challenging due to inherently poorly controllable polymerization characteristics of acrylamides. In this study, (N-(2-methacryloyloxyethyl)pyrrolidone (NMEP) is synthesized and polymerized under controlled conditions from silicon oxide substrates via surface-initiated atom transfer radical polymerization (SI-ATRP) to produce thermoresponsive poly(NMEP) brushes. The livingness of the brushes is demonstrated by reinitiation of poly(NMEP) brushes using oligo(ethylene glycol) methyl ether methacrylate to obtain diblock copolymer brushes. Following extensive characterization, the reversible thermoresponsive behavior of these poly(NMEP) brushes is demonstrated using phase-controlled AFM topography measurements in an aqueous liquid environment. These measurements indicate that at 27 °C the poly(NMEP) brushes are solvated and extend away from the surface, whereas at 60 °C the polymers are insoluble and reside in a collapsed conformation. Finally, to investigate the potential applicability of poly(NMEP) brushes in biomedical devices, the antifouling properties of the coating are tested in aqueous media containing BSA, fibrinogen, or 10% diluted human serum using quartz crystal microbalance with dissipation monitoring (QCM-D). These measurements reveal very good antifouling properties, even when exposed to 10% diluted human serum.
Keywords	bioactive surfaces ; copolymers ; smart coatings ; surface-initiated atom transfer radical polymerization ; thermoresponsive polymer brushes
Subject code	540
Language	English
Publishing country	nl
Document type	Article ; Online
ISSN	2196-7350
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The Nt17 Domain and its Helical Conformation Regulate the Aggregation, Cellular Properties and Neurotoxicity of Mutant Huntingtin Exon 1

Vieweg, Sophie / Mahul-Mellier, Anne-Laure / Ruggeri, Francesco S. / Riguet, Nathan / DeGuire, Sean M. / Chiki, Anass / Cendrowska, Urszula / Dietler, Giovanni / Lashuel, Hilal A.

Journal of molecular biology. 2021 Oct. 15, v. 433, no. 21

2021

Abstract: Converging evidence points to the N-terminal domain comprising the first 17 amino acids of the Huntingtin protein (Nt17) as a key regulator of its aggregation, cellular properties and toxicity. In this study, we further investigated the interplay between ...

Abstract	Converging evidence points to the N-terminal domain comprising the first 17 amino acids of the Huntingtin protein (Nt17) as a key regulator of its aggregation, cellular properties and toxicity. In this study, we further investigated the interplay between Nt17 and the polyQ domain repeat length in regulating the aggregation and inclusion formation of exon 1 of the Huntingtin protein (Httex1). In addition, we investigated the effect of removing Nt17 or modulating its local structure on the membrane interactions, neuronal uptake, and toxicity of monomeric or fibrillar Httex1. Our results show that the polyQ and Nt17 domains synergistically modulate the aggregation propensity of Httex1 and that the Nt17 domain plays important roles in shaping the surface properties of mutant Httex1 fibrils and regulating their poly-Q-dependent growth, lateral association and neuronal uptake. Removal of Nt17 or disruption of its transient helical conformations slowed the aggregation of monomeric Httex1 in vitro, reduced inclusion formation in cells, enhanced the neuronal uptake and nuclear accumulation of monomeric Httex1 proteins, and was sufficient to prevent cell death induced by Httex1 72Q overexpression. Finally, we demonstrate that the uptake of Httex1 fibrils into primary neurons and the resulting toxicity are strongly influenced by mutations and phosphorylation events that influence the local helical propensity of Nt17. Altogether, our results demonstrate that the Nt17 domain serves as one of the key master regulators of Htt aggregation, internalization, and toxicity and represents an attractive target for inhibiting Htt aggregate formation, inclusion formation, and neuronal toxicity.
Keywords	cell death ; exons ; molecular biology ; mutants ; neurons ; neurotoxicity ; phosphorylation
Language	English
Dates of publication	2021-1015
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2021.167222
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Article: Effects of sedimentation, microgravity, hydrodynamic mixing and air-water interface on α-synuclein amyloid formation.

Zhou, Jiangtao / Ruggeri, Francesco S / Zimmermann, Manuela R / Meisl, Georg / Longo, Giovanni / Sekatskii, Sergey K / Knowles, Tuomas P J / Dietler, Giovanni

Chemical science

2020 Volume 11, Issue 14, Page(s) 3687–3693

Abstract: The formation of amyloid fibrils is a characterizing feature of a range of protein misfolding diseases, including Parkinson's disease. The propensity of native proteins to form such amyloid fibril, ... ...

Abstract	The formation of amyloid fibrils is a characterizing feature of a range of protein misfolding diseases, including Parkinson's disease. The propensity of native proteins to form such amyloid fibril, both
Language	English
Publishing date	2020-03-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/d0sc00281j
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Article ; Online: Imaging protein aggregates in the serum and cerebrospinal fluid in Parkinson's disease.

Lobanova, Evgeniia / Whiten, Daniel / Ruggeri, Francesco S / Taylor, Christopher G / Kouli, Antonina / Xia, Zengjie / Emin, Derya / Zhang, Yu P / Lam, Jeff Y L / Williams-Gray, Caroline H / Klenerman, David

Brain : a journal of neurology

2021 Volume 145, Issue 2, Page(s) 632–643

Abstract: Aggregation of α-synuclein plays a key role in the development of Parkinson's disease. Soluble aggregates are present not only within human brain but also the CSF and blood. Characterizing the aggregates present in these biofluids may provide insights ... ...

Abstract	Aggregation of α-synuclein plays a key role in the development of Parkinson's disease. Soluble aggregates are present not only within human brain but also the CSF and blood. Characterizing the aggregates present in these biofluids may provide insights into disease mechanisms and also have potential for aiding diagnosis. We used two optical single-molecule imaging methods called aptamer DNA-PAINT and single-aggregate confocal fluorescence, together with high-resolution atomic force microscopy for specific detection and characterization of individual aggregates with intermolecular β-sheet structure, present in the CSF and serum of 15 early stage Parkinson's disease patients compared to 10 healthy age-matched controls. We found aggregates ranging in size from 20 nm to 200 nm, in both CSF and serum. There was a difference in aggregate size distribution between Parkinson's disease and control groups with a significantly increased number of larger aggregates (longer than 150 nm) in the serum of patients with Parkinson's disease. To determine the chemical composition of the aggregates, we performed aptamer DNA-PAINT on serum following α-synuclein and amyloid-β immunodepletion in an independent cohort of 11 patients with early stage Parkinson's disease and 10 control subjects. β-Sheet aggregates in the serum of Parkinson's disease patients were found to consist of, on average, 50% α-synuclein and 50% amyloid-β in contrast to 30% α-synuclein and 70% amyloid-β in control serum [the differences in the proportion of these aggregates were statistically significant between diseased and control groups (P = 1.7 × 10-5 for each species)]. The ratio of the number of β-sheet α-synuclein aggregates to β-sheet amyloid-β aggregates in serum extracted using our super-resolution method discriminated Parkinson's disease cases from controls with an accuracy of 98.2% (AUC = 98.2%, P = 4.3 × 10-5). Our data suggest that studying the protein aggregates present in serum can provide information about the disruption of protein homeostasis occurring in Parkinson's disease and warrants further investigation as a potential biomarker of disease.
MeSH term(s)	Amyloid beta-Peptides/metabolism ; Biomarkers/metabolism ; Brain/metabolism ; Humans ; Parkinson Disease/metabolism ; Protein Aggregates ; alpha-Synuclein/metabolism
Chemical Substances	Amyloid beta-Peptides ; Biomarkers ; Protein Aggregates ; alpha-Synuclein
Language	English
Publishing date	2021-08-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80072-7
ISSN	1460-2156 ; 0006-8950
ISSN (online)	1460-2156
ISSN	0006-8950
DOI	10.1093/brain/awab306
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Article ; Online: The Nt17 Domain and its Helical Conformation Regulate the Aggregation, Cellular Properties and Neurotoxicity of Mutant Huntingtin Exon 1.

Vieweg, Sophie / Mahul-Mellier, Anne-Laure / Ruggeri, Francesco S / Riguet, Nathan / DeGuire, Sean M / Chiki, Anass / Cendrowska, Urszula / Dietler, Giovanni / Lashuel, Hilal A

Journal of molecular biology

2021 Volume 433, Issue 21, Page(s) 167222

Abstract	Converging evidence points to the N-terminal domain comprising the first 17 amino acids of the Huntingtin protein (Nt17) as a key regulator of its aggregation, cellular properties and toxicity. In this study, we further investigated the interplay between Nt17 and the polyQ domain repeat length in regulating the aggregation and inclusion formation of exon 1 of the Huntingtin protein (Httex1). In addition, we investigated the effect of removing Nt17 or modulating its local structure on the membrane interactions, neuronal uptake, and toxicity of monomeric or fibrillar Httex1. Our results show that the polyQ and Nt17 domains synergistically modulate the aggregation propensity of Httex1 and that the Nt17 domain plays important roles in shaping the surface properties of mutant Httex1 fibrils and regulating their poly-Q-dependent growth, lateral association and neuronal uptake. Removal of Nt17 or disruption of its transient helical conformations slowed the aggregation of monomeric Httex1 in vitro, reduced inclusion formation in cells, enhanced the neuronal uptake and nuclear accumulation of monomeric Httex1 proteins, and was sufficient to prevent cell death induced by Httex1 72Q overexpression. Finally, we demonstrate that the uptake of Httex1 fibrils into primary neurons and the resulting toxicity are strongly influenced by mutations and phosphorylation events that influence the local helical propensity of Nt17. Altogether, our results demonstrate that the Nt17 domain serves as one of the key master regulators of Htt aggregation, internalization, and toxicity and represents an attractive target for inhibiting Htt aggregate formation, inclusion formation, and neuronal toxicity.
MeSH term(s)	Animals ; Cloning, Molecular ; Corpus Striatum/cytology ; Corpus Striatum/metabolism ; Cryoelectron Microscopy ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Exons ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; HEK293 Cells ; Humans ; Huntingtin Protein/chemistry ; Huntingtin Protein/genetics ; Huntingtin Protein/metabolism ; Microscopy, Atomic Force ; Mutation ; Neurons/cytology ; Neurons/metabolism ; Phosphorylation ; Primary Cell Culture ; Protein Aggregates ; Protein Conformation, alpha-Helical ; Protein Engineering/methods ; Protein Folding ; Rats ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism
Chemical Substances	HTT protein, human ; Huntingtin Protein ; Protein Aggregates ; Recombinant Proteins
Language	English
Publishing date	2021-09-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2021.167222
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Article ; Online: Identification of Oxidative Stress in Red Blood Cells with Nanoscale Chemical Resolution by Infrared Nanospectroscopy.

Ruggeri, Francesco S / Marcott, Curtis / Dinarelli, Simone / Longo, Giovanni / Girasole, Marco / Dietler, Giovanni / Knowles, Tuomas P J

International journal of molecular sciences

2018 Volume 19, Issue 9

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Cell Shape ; Erythrocyte Count ; Erythrocytes/chemistry ; Erythrocytes/cytology ; Humans ; Lipid Peroxidation ; Membrane Lipids/chemistry ; Microscopy, Atomic Force/methods ; Nanotechnology ; Oxidative Stress ; Spectrophotometry, Infrared/methods
Chemical Substances	Membrane Lipids
Language	English
Publishing date	2018-08-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms19092582
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Article ; Online: N-terminal Huntingtin (Htt) phosphorylation is a molecular switch regulating Htt aggregation, helical conformation, internalization, and nuclear targeting.

DeGuire, Sean M / Ruggeri, Francesco S / Fares, Mohamed-Bilal / Chiki, Anass / Cendrowska, Urszula / Dietler, Giovanni / Lashuel, Hilal A

The Journal of biological chemistry

2018 Volume 293, Issue 48, Page(s) 18540–18558

Abstract: Huntington's disease is a fatal neurodegenerative disorder resulting from a CAG repeat expansion in the first exon of the gene encoding the Huntingtin protein (Htt). Phosphorylation of this protein region (Httex1) has been shown to play important roles ... ...

Abstract	Huntington's disease is a fatal neurodegenerative disorder resulting from a CAG repeat expansion in the first exon of the gene encoding the Huntingtin protein (Htt). Phosphorylation of this protein region (Httex1) has been shown to play important roles in regulating the structure, toxicity, and cellular properties of N-terminal fragments and full-length Htt. However, increasing evidence suggests that phosphomimetic substitutions in Htt result in inconsistent findings and do not reproduce all aspects of true phosphorylation. Here, we investigated the effects of
MeSH term(s)	Animals ; Cell Nucleus/metabolism ; Cells, Cultured ; Circular Dichroism ; Huntingtin Protein/chemistry ; Huntingtin Protein/metabolism ; Molecular Mimicry ; Mutation ; Nerve Tissue Proteins/chemistry ; Nerve Tissue Proteins/metabolism ; Neurons/metabolism ; Nuclear Proteins/chemistry ; Nuclear Proteins/metabolism ; Phosphoproteins/metabolism ; Phosphorylation ; Protein Aggregates ; Protein Conformation ; Protein Structure, Secondary ; Protein Transport ; Rats, Sprague-Dawley ; Serine/metabolism ; Subcellular Fractions/metabolism
Chemical Substances	Htt protein, rat ; Huntingtin Protein ; Nerve Tissue Proteins ; Nuclear Proteins ; Phosphoproteins ; Protein Aggregates ; Serine (452VLY9402)
Language	English
Publishing date	2018-09-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA118.004621
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Article ; Online: Molecular determinants of the interaction of EGCG with ordered and disordered proteins.

Fusco, Giuliana / Sanz-Hernandez, Maximo / Ruggeri, Francesco S / Vendruscolo, Michele / Dobson, Christopher M / De Simone, Alfonso

Biopolymers

2018 Volume 109, Issue 10, Page(s) e23117

Abstract: The aggregation process of peptides and proteins is of great relevance as it is associated with a wide range of highly debilitating disorders, including Alzheimer's and Parkinson's diseases. The natural product (-)-epigallocatechin-3-gallate (EGCG) can ... ...

Abstract	The aggregation process of peptides and proteins is of great relevance as it is associated with a wide range of highly debilitating disorders, including Alzheimer's and Parkinson's diseases. The natural product (-)-epigallocatechin-3-gallate (EGCG) can redirect this process away from amyloid fibrils and towards non-toxic oligomers. In this study we used nuclear magnetic resonance (NMR) spectroscopy to characterize the binding of EGCG to a set of natively structured and unstructured proteins. The results show that the binding process is dramatically dependent on the conformational properties of the protein involved, as EGCG interacts with different binding modes depending on the folding state of the protein. We used replica exchange molecular dynamics simulations to reproduce the trends observed in the NMR experiments, and analyzed the resulting samplings to identify the dominant direct interactions between EGCG and ordered and disordered proteins.
MeSH term(s)	Catechin/analogs & derivatives ; Catechin/chemistry ; Catechin/metabolism ; Humans ; Intrinsically Disordered Proteins/chemistry ; Intrinsically Disordered Proteins/metabolism ; Muramidase/chemistry ; Protein Binding ; alpha-Synuclein/chemistry
Chemical Substances	Intrinsically Disordered Proteins ; alpha-Synuclein ; Catechin (8R1V1STN48) ; epigallocatechin gallate (BQM438CTEL) ; Muramidase (EC 3.2.1.17)
Language	English
Publishing date	2018-03-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	1123-x
ISSN	1097-0282 ; 0006-3525
ISSN (online)	1097-0282
ISSN	0006-3525
DOI	10.1002/bip.23117
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