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Book ; Online: Frontiers in Protein Folding and Related Areas - in Memory of Professor Sir Christopher M. Dobson (1949-2019)

Kuwajima, Kunihiro / Okamoto, Yuko / Knowles, Tuomas / Vendruscolo, Michele

2023

Keywords	Research & information: general ; Biology, life sciences ; 14-3-3 proteins ; molecular chaperone ; amyloid β ; α-synuclein ; NMR spectroscopy ; amyloid fibril ; amyloidogenesis ; aggregation ; adsorption ; Aβ 1-40 peptide ; boundary of liquid phase ; self-assembly ; extraction ; solubilization ; toxic oligomers ; Parkinson's disease ; familial mutations ; α-helical structure ; amyloid-beta ; mutants ; cholesterol ; simulations ; X-ray crystallography ; phospholipase A1 ; homodimer ; dimerization domain ; catalytic triad ; plant protein ; molecular dynamics simulation ; replica permutation method ; amyloid-β ; disaggregation ; β-sheet ; α-helix ; interface ; inhibitor ; polyphenol ; high-temperature reversible oligomerization ; amyloidogenicity ; oligomeric interface residues ; thermal denaturation ; mutational analysis ; RHIM ; TRIF ; necroptosis ; functional amyloid ; fibrils ; RIPK ; turbulent mixing ; continuous flow ; fluorescence ; reaction mechanism ; protein folding ; protein-ligand interactions ; protein design ; reverse fold ; minimum frustration ; protein structure prediction ; sequence-structure alignment ; template-based modeling ; conditional random fields ; boosted regression trees ; CASP ; hydrogen/deuterium exchange ; dimethylsulfoxide ; nuclear magnetic resonance ; chaperonin ; GroEL ; protease ; Lon protease ; proteomics ; proteostasis ; Hfq hexamer ; mutations ; unfolding intermediates ; thermodynamics ; amyloid ; insulin B chain ; nucleation ; prefibrillar aggregates ; protofibrils ; bacterial amyloid ; biofilm ; curli ; FapC ; imperfect repeats ; neurodegeneration ; oligomerisation ; native-like ; micelle ; globular protein ; rigid native state ; molten globule ; intrinsically disordered ; functional state ; unfolded state ; coil ; post-translational modifications ; membrane ; chaperone ; statistical mechanical model ; WSME model ; folding kinetics ; folding intermediates ; protein dynamics ; amyloid fibrils ; amorphous aggregation ; β2-microglobulin ; protein misfolding ; solubility ; supersaturation ; ultrasonication ; cryo-electron microscopy ; fibril ; ganglioside ; cancer ; prion ; folding ; pathway ; interdiction ; peptide ; enhanced sampling method ; molecular force fields ; van der Waals interaction ; CHARMM36m ; NBFIX ; intrinsically disordered proteins ; crowding simulations
Language	English
Size	1 electronic resource (418 pages)
Publisher	MDPI - Multidisciplinary Digital Publishing Institute
Publishing place	Basel
Document type	Book ; Online
Note	English
HBZ-ID	HT030376814
ISBN	9783036573205 ; 3036573208
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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Article ; Online: Thermodynamic and kinetic approaches for drug discovery to target protein misfolding and aggregation.

Vendruscolo, Michele

Expert opinion on drug discovery

2023 Volume 18, Issue 8, Page(s) 881–891

Abstract: Introduction: Protein misfolding diseases, including Alzheimer's and Parkinson's diseases, are characterized by the aberrant aggregation of proteins. These conditions are still largely untreatable, despite having a major impact on our healthcare systems ...

Abstract	Introduction: Protein misfolding diseases, including Alzheimer's and Parkinson's diseases, are characterized by the aberrant aggregation of proteins. These conditions are still largely untreatable, despite having a major impact on our healthcare systems and societies. Areas covered: We describe drug discovery strategies to target protein misfolding and aggregation. We compare thermodynamic approaches, which are based on the stabilization of the native states of proteins, with kinetic approaches, which are based on the slowing down of the aggregation process. This comparison is carried out in terms of the current knowledge of the process of protein misfolding and aggregation, the mechanisms of disease and the therapeutic targets. Expert opinion: There is an unmet need for disease-modifying treatments that target protein misfolding and aggregation for the over 50 human disorders known to be associated with this phenomenon. With the approval of the first drugs that can prevent misfolding or inhibit aggregation, future efforts will be focused on the discovery of effective compounds with these mechanisms of action for a wide range of conditions.
MeSH term(s)	Humans ; Protein Folding ; Proteins ; Proteostasis Deficiencies/drug therapy ; Proteostasis Deficiencies/prevention & control ; Thermodynamics ; Parkinson Disease ; Protein Aggregates
Chemical Substances	Proteins ; Protein Aggregates
Language	English
Publishing date	2023-06-05
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2259618-5
ISSN	1746-045X ; 1746-0441
ISSN (online)	1746-045X
ISSN	1746-0441
DOI	10.1080/17460441.2023.2221024
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Lipid Homeostasis and Its Links With Protein Misfolding Diseases.

Vendruscolo, Michele

Frontiers in molecular neuroscience

2022 Volume 15, Page(s) 829291

Abstract: The maintenance of lipid homeostasis is essential for the normal functioning of living organisms. Alterations of the lipid homeostasis system remodel the composition of the lipidome, potentially leading to the formation of toxic lipid species. In turn, ... ...

Abstract	The maintenance of lipid homeostasis is essential for the normal functioning of living organisms. Alterations of the lipid homeostasis system remodel the composition of the lipidome, potentially leading to the formation of toxic lipid species. In turn, lipidome changes can affect the protein homeostasis system by causing perturbations that elicit protein condensation phenomena such as protein liquid-liquid phase separation and protein aggregation. Lipids can also be more directly involved the formation of aberrant condensed states of proteins by facilitating the early events that initiate these processes and by stabilizing the condensed states themselves. These observations suggest that lipid-induced toxicity can contribute to protein misfolding diseases, including Alzheimer's and Parkinson's diseases. According to this view, an impairment of the lipid homeostasis system generates toxic states of lipids that disturb the protein homeostasis system and promote the formation of toxic states of proteins.
Language	English
Publishing date	2022-03-25
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2452967-9
ISSN	1662-5099
ISSN	1662-5099
DOI	10.3389/fnmol.2022.829291
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Towards sequence-based principles for protein phase separation predictions.

Vendruscolo, Michele / Fuxreiter, Monika

Current opinion in chemical biology

2023 Volume 75, Page(s) 102317

Abstract: The phenomenon of protein phase separation, which underlies the formation of biomolecular condensates, has been associated with numerous cellular functions. Recent studies indicate that the amino acid sequences of most proteins may harbour not only the ... ...

Abstract	The phenomenon of protein phase separation, which underlies the formation of biomolecular condensates, has been associated with numerous cellular functions. Recent studies indicate that the amino acid sequences of most proteins may harbour not only the code for folding into the native state but also for condensing into the liquid-like droplet state and the solid-like amyloid state. Here we review the current understanding of the principles for sequence-based methods for predicting the propensity of proteins for phase separation. A guiding concept is that entropic contributions are generally more important to stabilise the droplet state than they are for the native and amyloid states. Although estimating these entropic contributions has proven difficult, we describe some progress that has been recently made in this direction. To conclude, we discuss the challenges ahead to extend sequence-based prediction methods of protein phase separation to include quantitative in vivo characterisations of this process.
MeSH term(s)	Amyloid ; Amino Acid Sequence ; Cell Physiological Phenomena
Chemical Substances	Amyloid
Language	English
Publishing date	2023-05-17
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1439176-4
ISSN	1879-0402 ; 1367-5931
ISSN (online)	1879-0402
ISSN	1367-5931
DOI	10.1016/j.cbpa.2023.102317
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Article ; Online: Extracellular protein homeostasis: The dawning of a new age for human disease therapies?

Wilson, Mark R / Satapathy, Sandeep / Vendruscolo, Michele

Clinical and translational medicine

2023 Volume 13, Issue 6, Page(s) e1305

MeSH term(s)	Humans ; Proteostasis
Language	English
Publishing date	2023-06-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2697013-2
ISSN	2001-1326 ; 2001-1326
ISSN (online)	2001-1326
ISSN	2001-1326
DOI	10.1002/ctm2.1305
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Modulation of α-synuclein in vitro aggregation kinetics by its alternative splice isoforms.

Röntgen, Alexander / Toprakcioglu, Zenon / Tomkins, James E / Vendruscolo, Michele

Proceedings of the National Academy of Sciences of the United States of America

2024 Volume 121, Issue 7, Page(s) e2313465121

Abstract: The misfolding and aggregation of α-synuclein is linked to a family of neurodegenerative disorders known as synucleinopathies, the most prominent of which is Parkinson's disease (PD). Understanding the aggregation process of α-synuclein from a ... ...

Abstract	The misfolding and aggregation of α-synuclein is linked to a family of neurodegenerative disorders known as synucleinopathies, the most prominent of which is Parkinson's disease (PD). Understanding the aggregation process of α-synuclein from a mechanistic point of view is thus of key importance.
MeSH term(s)	Humans ; alpha-Synuclein/genetics ; alpha-Synuclein/metabolism ; Synucleinopathies ; Parkinson Disease/genetics ; Parkinson Disease/metabolism ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; Kinetics
Chemical Substances	alpha-Synuclein ; Protein Isoforms
Language	English
Publishing date	2024-02-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2313465121
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Article ; Online: Protein condensation diseases: therapeutic opportunities.

Vendruscolo, Michele / Fuxreiter, Monika

Nature communications

2022 Volume 13, Issue 1, Page(s) 5550

Abstract: Condensed states of proteins, including liquid-like membraneless organelles and solid-like aggregates, contribute in fundamental ways to the organisation and function of the cell. Perturbations of these states can lead to a variety of diseases through ... ...

Abstract	Condensed states of proteins, including liquid-like membraneless organelles and solid-like aggregates, contribute in fundamental ways to the organisation and function of the cell. Perturbations of these states can lead to a variety of diseases through mechanisms that we are now beginning to understand. We define protein condensation diseases as conditions caused by the disruption of the normal behaviour of the condensed states of proteins. We analyze the problem of the identification of targets for pharmacological interventions for these diseases and explore opportunities for the regulation of the formation and organisation of aberrant condensed states of proteins.
MeSH term(s)	Organelles/metabolism ; Proteins/metabolism
Chemical Substances	Proteins
Language	English
Publishing date	2022-09-22
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-32940-7
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases.

Rinauro, Dillon J / Chiti, Fabrizio / Vendruscolo, Michele / Limbocker, Ryan

Molecular neurodegeneration

2024 Volume 19, Issue 1, Page(s) 20

Abstract: The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid ... ...

Abstract	The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
MeSH term(s)	Humans ; Amyloid/metabolism ; Parkinson Disease/metabolism ; Proteostasis Deficiencies ; Amyloid beta-Peptides
Chemical Substances	Amyloid ; Amyloid beta-Peptides
Language	English
Publishing date	2024-02-20
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2244557-2
ISSN	1750-1326 ; 1750-1326
ISSN (online)	1750-1326
ISSN	1750-1326
DOI	10.1186/s13024-023-00651-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Probing the effects of N-terminal acetylation on α-synuclein structure, aggregation and cytotoxicity.

Bell, Rosie / Vendruscolo, Michele / Kumita, Janet R

Methods in enzymology

2023 Volume 686, Page(s) 45–65

Abstract: Parkinson's disease is associated with the aberrant aggregation of α-synuclein within brain cells. Although the causes of this process are still unclear, post-translational modifications of α-synuclein are likely to play a modulatory role. Since α- ... ...

Abstract	Parkinson's disease is associated with the aberrant aggregation of α-synuclein within brain cells. Although the causes of this process are still unclear, post-translational modifications of α-synuclein are likely to play a modulatory role. Since α-synuclein is constitutively N-terminally acetylated, we previously investigated how this protein modification affects the aggregation behavior of the protein using a variety of methods in vitro and in cell systems. This chapter describes the production of N-terminally acetylated (NTA) α-synuclein, the preparation of different seeds of NTA α-synuclein for aggregation assays and the experimental methods for the kinetic analysis of the aggregation process of NTA α-synuclein. We also detail our protocol to evaluate the effects of preformed protofibrils of NTA α-synuclein in cell-based assays. These methods can be applied to study other post-translational modifications of α-synuclein, or adapted for the study of N-acetylation of other aggregation-prone proteins.
MeSH term(s)	alpha-Synuclein/chemistry ; Acetylation ; Kinetics ; Protein Processing, Post-Translational
Chemical Substances	alpha-Synuclein
Language	English
Publishing date	2023-03-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1557-7988
ISSN (online)	1557-7988
DOI	10.1016/bs.mie.2022.09.003
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Bayesian Optimization in the Latent Space of a Variational Autoencoder for the Generation of Selective FLT3 Inhibitors.

Chandra, Raghav / Horne, Robert I / Vendruscolo, Michele

Journal of chemical theory and computation

2023 Volume 20, Issue 1, Page(s) 469–476

Abstract: The process of drug design requires the initial identification of compounds that bind their targets with high affinity and selectivity. Advances in generative modeling of small molecules based on deep learning are offering novel opportunities for making ... ...

Abstract	The process of drug design requires the initial identification of compounds that bind their targets with high affinity and selectivity. Advances in generative modeling of small molecules based on deep learning are offering novel opportunities for making this process faster and cheaper. Here, we propose an approach to achieve this goal, where predictions of binding affinity are used in conjunction with the Junction Tree Variational Autoencoder (JTVAE) whose latent space is used to facilitate the efficient exploration of the chemical space using a Bayesian optimization strategy. The exploration identifies small molecules predicted to have both high affinity and high selectivity by using an objective function that optimizes the binding to the target while penalizing the binding to off-targets. The framework is demonstrated for FMS-like tyrosine kinase 3 (FLT3) and shown to predict small molecules with predicted affinity and selectivity comparable to those of clinically approved drugs for this target.
MeSH term(s)	fms-Like Tyrosine Kinase 3 ; Bayes Theorem ; Drug Design
Chemical Substances	fms-Like Tyrosine Kinase 3 (EC 2.7.10.1)
Language	English
Publishing date	2023-12-19
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.3c01224
Database	MEDical Literature Analysis and Retrieval System OnLINE

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