Thomas Michaels

Last Name

Michaels

First Name

Thomas

ORCID

0000-0001-6931-5041

Organisational unit

09791 - Michaels, Thomas / Michaels, Thomas

Show all metadata

Search Results

Publications 1 - 10 of 17

A solid beta-sheet structure is formed at the surface of FUS droplets during aging
Emmanouilidis, Leonidas; Bartalucci, Ettore; Kan, Yelena; et al. (2024)
Nature Chemical Biology
Phase transitions are important to understand cell dynamics, and the maturation of liquid droplets is relevant to neurodegenerative disorders. We combined NMR and Raman spectroscopies with microscopy to follow, over a period of days to months, droplet maturation of the protein fused in sarcoma (FUS). Our study reveals that the surface of the droplets plays a critical role in this process, while RNA binding prevents it. The maturation kinetics are faster in an agarose-stabilized biphasic sample compared with a monophasic condensed sample, owing to the larger surface-to-volume ratio. In addition, Raman spectroscopy reports structural differences upon maturation between the inside and the surface of droplets, which is comprised of beta-sheet content, as revealed by solid-state NMR. In agreement with these observations, a solid crust-like shell is observed at the surface using microaspiration. Ultimately, matured droplets were converted into fibrils involving the prion-like domain as well as the first RGG motif.
Self-replication of Aβ₄₂ aggregates occurs on small and isolated fibril sites
Curk, Samo; Krausser, Johannes; Meisl, Georg; et al. (2024)
Proceedings of the National Academy of Sciences of the United States of America
Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer's A[Formula: see text] amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A[Formula: see text] fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.
A solid beta-sheet structure is formed at the surface of FUS liquid droplets during aging
Emmanouilidis, Leonidas; Bartalucci, Ettore; Kan, Yelena; et al. (2023)
bioRxiv
Insights into liquid droplet formation via liquid-liquid phase separation and the subsequent liquid-to-solid phase transition are important for understanding cell dynamics, as well as a number of neurodegenerative disorders. We report here, using the example of the FUsed in Sarcoma (FUS) protein, an investigation of the liquid droplet maturation process combining solution- and solid-state NMR spectroscopy, Raman spectroscopy, and light and electron microscopies. Our study reveals that the surface of the droplets plays a critical role in this process. Indeed, when comparing a biphasic sample, in which liquid droplets are stabilized in an agarose matrix, with a pure monophasic condensed phase sample, we find that the liquid-droplet maturation kinetics is faster in the biphasic FUS sample, owing to the larger surface-to-volume ratio. In addition, using Raman spectroscopy, we observe structural differences upon liquid-droplet maturation between the inside and the surface of liquid droplets, which is of β-sheet content as revealed by solid-state NMR. This is detected very early on and increases over time. In agreement with these observations, a solid crust-like shell is visually seen by microaspiration experiments. After several months, electron microscopy reveals that the matured FUS droplets have converted into solid linear fibrils distinct from the fibril core of seeded fibrils reported previously, as arginine side-chains from the arginine-and-glycine-rich domain (RGG) motif are partially rigidified, highlighting the participation of this motif in the liquid-to-solid transition. In presence of RNA, this aging process is not taking place.
Approximate analytical solution to the Flory-Huggins model
Qian, Daoyuan; Michaels, Thomas; Knowles, Tuomas P.J. (2023)
Biophysical Journal
Spontaneous nucleation and fast aggregate-dependent proliferation of α-synuclein aggregates within liquid condensates at neutral pH
Dada, Samuel T.; Hardenberg, Maarten C.; Toprakcioglu, Zenon; et al. (2023)
Proceedings of the National Academy of Sciences of the United States of America
The aggregation of α-synuclein into amyloid fibrils has been under scrutiny in recent years because of its association with Parkinson's disease. This process can be triggered by a lipid-dependent nucleation process, and the resulting aggregates can proliferate through secondary nucleation under acidic pH conditions. It has also been recently reported that the aggregation of α-synuclein may follow an alternative pathway, which takes place within dense liquid condensates formed through phase separation. The microscopic mechanism of this process, however, remains to be clarified. Here, we used fluorescence-based assays to enable a kinetic analysis of the microscopic steps underlying the aggregation process of α-synuclein within liquid condensates. Our analysis shows that at pH 7.4, this process starts with spontaneous primary nucleation followed by rapid aggregate-dependent proliferation. Our results thus reveal the microscopic mechanism of α-synuclein aggregation within condensates through the accurate quantification of the kinetic rate constants for the appearance and proliferation of α-synuclein aggregates at physiological pH.
The Alzheimer’s Aβ peptide forms biomolecular condensates that trigger amyloid aggregation
Šneiderienė, Greta; González Díaz, Alicia; Das Adhikari, Sourav; et al. (2024)
bioRxiv
The onset and development of Alzheimer’s disease (AD) is linked to the accumulation of pathological aggregates formed from the normally monomeric amyloid-β peptide within the central nervous system. These Aβ aggregates are increasingly successfully targeted with clinical therapies, but the fundamental molecular steps that trigger the initial nucleation event leading to the conversion of monomeric Aβ peptide into pathological aggregates remain unknown. Here we show that the Aβ peptide can form biomolecular condensates on lipid bilayers both in molecular assays and in living cells. Our results reveal that these Aβ condensates can significantly accelerate the primary nucleation step in the amyloid conversion cascade that leads to the formation of amyloid aggregates and plaque. We show that Aβ condensates contain phospholipids, are intrinsically heterogenous, and are prone to undergo a liquid-to-solid transition leading to the formation amyloid fibrils. These findings uncover the liquid-liquid phase separation behaviour of the Aβ peptide, and reveal a new molecular step very early in the amyloid-β aggregation cascade that can form the basis for novel therapeutic intervention strategies. Significance statement The hallmark of Alzheimer’s disease is the abnormal buildup of the normally soluble amyloid β protein aggregates in the central nervous system. While the molecular mechanisms at the late stages of the amyloid β aggregation cascade are well understood, the initial steps remained elusive until now. Our current study demonstrates that amyloid β undergoes liquid-liquid phase separation on lipid surfaces, which triggers primary nucleation and initiates the amyloid β aggregation cascade. This newly identified step in the molecular mechanism of Alzheimer’s disease represents a promising target for the development of alternative innovative therapeutic strategies.
Understanding and controlling the molecular mechanisms of protein aggregation in mAb therapeutics
Pang, Kuin Tian; Yang, Yuan Sheng; Zhang, Wei; et al. (2023)
Biotechnology Advances
In antibody development and manufacturing, protein aggregation is a common challenge that can lead to serious efficacy and safety issues. To mitigate this problem, it is important to investigate its molecular origins. This review discusses (1) our current molecular understanding and theoretical models of antibody aggregation, (2) how various stress conditions related to antibody upstream and downstream bioprocesses can trigger aggregation, and (3) current mitigation strategies employed towards inhibiting aggregation. We discuss the relevance of the aggregation phenomenon in the context of novel antibody modalities and highlight how in silico approaches can be exploited to mitigate it.
Enhanced potency of aggregation inhibitors mediated by liquid condensates
Michaels, Thomas; Mahadevan, Lakshminarayana; Weber, Christoph A. (2022)
Physical Review Research
Liquid condensates are membraneless organelles that form via phase separation in living cells. These condensates provide unique heterogeneous environments that have much potential in regulating a range of biochemical processes from gene expression to filamentous protein aggregation - a process linked to Alzheimer's and Parkinson's diseases. Here we theoretically study the physical interplay between protein aggregation, its inhibition, and liquid-liquid phase separation. Our key finding is that the action of protein aggregation inhibitors can be strongly enhanced by liquid condensates. The physical mechanism of this enhancement relies on the partitioning and colocalization of inhibitors with their targets inside the liquid condensate. Our theory uncovers how the physicochemical properties of condensates can be used to modulate inhibitor potency, and we provide experimentally testable conditions under which drug potency is maximal. Our findings suggest design principles for protein aggregation inhibitors with respect to their phase-separation properties.
Physical limits to acceleration of enzymatic reactions inside phase-separated compartments
Schmit, Jeremy D.; Michaels, Thomas (2024)
Physical Review E
We present a theoretical analysis of phase-separated compartments to facilitate enzymatic chemical reactions. While phase separation can facilitate reactions by increasing local concentration, it can also hinder the mobility of reactants. In particular, we find that the attractive interactions that concentrate reactants within the dense phase can inhibit reactions by lowering the mobility of the reactants. This mobility loss severely limits the potential to enhance reaction rates. Phase separation provides greater benefit in situations where multiple sequential reactions occur and/or high order reactions, provided the enzymes are unsaturated, transport to the condensate is not limiting, and the reactants are mobile. We show that mobility can be maintained if recruitment to the condensed phase is driven by multiple attractive moieties that can bind and release independently. However, the spacers necessary to ensure independence between stickers are prone to entangle with the dense phase scaffold. We find an optimal sticker affinity that balances the need for rapid binding/unbinding kinetics and minimal entanglement. Reaction rates can be accelerated by shrinking the size of the dense phase with a corresponding increase in the number of stickers. Our results showcase the potential capabilities of phase-separated compartments to act as biochemical reaction crucibles within living cells.
Amyloid formation as a protein phase transition
Michaels, Thomas; Qian, Daoyuan; Šarić, Andela; et al. (2023)
Nature Reviews Physics
The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases.

Publications 1 - 10 of 17

Thomas Michaels

Last Name

First Name

ORCID

Organisational unit

Filters

Search Results