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New Insights into Protein Aggregation in Condensed and Amyloid States

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Prof. Dr. Eva Žerovnik

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Guest Editor

1. Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
2. Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia
Interests: mechanisms of protein folding and aggregation, amyloid metal interaction, amyloid-membrane interaction; amyloid pore formation; lipid composition modulation of protein aggregation; proteomics and bioinformatics; interactomes and protein function annotation
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Dear Colleagues,

Protein aggregation has two pathways: the condensation pathway and the amyloid aggregation pathway. Recently, protein condensates formed by LLPS (liquid–liquid phase separation) are being discovered anew. The dense bodies in the cytoplasm and nucleus are formed mostly from intrinsically disordered proteins, which interact with RNAs, but they can also form from globular proteins. The condensates (membrane-less organelles) serve functional roles in cell storage and regulation. Another pathway of protein aggregation ends in irreversible amyloid fibrils. The mature amyloid fibrils have very compact and regular structures. Due to their stability and special mechanical and electrical properties, they are used as scaffolding materials, both in cells and in biotechnology. The amyloid fibrils also exhibit special opto-physical properties from bioluminescence, enhanced absorption, enhanced fluorescence of bound dyes, interaction with laser light, and, interestingly, the laser (from visible to IR) induces degradation of amyloid fibers (J. Chem. Phys. (2015), DOI: 10.1063/1.4933207). Amyloid structures exert some functional roles in different organisms, but by the majority they are seen as cytotoxic and therefore sequestered.

We welcome papers exploring new insights into the special optical and physico-chemical properties or papers on the biological roles of protein oligomers, condensates, and amyloid. Also, papers on specific inhibitory compounds for the process of amyloid or condensate formation would be welcome. Bioinformatic or experimental studies of the interaction of the aggregates with lipid membranes and other proteins would be considered. Theoretical methods can include interactome analysis and signaling pathways affected by the aggregated proteins, as well as molecular dynamics calculations.

Prof. Dr. Eva Žerovnik
Guest Editor

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Keywords

proteinopathies
protein aggregation
physico-chemical and biological properties of amyloid fibrils and protein condensates
signal and light transduction
interaction with lipid membranes
aggregating protein interactomes
bioinformatics and machine learning
molecular dynamics

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Research

21 pages, 7608 KiB

Open AccessArticle

Oligomer Formation by Physiologically Relevant C-Terminal Isoforms of Amyloid β-Protein

by Rachit Pandey and Brigita Urbanc

Biomolecules 2024, 14(7), 774; https://doi.org/10.3390/biom14070774 - 28 Jun 2024

Viewed by 203

Abstract

Alzheimer’s disease (AD) is a neurological disorder associated with amyloid

β

-protein (A

β

) assembly into toxic oligomers. In addition to the two predominant alloforms, A

β_{1 - 40}

and A

β_{1 - 42}

, other C-terminally truncated A

β

[...] Read more.

Alzheimer’s disease (AD) is a neurological disorder associated with amyloid

β

-protein (A

β

) assembly into toxic oligomers. In addition to the two predominant alloforms, A

β_{1 - 40}

and A

β_{1 - 42}

, other C-terminally truncated A

β

peptides, including A

β_{1 - 38}

and A

β_{1 - 43}

, are produced in the brain. Here, we use discrete molecular dynamics (DMD) and a four-bead protein model with amino acid-specific hydropathic interactions, DMD4B-HYDRA, to examine oligomer formation of A

β_{1 - 38}

, A

β_{1 - 40}

, A

β_{1 - 42}

, and A

β_{1 - 43}

. Self-assembly of 32 unstructured monomer peptides into oligomers is examined using 32 replica DMD trajectories for each of the four peptides. In a quasi-steady state, A

β_{1 - 38}

and A

β_{1 - 40}

adopt similar unimodal oligomer size distributions with a maximum at trimers, whereas A

β_{1 - 42}

and A

β_{1 - 43}

oligomer size distributions are multimodal with the dominant maximum at trimers or tetramers, and additional maxima at hexamers and unidecamers (for A

β_{1 - 42}

) or octamers and pentadecamers (for A

β_{1 - 43}

). The free energy landscapes reveal isoform- and oligomer-order specific structural and morphological features of oligomer ensembles. Our results show that oligomers of each of the four isoforms have unique features, with A

β_{1 - 42}

alone resulting in oligomers with disordered and solvent-exposed N-termini. Our findings help unravel the structure–function paradigm governing oligomers formed by various A

β

isoforms. Full article

(This article belongs to the Special Issue New Insights into Protein Aggregation in Condensed and Amyloid States)

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New Insights into Protein Aggregation in Condensed and Amyloid States

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