Biology subjects

Dekker, F. A.

Publications and source records attributed to Dekker, F. A..

3 recordsLinked to original sources

bioRxiv2024

FibrilPaint targets amyloid fibrils for ubiquitination

Failure of the Protein Quality Control (PQC) System to control the Tau protein leads to amyloid fibrils that are at the basis of various Tauopathies, including Alzheimers Disease (AD). Reinstating the PQC for Tau is desirable. Here we show that the PROTAC peptide FibrilPaint20 (FP20) recruits the ubiquitination system to Tau amyloid fibrils. We reconstituted the ubiquitin-proteasome cascade and monitored the stepwise ubiquitin transfer using the microfluidics technique FIDA. To direct ubiquitination specifically to amyloids, we discovered FP20, a bifunctional peptide that connects amyloid fibrils to the E3 ligase CHIP. FP20 mediated ubiquitination of recombinant and patient derived fibrils from various tauopathies, ultimately enabling the 26S proteasome to target CHIP-ubiquitinated Tau fibrils. This shows that FP20 cooperates with the PQC system and can initiate fibril cleavage. This offers a strategy to target amyloid diseases by cooperation with the PQC system exploiting key cellular systems.

biochemistry↗

bioRxiv2024

Fibril Paint: a class of amyloid-targeting peptides

Amyloid fibrils are a common pathological hallmark in multiple neurodegenerative diseases, yet molecular tools to selectively recognise and manipulate them remain scarce. We report FibrilPaints, a family of modular peptides designed for selective amyloid binding and adaptable chemical functionality. The degenerative amyloid-targeting unit of FibrilPaints, W5P4H3R2, has a high content of {pi}-stacking and aromatic side chains. Systematic sequence variation, altering charge, termini, and residue order, revealed the importance of the composition of the amyloid-targeting unit for high-affinity binding across Tau and Huntingtin fibrils. Importantly, sequence changes outside this unit do not preclude fibril binding, which permits attachment of fluorophores or E3-recruiting motifs for targeted protein degradation. This work establishes FibrilPaint as a modular peptide system for the detection and modulation of amyloids. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/609586v4_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1e9cadborg.highwire.dtl.DTLVardef@50f9eorg.highwire.dtl.DTLVardef@446ee8org.highwire.dtl.DTLVardef@cd47a2_HPS_FORMAT_FIGEXP M_FIG Figure of content The modular design of FibrilPaints enables systematic evaluation of their functionality by testing the binding capacity of each variant (FibrilPaintX) to distinct amyloid fibrils. Successful binding results in visible painting of the fibrils, facilitating their detection and downstream research. C_FIG

biochemistry↗

bioRxiv2023

Fibril Paint to detect Amyloids and determine Fibril Length

Tau aggregation into amyloid fibrils is linked to the development of neurodegenerative diseases, including Alzheimers Disease. The molecular processes underlying aggregation in disease are poorly understood. Here, we introduce FibrilPaint1 as a tool to measure the size of Tau amyloid fibrils in fluids, from early aggregation stages to mature fibrils. FibrilPaint1 is a 22mer peptide with many exciting properties, which makes it a tool for diagnostics and an attractive start point for developing a class of effective fibril targeting degraders: (i) FibrilPaint1 binds fibrils with nanomolar affinity; (ii) it does also bind to oligomeric precursors, down to a size of only 4 layers; (iii) it does not bind to monomers (KD > 100 {micro}M); (iv) it is fluorescently labelled, which allows monitoring and localising interactions. (v) FibrilPaint1 recognises various Tau fibrils, including patient derived fibrils from Alzheimer, Corticobasal degeneration and Frontotemporal dementia; (vi) FibrilPaint1 is selective for the amyloid state and does not have background binding to amorphous aggregates, blood serum or cell lysate. In combination with Flow Induced Dispersion Analysis (FIDA), a microfluidics technology, we determined the molecular size of amyloid fibrils with sub-microliter sample volumes. This set-up acts as a molecular ruler at layer resolution - we determined Tau fibril length from 4 to 1100 layers in solution. This is an interesting parameter that can be used for diagnostic applications and biochemical research in dementia.

biochemistry↗