Biology subjects

Riedel, D.

Publications and source records attributed to Riedel, D..

At least 19 recordsLinked to original sources

bioRxiv2025

The clinical drug candidate anle138b binds predominantly to the central cavity in lipidic Aβ fibrils and modulates fibril formation.

Alzheimers disease is a specific neurodegenerative disorder, distinct from normal aging, with a growing unmet medical need. It is characterized by the accumulation of amyloid plaques in the brain, primarily consisting of amyloid beta (A{beta}) fibrils. Therapeutic antibodies can slow down the disease, but are associated with potential severe side effects, motivating the development of small molecules to halt disease progression. This study investigates the interaction between the clinical drug candidate small molecule anle138b and lipidic A{beta}40 fibrils of type 1 (L1). L1 fibrils were previously shown to closely resemble fibrils from Alzheimers patients18. Using high-resolution structural biology techniques, including cryo-electron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy enhanced by dynamic nuclear polarization (DNP), and molecular dynamics (MD) simulations, we find that anle138b selectively binds to a cavity within the fibril. This structural insight provides a deeper understanding of a potential drug-binding mechanism at the atomic level and may inform the development of novel therapies and diagnostic approaches. In addition, anle138b reduces fibril formation in the presence of lipids by approximately 75%. This may suggest a mechanistic connection to its previously reported activity in animal models of Alzheimers disease15.

biochemistry↗

bioRxiv2025

Membrane curvature regulates Ups1 dependent phosphatidic acid transfer across lipid bilayers

Mitochondria are essential organelles in eukaryotic cells, enclosed by two membranes with distinct compositions and functions. In addition to the endoplasmic reticulum, mitochondria are major sites of cellular lipid production. Cardiolipin, for example, is exclusively synthesized in the mitochondrial inner membrane. This requires the precursor lipid phosphatidic acid to be imported from the endoplasmic reticulum to the mitochondrial outer membrane. Subsequently phosphatidic acid is transferred to the inner membrane by the lipid transfer protein Ups1/PRELID1. The regulation of this process, the role of membrane physico-chemical properties, and the mechanisms by which energy barriers are overcome during lipid extraction and insertion remain poorly understood. Here, we demonstrate that Ups1 exhibits a strong preference for binding to positively curved membrane regions. Our findings reveal that phosphatidic acid extraction is energetically favored at these membrane domains, leading to enhanced lipid transfer between membranes with high positive curvature and we show that events at the donor membrane are rate limiting for the transfer cycle. Our data suggest that Ups1 membrane binding is modulated by pH, lipid composition, and membrane morphology, pointing to a complex, multipartite regulatory network underlying intra-mitochondrial lipid transfer.

biochemistry↗

bioRxiv2025

Governed by surface amino acid composition: HIV capsid passage through the NPC barrier

Nuclear transport receptors (NTRs) carry cargo across the permeability barrier of nuclear pore complexes (NPCs) - an FG phase condensed from disordered but cohesive FG repeats. This phase repels normal macromolecules but allows NTR passage. When HIV infects non-dividing cells, its capsid is transported into nuclei not like cargo but crosses NPCs like NTRs. We now uncovered the molecular determinants of the capsids NTR behavior: The FG-binding pocket is insufficient. Hexameric and pentameric capsomers contribute. The highly exposed outer capsid surface is key. It lacks FG-repulsive charged residues (K,D,E) that are very abundant on normal protein surfaces. FG-attractive residues dominate the capsid surface. Introducing FG-repulsive ones impedes FG phase-partitioning, NPC-targeting and NPC-passage of assembled capsids. Capsids are thus made FG phase-soluble by myriads of transient FG-attractive interactions originating from individual surface sidechains. We discuss that CPSF6 releases the capsid from NPCs by switching its surface from FG-attractive to FG-repulsive.

cell biology↗

bioRxiv2024

In-situ architecture of the human prohibitin complex

Prohibitins are a highly conserved family of proteins that have been implicated in a variety of functions including mitochondrial stress signalling and housekeeping, cell cycle progression, apoptosis, lifespan regulation and many others1, 2. The human prohibitins PHB1 and PHB2 have been proposed to act as scaffolds within the mitochondrial inner membrane, but their molecular organisation remained elusive. Using an integrative structural biology approach combining quantitative Western blotting, cryo-electron tomography, subtomogram averaging and molecular modelling, we determined the molecular organisation of the human prohibitin complex within the mitochondrial inner membrane. The proposed bell-shaped structure consists of eleven alternating PHB1 and PHB2 molecules. This study reveals an average of about 43 prohibitin complexes per crista, covering 1-3 % of the cristae membranes. These findings provide a structural basis for understanding the functional contributions of prohibitins to the integrity and spatial organisation of the mitochondrial inner membrane.

cell biology↗

bioRxiv2024

Localising elements in single-particle reconstructions by REEL-EM: Reconstructed Electron Energy-Loss - Elemental Mapping

For structures determined by single particle cryo-EM, no technique currently exists for mapping elements to defined locations, leading to errors in the assignment of metals and other ions, cofactors, substrates, inhibitors, and lipids that play essential roles in activity and regulation. Elemental mapping in the electron microscope is well established for dose-tolerant samples but is challenging for biological samples, especially in a cryo-preserved state. Here, we combine electron energy-loss spectroscopy (EELS) with single-particle image processing to allow elemental mapping in cryo-preserved macromolecular complexes. Proof-of-principle data show that our method, REEL-EM, allows 3D reconstruction of EELS data, such that a high total electron dose is accumulated across many copies of a complex. Working with two test samples, we demonstrate that we can reliably localise abundant elements. We discuss the current limitations of the method and potential future developments.

biophysics↗

bioRxiv2023

The proteolysis of ZP proteins is essential to control cell membrane structure and integrity of developing tubes

Membrane expansion integrates multiple forces to mediate precise tube growth and network formation. Defects lead to deformations, as found in diseases such as polycystic kidney diseases, aortic aneurysms, stenosis, and tortuosity. We identified a mechanism of sensing and responding to the membrane expansion of tracheal tubes. We show in Drosophila that Zona Pellucida domain proteins Piopio and Dumpy cooperate to integrate mechanical stress at cell membranes and luminal matrix. When tension appears at the apical membrane due to tracheal tube length expansion, Piopio undergoes ectodomain shedding by the Matriptase homolog Notopleural, which releases Piopio-mediated linkages between membranes and extracellular matrix. Failure of this process leads to deformations of the apical membrane and comprises tubular network function. We also show conserved ectodomain shedding by the human matriptase during TGF-{beta} signaling, both of which are required in the lung, providing novel approaches for in-depth analysis of pulmonary diseases caused by cell and tube shape changes.

developmental biology↗

bioRxiv2023

Cryo-EM structures of lipidic fibrils of amyloid-β (1-40)

Alzheimers disease (AD) is a progressive and incurable neurodegenerative disease characterized by the extracellular deposition of amyloid plaques. Investigation into the composition of these plaques revealed a high amount of amyloid-{beta} (A{beta}) fibrils and a high concentration of lipids, suggesting that fibril-lipid interactions may also be relevant for the pathogenesis of AD. Therefore, we grew A{beta}40 fibrils in the presence of lipid vesicles and determined their structure by cryo-electron microscopy (cryo-EM) to high resolution. The fold of the major polymorph is similar to the structure of brain-seeded fibrils reported previously. The majority of the lipids are bound to the fibrils as we show by cryo-EM and NMR spectroscopy. This apparent lipid extraction from vesicles observed here in vitro provides structural insights into potentially disease-relevant fibril-lipid interactions.

molecular biology↗

bioRxiv2023

The Drosophila MIC10 orthologue has a propensity to polymerize into cristae-shaping filaments

Mitochondria are essential eukaryotic double-membrane organelles. The convoluted mitochondrial inner membrane forms highly organized invaginations, termed cristae, which are crucial for energy metabolism. Cristae formation requires MICOS, a conserved hetero-oligomeric inner membrane complex. The MICOS core subunit MIC10 is a small transmembrane protein that oligomerizes through highly conserved glycine-rich motifs to control cristae formation. Sequence alignments show that D. melanogaster exhibits three MIC10-like proteins with different tissue-specific expression patterns. Here, we show that the ubiquitously expressed Dmel_CG41128/MINOS1b/DmMIC10b is the major MIC10 orthologue in flies. Loss of DmMIC10b disturbs cristae architecture of mitochondria and reduces the life-span and fertility of flies. Moreover, using fluorescence nanoscopy and electron tomography, we demonstrate that despite its high similarity to the MIC10 proteins from yeast and humans, DmMIC10b exhibits the unique ability to polymerize into elongated filaments upon overexpression. DmMIC10b filaments form bundles which accumulate in the intermembrane space and alter the shape of mitochondrial cristae membranes. We show that the formation of the filaments relies on conserved glycine and cysteine residues and is suppressed by co-expression of other MICOS proteins. Thereby, our findings provide new insights into the regulation of MICOS in flies.

cell biology↗

bioRxiv2022

LUBAC assembles a signaling platform at mitochondria for signal amplification and shuttling of NF-ĸB to the nucleus

Mitochondria are increasingly recognized as cellular hubs to orchestrate signaling pathways that regulate metabolism, redox homeostasis, and cell fate decisions. Recent research revealed a role of mitochondria also in innate immune signaling, however, the mechanisms of how mitochondria affect signal transduction are poorly understood. Here we show that the NF-B pathway activated by TNF employs mitochondria as a platform for signal amplification and shuttling of activated NF-B to the nucleus. TNF induces the recruitment of HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), and its substrate NEMO to the outer mitochondrial membrane, where M1- and K63-linked ubiquitin chains are generated. NF-B is locally activated and transported to the nucleus by mitochondria, resulting in an increase in mitochondria-nucleus contact sites in a HOIP-dependent manner. Notably, TNF-induced stabilization of the mitochondrial kinase PINK1 contributes to signal amplification by antagonizing the M1-ubiquitin-specific deubiquitinase OTULIN.

cell biology↗

bioRxiv2022

Multi-color live-cell STED nanoscopy of mitochondria with a gentle inner membrane stain

Capturing mitochondrias intricate and dynamic structure poses a daunting challenge for optical nanoscopy. Different labeling strategies have been demonstrated for live-cell stimulated emission depletion (STED) microscopy of mitochondria, but orthogonal strategies are yet to be established, and image acquisition has suffered either from photodamage to the organelles or from rapid photobleaching. Therefore, live-cell nanoscopy of mitochondria has been largely restricted to 2D single-color recordings of cancer cells. Here, by conjugation of cyclooctatetraene to a benzo-fused cyanine dye, we report a mitochondrial inner-membrane (IM) fluorescent marker, PK Mito Orange (PKMO), featuring efficient STED at 775 nm, strong photostability and markedly reduced phototoxicity. PKMO enables super-resolution recordings of inner-membrane dynamics for extended periods in immortalized mammalian cell lines, primary cells, and organoids. Photostability and reduced phototoxicity of PKMO open the door to live-cell 3D STED nanoscopy of mitochondria for three-dimensional analysis of the convoluted IM. PKMO is optically orthogonal with green and far-red markers allowing multiplexed recordings of mitochondria using commercial STED microscopes. Using multi-color STED, we demonstrate that imaging with PKMO can capture the sub-mitochondrial localization of proteins, or interactions of mitochondria with different cellular components, such as the ER or the cytoskeleton at sub-100 nm resolution. Thereby, this work offers a versatile tool for studying mitochondrial inner-membrane architecture and dynamics in a multiplexed manner.

cell biology↗

bioRxiv2022

Membrane interactions of mitochondrial lipid transfer proteins

The mitochondrial inner membrane is an integral part of the cellular lipid biosynthesis network. Intramitochondrial lipid transfer shuttles specific lipid species between the two mitochondrial membranes. This pathway is facilitated by designated protein complexes in the intermembrane space. A hetero-dimeric complex of Ups1 and Mdm35 has been identified in yeast to transfer phosphatidic acid from the outer to the inner membrane. Here, we define pH and lipid charge dependency of Ups1 membrane interaction. We show that Ups1 interacts with membranes in a membrane curvature dependent manner. Ups1 predominantly binds to membrane domains of positive curvature. Desorption of phosphatidic acid from positively curved membranes is energetically favorable over flat or negatively curved membranes. Hence, our results demonstrate that Ups1 specifically binds to membrane regions where extraction and insertion of lipids is enhanced.

biophysics↗

bioRxiv2022

Structural insights into crista junction formation by the Mic60-Mic19 complex

Mitochondrial cristae membranes are the oxidative phosphorylation sites in cells. Crista junctions (CJs) form the highly curved neck regions of cristae and are thought to function as selective entry gates into the cristae space. Little is known about how CJs are generated and maintained. We show that the central coiled-coil domain of the mitochondrial contact and cristae organizing system (MICOS) subunit Mic60 forms an elongated, bow tie-shaped tetrameric assembly. Mic19 promotes Mic60 tetramerization via a conserved interface between the Mic60 mitofilin and Mic19 CHCH domains. Dimerization of mitofilin domains exposes a crescent-shaped membrane-binding site with convex curvature tailored to interact with curved CJ necks. Our study suggests that the Mic60-Mic19 subcomplex transverses CJs as a molecular strut, thereby controlling CJ architecture and function.

cell biology↗

bioRxiv2021

Common molecular mechanisms underlie the transfer of alpha-synuclein, Tau and huntingtin and modulate spontaneous activity in neuronal cells

The misfolding and accumulation of disease-related proteins are common hallmarks among several neurodegenerative diseases. Alpha-synuclein (aSyn), Tau and huntingtin (wild-type and mutant, 25QHtt and 103QHtt, respectively) were recently shown to be transferred from cell-to-cell through different cellular pathways, thereby contributing to disease progression and neurodegeneration. However, the relative contribution of each of these mechanisms towards the spreading of these different proteins and the overall effect on neuronal function is still unclear. To address this, we exploited different cell-based systems to conduct a systematic comparison of the mechanisms of release of aSyn, Tau and Htt, and evaluated the effects of each protein upon internalization in microglial, astrocytic, and neuronal cells. In the models used, we demonstrate that 25QHtt, aSyn and Tau are released to the extracellular space at higher levels than 103QHtt, and their release can be further augmented with the co-expression of USP19. Furthermore, cortical neurons treated with recombinant monomeric 43QHtt exhibited alterations in neuronal activity that correlated with the toxicity of the polyglutamine expansion. Tau internalization resulted in an increase in neuronal activity, in contrast to slight effects observed with aSyn. Interestingly, all these disease-associated proteins were present at higher levels in ectosomes than in exosomes. The internalization of both types of extracellular vesicles (EVs) by microglial or astrocytic cells elicited the production of pro-inflammatory cytokines and promoted an increase in autophagy markers. Additionally, the uptake of the EVs modulated neuronal activity in cortical neurons. Overall, our systematic study demonstrates the release of neurodegenerative disease-associated proteins through similar cellular pathways. Furthermore, it emphasizes that protein release, both in a free form or in EVs, might contribute to a variety of detrimental effects in receiving cells and to progression of pathology, suggesting they may be exploited as valid targets for therapeutic intervention in different neurodegenerative diseases. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/452825v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1400e8org.highwire.dtl.DTLVardef@1478fccorg.highwire.dtl.DTLVardef@1319abcorg.highwire.dtl.DTLVardef@1a5ad40_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2021

Co-localization of different Neurotransmitter Transporters on the same Synaptic Vesicle is Bona-fide yet Sparse

Vesicular transporters (VTs) define the type of neurotransmitter that synaptic vesicles (SVs) store and release. While certain neurons in mammalian brain release multiple transmitters, the prevalence, physiology of such pluralism and if the release occurs from same or distinct vesicle pools is not clear. Using quantitative single vesicle imaging, we show that a small population of neuronal SVs indeed contain different VTs to accomplish corelease. Surprisingly, this population is highly diverse (27 types), expressing distinct dual transporters suggesting corelease of various combinations of neurotransmitters. Using glutamatergic vesicles as an example, we demonstrate that transporter colocalization not only determine the transmitter type but also influences the SV content and synaptic quantal size. Thus, presence of diverse transporters on the same vesicle is bona-fide and, depending on the VT types, this may act as one mechanism to regulate neurotransmitter type, content and release in space and time.

neuroscience↗

bioRxiv2021

Ectosomes and exosomes are distinct proteomic entities that modulate spontaneous activity in neuronal cells

Extracellular vesicles (EVs) are important mediators in intercellular communication. However, understanding the biological origin and functional effects of EVs subtypes has been challenging due to the moderate differences in their physical properties and absence of reliable markers. Here, we characterize the proteomes of ectosomes and exosomes using an improved differential ultracentrifugation protocol and quantitative proteomics. Cytoskeleton and glycolytic proteins are distinctively present in ectosomes, while endosomal sorting complexes proteins and tetraspanins are enriched in exosomes. Furthermore, annexin-A2 was identified as a specific marker for ectosomes derived from cell media and human cerebrospinal fluid. Expression of EGFP as a cytosolic reporter leads to its incorporation in EVs and enables their imaging with higher resolution. Importantly, ectosomes and exosomes internalization in neuronal cells results in the modulation of neuronal spontaneous activity. Our findings suggest that EVs cargoes reflect core intracellular processes, and their functional properties might regulate basic biological and pathological processes.

neuroscience↗

bioRxiv2021

Resolving the molecular architecture of the photoreceptor active zone by MINFLUX nanoscopy

Cells assemble macromolecular complexes into scaffoldings that serve as substrates for catalytic processes. Years of molecular neurobiology indicate that neurotransmission depends on such optimization strategies, yet the molecular topography of the presynaptic Active Zone (AZ) where transmitter is released upon synaptic vesicle (SV) fusion remains to be visualized. Therefore, we implemented MINFLUX optical nanoscopy to resolve the AZ of rod photoreceptors. To facilitate MINFLUX nanoscopy of the AZ, we developed and verified an immobilization technique, we name Heat Assisted Rapid Dehydration (HARD). Here fresh retinal slices are directly stamped onto glass coverslips yielding a single layer of rod AZs. These AZs exhibited excellent labeling efficiency and minimal signal redundancy in the Z-direction. Our data indicate that the SV release site is a molecular complex of bassoon-Rab3-binding molecule 2 (RIM2)-ubMunc13-2-CAST. The complexes are serially duplicated longitudinally, and reflected in register along the axis of symmetry of the synaptic ribbon. One sentence summaryStructural motifs formed by active zone proteins at the photoreceptor synapse.

neuroscience↗

bioRxiv2021

Germ plasm anchors at tight junctions in the early zebrafish embryo

The zebrafish germline is specified during early embryogenesis by inherited maternal RNAs and proteins collectively called germ plasm. Only the cells containing germ plasm will become part of the germline, whereas other cells will commit to somatic cell fates. Therefore, proper localization of germ plasm is key for germ cell specification and its removal is critical for the development of soma. The molecular mechanism underlying this process in vertebrates is largely unknown. Here we show that germ plasm localization in zebrafish is similar to Xenopus and amniotes but distinct from Drosophila. We identified non muscle myosin II (NMII) and tight junction (TJ) components as interaction candidates of Bucky ball (Buc), which is the germ plasm organizer in zebrafish. Remarkably, we also found that TJ protein ZO1 colocalizes with germ plasm and electron microscopy (EM) of zebrafish embryos uncovered TJ like structures at early cleavage furrows. In addition, injection of the TJ-receptor Claudin-d (Cldn-d) produced extra germ plasm aggregates. Our findings discover for the first time a role of TJs in germ plasm localization.

developmental biology↗

bioRxiv2020

Correlative fluorescence microscopy, transmission electron microscopy and secondary ion mass spectrometry (CLEM-SIMS) for cellular imaging

Electron microscopy (EM) has been employed for decades to analyze cell structure. To also analyze the positions and functions of specific proteins, one typically relies on immuno-EM or on a correlation with fluorescence microscopy, in the form of correlated light and electron microscopy (CLEM). Nevertheless, neither of these procedures is able to also address the isotopic composition of cells. To solve this, a correlation with secondary ion mass spectrometry (SIMS) would be necessary. SIMS has been correlated in the past to EM or to fluorescence microscopy in biological samples, but not to CLEM. We achieved this here, using a protocol based on transmission EM, conventional epifluorescence microscopy and nanoSIMS. The protocol is easily applied, and enables the use of all three technologies at high performance parameters. We suggest that CLEM-SIMS will provide substantial information that is currently beyond the scope of conventional correlative approaches.

cell biology↗