Biology subjects

Naschberger, A.

Publications and source records attributed to Naschberger, A..

10 recordsLinked to original sources

bioRxiv2026

The Posidonia oceanica Large PSI-LHCII supercomplex reveals the molecular basis of PSI spectral diversification in higher plants

Higher plant Photosystem I (PSI) can capture low-energy photons and convert them into chemical energy through special far-red absorbing chlorophylls, the red-forms. Across higher-plant evolution, red-form spectral range has shifted to match differences in far-red availability across various habitats, despite broad conservation of the antenna system and canonical red-form architecture. Here, we report the 1.9 A cryo-EM structure of a large and blue shifted PSI light-harvesting complex I and II supercomplex (L-PSI-LHCI-LHCII) from the Mediterranean seagrass Posidonia oceanica, a marine angiosperm adapted to blue-enriched underwater light depleted in far-red wavelengths. Although the PSI core remains conserved, the antenna system was selectively remodeled through incorporation of an additional Lhca1-Lhca4 heterodimer at a previously undescribed binding site, together with pigment remodeling in the LHCI and the LHCII that enhanced blue-cyan light harvesting. Comparative structural analyses identified recurrent amino-acid sites within the far-red domains that influence red-forms geometry and whose residue composition diverges strongly among blue-shifted and red-shifted plant species. These findings establish a common structural basis underlying the spectral diversification of PSI toward contrasting light environments, accounting for both seagrass adaptation to the seawater light regime and the broad range of far-red absorption in higher plants.

plant biology↗

bioRxiv2025

Cryo-EM Structure of Photosystem I from mangroves in their natural environment

Photosystem I (PSI) is a multi-subunit pigment-protein supercomplex responsible for light driven electron transport in photosynthesis. Its structural plasticity under natural environmental stress remains poorly understood. Here, we present a 2.1 [A] cryo-EM structure of the PSI-LHCI supercomplex from Avicennia marina, a halotolerant, dominant mangrove species native to the Arabian Gulf that thrives in harsh coastal environments. Unlike structures derived from laboratory grown specimens, our analysis captures PSI directly from wild-grown plant leaves, offering an in-situ snapshot of plant adaptation. The core architecture comprising twelve protein subunits and four Lhca antenna proteins coordinating 157 chlorophylls, 36 carotenoids and 24 lipids is highly conserved relative to model angiosperms yet exhibits subtle shifts in antenna core coupling and pigment organization. Red-shifted chlorophylls in Lhca3, conserved among far red adapted plants, suggest an ancestral photoprotective mechanism retained in high light, high-salinity environments. Lipid mediated stabilization at interfaces likely counteracts salinity-induced membrane fluidity changes enhancing resilience under fluctuating light and salt stress. Comparative analysis with PSI structures from other vascular plants highlights both evolutionary conservation and distinct ecological tuning of LHCI organization and cofactor binding in mangroves. These insights reveal molecular strategies enabling A. marina to maintain efficient photosynthesis under extreme conditions, offering strategies for engineering photosystems in crops.

plant biology↗

bioRxiv2025

In situ structure of bacterial 50S ribosomes at 2.98 A resolution from vitreous sections.

In situ high-resolution structure determination is limited to samples thin enough to be penetrated by the electron beam during imaging. Sample thinning involves focused ion or plasma beam milling of specimens to produce lamellae with thicknesses as low as 100-150 nm. However, surface damage caused by the milling process can extend 30-60 nm deep, restricting the usable lamella thickness. This imposes limitations on single-particle analysis of macromolecular complexes due to elevated structural noise, which cannot be avoided in situ because of the dense cellular environment. Alternative methods capable of producing thinner samples are needed to reduce background. Here, we demonstrate that high-resolution structures at side-chain level, free of orientation bias, can be obtained from vitreous sections prepared by cryo-ultramicrotomy, both in vitro and in situ. We optimized the method to produce sections as thin as [~]40 nm, free from significant surface damage. Using this approach, we determined the structure of the 50S ribosomal subunit in vitro at 2.8 [A] and in situ at 3 [A] from bacterial cells. These results lay the foundation for future in situ studies of smaller complexes using CEMOVIS, as well as for methodological advances aimed at achieving compression-free sectioning.

biochemistry↗

bioRxiv2023

Identification of key residues in MERS-CoV and SARS-CoV-2 main proteases for resistance against clinically applied inhibitors nirmatrelvir and ensitrelvir

The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an epidemic, zoonotically emerging pathogen initially reported in Saudi Arabia in 2012. MERS-CoV has the potential to mutate or recombine with other coronaviruses, thus acquiring the ability to efficiently spread among humans and become pandemic. Its high mortality rate of up to 35 % and the absence of effective targeted therapies call for the development of antiviral drugs for this pathogen. Since the beginning of the SARS-CoV-2 pandemic, extensive research has focused on identifying protease inhibitors for the treatment of SARS-CoV-2. Our intention was therefore to assess whether these protease inhibitors are viable options for combating MERS-CoV. To that end, we used previously established protease assays to quantify inhibition of the SARS-CoV-2 and MERS-CoV main proteases. Furthermore, we selected MERS-CoV-Mpro mutants resistant against nirmatrelvir, the most effective inhibitor of this protease, with a safe, surrogate virus-based system, and suggest putative resistance mechanisms. Notably, nirmatrelvir demonstrated effectiveness against various viral proteases, illustrating its potential as a broad-spectrum coronavirus inhibitor. To adress the inherent resistance of MERS-CoV-Mpro to ensitrelvir, we applied directed mutagenesis to a key ensitrelvir-interacting residue and provided structural models. One-Sentence SummaryWe investigate antivirals for MERS-CoV with a pool of SARS-CoV-2 antiviral drugs and study potential resistances developing against those drugs.

molecular biology↗

bioRxiv2023

Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications

The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 [A] resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNAVal. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transition in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide the most complete description so far of the structure and function of the human mitoribosome.

biochemistry↗

bioRxiv2022

dgram2dmap: Extraction, visualisation and formatting of distance constraints from AlphaFold distograms

Distograms are data structures output by AlphaFold, along with the predicted 3D coordinates of the target protein, that encode predictions about Euclidean distances between pairs of amino acids. Although distograms are often overlooked, they do provide information that is to some extent complementary to that of the final 3D model. Here, we introduce dgram2dmap, a simple tool to convert distograms into distance maps that can be visualised and used in external tools for further downstream analyses. dgram2dmap runs within seconds to minutes, is open source and available on GitHub: https://github.com/clami66/dgram2dmap.

bioinformatics↗

bioRxiv2022

Structural basis of streptomycin off-target binding to human mitoribosome

The ribosome in mitochondria regulates cellular energy production, and its deactivation is associated with pathologies and ageing. Inhibition of human mitoribosome can be caused by antimicrobial off-target binding, which leads to clinical appearances. The anti-tuberculosis drug aminoglycoside streptomycin targets the small subunit and was shown to be coupled with a bilateral decreased visual acuity with central scotomas and an altered mitochondrial structure. Previously, we reported mitochondria-specific aspects of translation related to specialties of the human mitoribosome (Aibara et al., 2020). In this Research advance article, we report 2.23-[A] resolution structure of the human mitoribosomal small subunit in complex with streptomycin. The structural data reveals new details of the streptomycin interactions, including specific water molecules and metal ions involved in the coordination. The density for the streptose moiety reveals that previously modeled aldehyde group appears as a loosely bound density, and the hydroxyl group is not resolved. The density replacing the aldehyde group is within hydrogen bonding distance of four phosphate groups of rRNA, suggesting that the ribosome-bound streptomycin is likely to be in the hydrated gem-diol form rather than in the free aldehyde form. Since streptomycin is a widely used drug for treatment, the newly resolved fine features can serve as determinants for targeting.

molecular biology↗

bioRxiv2021

Chloroplast photosystem I dimer and high resolution model of the complex with plastocyanin

Photosystem I (PSI) enables photo-electron transfer and regulates photosynthesis in the bioenergetic membranes of cyanobacteria and chloroplasts. Being a multi-subunit complex, its macromolecular organization affects the dynamics of photosynthetic membranes. Here, we reveal a chloroplast PSI from the green alga Chlamydomonas reinhardtii that is organized as a homodimer, comprising 40 protein subunits with 118 transmembrane helices that provide scaffold for 568 pigments. Our cryo-EM structure identifies that the absence of PsaH and Lhca2 gives rise to a head-to-head relative orientation of the PSI-LHCI monomers in a way that is essentially different from the oligomer formation in cyanobacteria. The light-harvesting protein Lhca9 is the key element for mediating this dimerization. The interface between the monomers is lacking PsaH, and thus partially overlaps with the surface area that would bind one of the LHCII complexes in state transitions. We also define the most accurate available PSI-LHCI model at 2.3 [A] resolution, including a flexibly bound electron donor plastocyanin, and assign correct identities and orientations of all the pigments, as well as 621 water molecules that affect energy transfer pathways.

plant biology↗

bioRxiv2020

Analysis of translating mitoribosome reveals functional characteristics of protein synthesis in mitochondria of fungi

Mitoribosomes are specialized protein synthesis machineries in mitochondria. However, how mRNA binds to its dedicated channel, and tRNA moves as the mitoribosomal subunit rotate with respect to each other is not understood. We report models of the translating fungal mitoribosome with mRNA, tRNA and nascent polypeptide, as well as an assembly intermediate. Nicotinamide adenine dinucleotide (NAD) is found in the central protuberance of the large subunit, and the ATPase inhibitory factor 1 (IF1) in the small subunit. The models of the active mitoribosome explain how mRNA binds through a dedicated protein platform on the small subunit, tRNA is translocated with the help of the protein mL108, bridging it with L1 stalk on the large subunit, and nascent polypeptide paths through a newly shaped exit tunnel involving a series of structural rearrangements. An assembly intermediate is modeled with the maturation factor Atp25, providing insight in to the biogenesis of the mitoribosomal large subunit and translation regulation.

biochemistry↗

bioRxiv2019

Controlled dehydration, structural flexibility, and Gadolinium MRI contrast compound binding in human plasma glycoprotein afamin

Afamin, a human blood plasma glycoprotein, a putative multi-functional transporter of hydrophobic molecules and a marker for metabolic syndrome, poses multiple challenges for crystallographic structure determination, both practically and in analysis of the models. Several hundred crystals were analysed, and unusual variability in cell volume and difficulty solving the structure despite a ~34% sequence identity with non-glycosylated human serum albumin indicated that the molecule exhibits variable and context-sensitive packing, despite greatly simplified glycosylation in insect cell expressed recombinant afamin. Controlled dehydration of the crystals was able to stabilise the orthorhombic crystal form reducing the number of molecules in the asymmetric unit from the monoclinic form and changing the conformational states of the protein. An iterative strategy, using fully automatic experiments available on MASSIF-1, was used to quickly determine the optimal protocol to achieve the phase transition that should be readily applicable to many types of sample. The study also highlights the drawback of using a single crystallographic structure model for computation modelling purposes given that conformational state of the binding sites and electron density in the binding site, likely resulting from PEGs, greatly varies between models. This also holds for the analysis of unspecific low-affinity ligands, where often a variety fragments with similar uncertainty can be modelled, inviting interpretative bias. As a promiscuous transporter, afamin also seems to bind Gadoteridol, a magnetic resonance imaging contrast compound, in at least two sites. One pair of Gadoteridol molecules is located near the human albumin Sudlow-site, and a second Gadoteridol at an intermolecular site in proximity of domain IA. The data from the co-crystals provide an opportunity to evaluate modern metrics of data quality in the context of the information that can be gleaned from data sets that would be abandoned on classical measures.\n\nSynopsisControlled dehydration experiments have revealed a new crystal form of afamin, a human blood plasma glycoprotein and transporter of hydrophobic molecules. The comparison shows substantial molecular plasticity and amplifies the necessity to examine multiple crystal forms and to refine multiple models, while at the same time the new structure cautions against interpretation of fatty acid ligand density in crystals derived from PEG as major precipitants. An isomorphic low-resolution structure model suggests that afamin is capable of transporting Gadolinium-DO3A, a magnetic resonance imaging compound.

biochemistry↗