Biology subjects

Marabini, R.

Publications and source records attributed to Marabini, R..

7 recordsLinked to original sources

bioRxiv2026

Protease-driven remodeling of stabilization networks during adenovirus assembly

At least thirteen different proteins form the adenovirus virion, including those bound to the dsDNA genome in the core. To produce infectious particles, the adenovirus protease (AVP) cleaves many of these proteins during genome packaging, using the viral genome as a cofactor. Here, we determine high-resolution structures of two types of adenovirus particles devoid of genome and core proteins and stalled at different AVP processing stages. We find that the N-terminal regions of penton base and internal minor coat protein IIIa are disordered when the core is absent and uncleaved packaging protein L1 52/55 kDa is present, likely enabling correction of early assembly errors at the vertex. Assignment of previously unmodeled densities reveals that proteins IIIa and VIII form long-range bridges linking vertex capsomers to the facet center before proteolytic maturation. Cleavage by AVP remodels these connections, diminishing capsid-wide stabilizing interactions and promoting the metastable state that prepares the mature virion for uncoating. Significance statementAdenoviruses cause disease and are major platforms for gene delivery, yet how their capsids are built and primed for infection remains incompletely understood. High-resolution cryo-EM structures of empty particles arrested at successive proteolytic maturation stages show previously unrecognized interactions that regulate capsid stability. Uncleaved packaging protein L1 52/55 kDa induces disorder at the icosahedral vertex during early assembly, likely facilitating error correction, while minor coat proteins IIIa and VIII serve as transient scaffolds stabilizing the capsid before proteolytic remodeling. Maturation thereby converts a stable assembly intermediate into a metastable particle ready for uncoating. These findings reveal how structural plasticity of minor coat proteins coordinates adenovirus assembly, maturation, and infectivity.

microbiology↗

bioRxiv2025

Aviadenovirus structure: a highly thermostable capsid in the absence of stabilizing proteins

High-resolution structural studies have mainly focused on two out of the six adenovirus genera: mastadenoviruses and atadenoviruses. Here we report the high-resolution structure of an aviadenovirus, the poultry pathogen fowl adenovirus serotype 4 (FAdV-C4). FAdV-C4 virions are highly thermostable, despite lacking minor coat and core proteins shown to stabilize the mast- and atadenovirus particles, and having no genus-specific cementing proteins. Unique structural features of the FAdV-C4 hexon include a large insertion at the trimer equatorial region, and a long N-terminal tail. Protein IIIa conformation is closer to atadenoviruses than to mastadenoviruses, while protein VIII diverges from all previously reported structures. We interpret these differences in light of adenovirus evolution. Finally, we discuss the possible role of core composition in determining capsid stability properties. These results enlarge our view on the structural diversity of adenoviruses, and provide useful information to counteract fowl pathogens or use non-human adenoviruses as vectors.

molecular biology↗

bioRxiv2023

Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs

DNA regulation, replication and repair are processes fundamental to all known organisms and the sliding clamp proliferating cell nuclear antigen (PCNA) is central to all these processes. S-phase delaying protein 1 (Spd1) from S. pombe, an intrinsically disordered protein that causes checkpoint activation by inhibiting the enzyme ribonucleotide reductase, has one of the most divergent PCNA binding motifs known. Using NMR spectroscopy, in vivo assays, X-ray crystallography, calorimetry, and Monte Carlo simulations, an additional PCNA binding motif in Spd1, a PIP-box, is revealed. The two tandemly positioned, low affinity sites exchange rapidly on PCNA exploiting the same binding sites. Increasing or decreasing the binding affinity between Spd1 and PCNA through mutations of either motif compromised the ability of Spd1 to cause checkpoint activation in yeast. These results pinpoint a role for PCNA in Spd1-mediated checkpoint activation and suggest that its tandemly positioned short linear motifs create a neatly balanced competition-based system, involving PCNA, Spd1 and the small ribonucleotide reductase subunit, Suc22R2. Similar mechanisms may be relevant in other PCNA binding ligands where divergent binding motifs so far have gone under the PIP-box radar.

biophysics↗

bioRxiv2020

Near Atomic Structure of an Atadenovirus Reveals a Conserved Capsid-Binding Motif and Intergenera Variations in Cementing Proteins

Little is known about the basic biology of non-human adenoviruses, which could be alternative vectors free of issues posed by preexisting immunity to human adenoviruses. We present the cryo-EM structure of a lizard atadenovirus, LAdV-2, at 3.4 [A] resolution. This is the first high resolution structure of an adenovirus with non-mammalian host, and of an adenovirus not belonging to the Mastadenovirus genus. Atadenovirus capsids contain genus specific proteins LH3, p32k, and LH2, and are more thermostable than the more studied human adenoviruses. We find a large conformational difference in the internal vertex protein IIIa between mast- and atadenoviruses, induced by the presence of an extended polypeptide in the region. This polypeptide, as well as -helical clusters located beneath the icosahedral facet, likely correspond to proteins LH2 and p32k. The external genus specific protein LH3, with a trimeric {beta}-helix fold typical of bacteriophage host attachment proteins, contacts the hexon shell surface via a triskelion structure identical to that used by protein IX in human AdV, revealing a conserved capsid-binding motif and a possible gene duplication event. Altogether, this work shows how the network of minor coat proteins differs between AdV genera and relates to virus evolution and capsid stability properties.

microbiology↗

bioRxiv2020

Cryo-EM structure of enteric adenovirus HAdV-F41 highlights structural divergence among human adenoviruses

Enteric adenoviruses are one of the main causes of viral gastroenteritis in the world. To carry out a successful infection, the virions must withstand the harsh conditions found in the gut. This requirement suggests that capsid stability must be different from that of other adenoviruses. We have determined the structure of a human enteric adenovirus, HAdV-F41, at 4.0 [A] resolution by single particle averaging cryo-electron microscopy, and compared it with that of other adenoviruses with respiratory (HAdV-C5) and ocular (HAdV-D26) tropisms. While the overall structures of hexon, penton base and internal minor coat proteins IIIa and VIII are conserved, we observe partially ordered elements reinforcing the vertex region, which suggests their role in enhancing the physicochemical capsid stability of HAdV-F41. Unexpectedly, we find an organization of the external minor coat protein IX different from all previously characterized human and non-human mastadenoviruses. Knowledge of the structure of enteric adenoviruses can provide a starting point for the design of vectors suitable for oral delivery or intestinal targeting.

microbiology↗

bioRxiv2020

FSC-Q: A CryoEM map-to-atomic model quality validation based on the local Fourier Shell Correlation

In recent years, advances in cryoEM have dramatically increased the resolution of Coulomb potential maps and, with it, the number of solved atomic models. It is widely accepted that the quality of cryoEM maps varies locally; therefore, the evaluation of the maps-derived structural models must be done locally as well. In this article, a method for the local analysis of the map-to-model fit is presented. The algorithm uses a comparison of two local resolution maps. The first is the local FSC (Fourier shell correlation) between the full map and the model, while the second is calculated between the half maps normally used in typical single particle analysis workflows. We call the new quality measure "FSC-Q", and it is a quantitative estimation of how much of the model is supported by the signal content of the map. Furthermore, we show that FSC-Q may be helpful to avoid overfitting. It can be used to complement other methods, such as the Q-score method that estimates the resolvability of atoms.

biophysics↗

bioRxiv2018

Automatic local resolution-based sharpening of cryo-EM maps.

Recent technological advances and computational developments, have allowed the reconstruction of cryo-EM maps at near-atomic resolution structures. Cryo-EM maps benefit significantly of a \"postprocessing\" step, normally referred to as \"sharpening\", that tends to increase signal at medium/high resolution. Here, we propose a new method for local sharpening of volumes generated by cryo-EM. The algorithm (LocalDeblur) is based on a local resolution-guided Wiener restoration approach, does not need any prior atomic model and it avoids artificial structure 1 factor corrections. LocalDeblur is fully automatic and parameter free. We show that the new method significantly and quantitatively improving map quality and interpretability, especially in cases of broad local resolution changes (as is often the case of membrane proteins).

biophysics↗