Biology subjects

Di Iorio, D.

Publications and source records attributed to Di Iorio, D..

3 recordsLinked to original sources

bioRxiv2025

Mechanistic Plasticity of the RabGEFs Mon1-Ccz1 and Fuzzy-Inturned

Rab GTPases organize intracellular trafficking and provide identity to organelles. Their spatiotemporal activation by guanine nucleotide exchange factors (GEFs) is tightly controlled to ensure fidelity. Our structural and functional comparison of the tri-longin domain RabGEFs Mon1-Ccz1 and Fuzzy-Inturned reveals the molecular basis for their target specificity. Both complexes rely on a conserved sequence motif of their substrate GTPases for the catalytic mechanism, while secondary interactions allow discrimination between targets. We also find that dimeric Mon1-Ccz1 from fungi and the metazoan homologs with the additional third subunit RMC1/Bulli bind membranes through electrostatic interactions via distinct interfaces. Protein-lipid interaction studies thus reveal a function of RMC1/Bulli in the complex as mediator of membrane recruitment. In the case of Fuzzy-Inturned, reconstitution experiments demonstrate that the BAR (Bin-Amphiphysin-Rvs) domain protein CiBAR1 can support membrane recruitment of the GEF. Collectively, our study demonstrates the molecular basis for the adaptation of TLD-RabGEFs to different cellular functions.

biochemistry↗

bioRxiv2025

Heparin flexibility within the extracellular matrix determines the bioactivity of bound vascular endothelial growth factor

Vascular endothelial growth factor (VEGF), a major regulator of blood vessel formation, is naturally bound to heparan sulfate proteoglycans in the extracellular matrix (ECM). Yet, how the physical presentation of VEGF by the matrix impacts its signaling potential remains fully unknown. To address this question, we have developed a tunable heparin-containing hydrogel model that recapitulates natural VEGF binding modes with full and independent control over physical properties. Using this model, we show that the degree of heparin flexibility in the hydrogel network determines the mobility of bound VEGF and, in turn, its ability to interact with VEGF receptor 2. We demonstrate that VEGF mobility is driven by a relay mechanism, in which VEGF molecules directly switch from one heparin chain to another. When strong electrostatic interactions between heparin and other hydrogel constituents immobilize the sugar backbone, this relay mechanism is impeded, in turn reducing VEGFs ability to reach its target receptor at the cell membrane, thereby reducing its bioactivity. This work identifies heparin flexibility within the ECM as a previously unknown regulator of the microenvironment, which will not only contribute to a better mechanistic understanding of how the ECM regulates growth factor bioactivity, but it will also provide an important design criterion for the development of tissue-engineered biomaterials that require vascularization.

bioengineering↗

bioRxiv2024

Evolution of SARS-CoV-2 spike trimers towards optimized heparan sulfate cross-linking and inter-chain mobility

The heparan sulfate (HS)-rich extracellular matrix (ECM) serves as an initial interaction site for the homotrimeric spike (S)-protein of SARS-CoV-2 to facilitate subsequent docking to angiotensin-converting enzyme 2 (ACE2) receptors and cellular infection. Recent variants of concern (VOCs), notably Omicron, have evolved by swapping several amino acids to positively charged residues to enhance the S-protein trimers interaction with the negatively charged HS polysaccharide chains in the matrix. These increased interactions, however, may reduce Omicrons ability to move through the HS-rich ECM to effectively find ACE2 receptors and infect cells, and raise the question of how HS-associated virus movement can be mechanistically explained. In this work, we show that Omicron S-proteins have evolved to balance HS interaction stability and dynamics, resulting in enhanced mobility on an HS-functionalized artificial matrix. Both properties are achieved by the ability of Omicrons S-proteins to cross-link at least two HS chains, providing both high avidity to retain the protein inside the HS-rich matrix, and fast dynamics, thus enabling direct S-protein switching between HS chains as a prerequisite for mobility at the cell surface. Optimized HS interactions can be targeted pharmaceutically, because an HS mimetic significantly suppressed surface binding and cellular infection specifically of the Omicron VOC. These findings suggest a robust way to interfere with SARS-CoV-2 Omicron infection and, potentially, future variants.

molecular biology↗