Biology subjects

Lambrughi, M.

Publications and source records attributed to Lambrughi, M..

3 recordsLinked to original sources

bioRxiv2019

Alterations of the pro-survival Bcl-2 protein interactome in breast cancer at the transcriptional, mutational and structural level

Apoptosis is an essential defensive mechanism against tumorigenesis. Proteins of the B-cell lymphoma-2 (Bcl-2) family regulates programmed cell death by the mitochondrial apoptosis pathway. In response to intracellular stresses, the apoptotic balance is governed by interactions of three distinct subgroups of proteins; the activator/sensitizer BH3 (Bcl-2 homology 3)-only proteins, the pro-survival, and the pro-apoptotic executioner proteins. Changes in expression levels, stability, and functional impairment of pro-survival proteins can lead to an imbalance in tissue homeostasis. Their overexpression or hyperactivation can result in oncogenic effects. Pro-survival Bcl-2 family members carry out their function by binding the BH3 short linear motif of pro-apoptotic proteins in a modular way, creating a complex network of protein-protein interactions. Their dysfunction enables cancer cells to evade cell death. The critical role in homeostasis and tumorigenesis coupled with progress in their structural elucidation, has led to consider pro-survival Bcl-2 proteins as therapeutic targets.\n\nA better understanding of the transcriptomic level, mutational status and molecular mechanism underlying pro-survival Bcl-2 proteins in different cancer types, could help to clarify their role in cancer development and may guide advancement in drug discovery, targeting these proteins. Here, we shed light on pro-survival Bcl-2 proteins in breast cancer by proposing a multiscale bioinformatic approach. We analyzed the changes in expression of the Bcl-2 proteins and their BH3-containing interactors, in breast cancer samples. We then studied, at the structural level, a selection of interactions, also accounting for effects induced by mutations found in the breast cancer samples. We identified the complexes between the up-regulated BCL2A1 and two down-regulated BH3-only candidates (HRK and NR4A1) as targets associated with reduced apoptosis in breast cancer samples, which could deserve future experimental validation. We predicted as damaging mutations altering protein stability L99R, M75R, along with Y120C as a possible allosteric mutation from an exposed surface to the BH3-binding site.

bioinformatics↗

bioRxiv2019

The conformational and mutational landscape of the ubiquitin-like marker for the autophagosome formation in cancer

Autophagy is a cellular process to recycle damaged cellular components and its modulation can be exploited for disease treatments. A key autophagy player is a ubiquitin-like protein, LC3B. Compelling evidence attests the role of autophagy and LC3B in different cancer types. Many LC3B structures have been solved, but a comprehensive study, including dynamics, has not been yet undertaken. To address this knowledge gap, we assessed ten physical models for molecular dynamics for their capabilities to describe the structural ensemble of LC3B in solution using different metrics and comparison with NMR data. With the resulting LC3B ensembles, we characterized the impact of 26 missense mutations from Pan-Cancer studies with different approaches. Our findings shed light on driver or neutral mutations in LC3B, providing an atlas of its modifications in cancer. Our framework could be used to assess the pathogenicity of mutations by accounting for the different aspects of protein structure and function altered by mutational events.

cancer biology↗

bioRxiv2019

Conformational gating in ammonia lyases

Ammonia lyases (AL) are enzymes of industrial and biomedical interest. Knowledge of AL structure-dynamics-function relationship would be instrumental for making use of the application potential of these enzymes. We investigated, using microsecond molecular dynamics, the conformational changes in the proximity of the catalytic pocket of a 3-methylaspartate ammonia lyase (MAL) as a model system. In particular, we identified two regulatory elements in the MAL structure, i.e., the {beta}5-2 loop, and the helix-hairpin-loop subdomain. We showed that they undergo conformational changes switching from occluded to open states. We observed that these rearrangements are coupled to changes in the accessibility of the active site. The {beta}5-2 loop and the helix-hairpin-loop subdomain modulate the formation of tunnels from the protein surface to the substrate binding site, making the active site more accessible to the substrate when they are in an open state. We pinpointed a sequential mechanism, in which the helix-hairpin-loop subdomain needs to break a subset of intramolecular interactions first, to then allow the opening of the {beta}5-2 loop and, as a consequence, make the AL catalytic pocket accessible for the substrate. Our data suggest that protein dynamics need to be considered in the design of new AL variants for protein engineering and therapeutic purposes.

biophysics↗