Lambrughi, M. | bioRxiv Science

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↗