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

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posted on 13.10.2021, 19:21 by Burcu Aykac Fas, Emiliano Maiani, Valentina Sora, Mukesh Kumar, Maliha Mashkoor, Matteo Lambrughi, Matteo Tiberti, Elena Papaleo

Macroautophagy/autophagy is a cellular process to recycle damaged cellular components, and its modulation can be exploited for disease treatments. A key autophagy player is the ubiquitin-like protein MAP1LC3B/LC3B. Mutations and changes in MAP1LC3B expression occur in cancer samples. However, the investigation of the effects of these mutations on MAP1LC3B protein structure is still missing. Despite many LC3B structures that have been solved, a comprehensive study, including dynamics, has not yet been undertaken. To address this knowledge gap, we assessed nine physical models for biomolecular simulations for their capabilities to describe the structural ensemble of MAP1LC3B. With the resulting MAP1LC3B structural ensembles, we characterized the impact of 26 missense mutations from pan-cancer studies with different approaches, and we experimentally validated our prediction for six variants using cellular assays. Our findings shed light on damaging or neutral mutations in MAP1LC3B, providing an atlas of its modifications in cancer. In particular, P32Q mutation was found detrimental for protein stability with a propensity to aggregation. In a broader context, our framework can be applied to assess the pathogenicity of protein mutations or to prioritize variants for experimental studies, allowing to comprehensively account for different aspects that mutational events alter in terms of protein structure and function.

Abbreviations: ATG: autophagy-related; Cα: alpha carbon; CG: coarse-grained; CHARMM: Chemistry at Harvard macromolecular mechanics; CONAN: contact analysis; FUNDC1: FUN14 domain containing 1; FYCO1: FYVE and coiled-coil domain containing 1; GABARAP: GABA type A receptor-associated protein; GROMACS: Groningen machine for chemical simulations; HP: hydrophobic pocket; LIR: LC3 interacting region; MAP1LC3B/LC3B microtubule associated protein 1 light chain 3 B; MD: molecular dynamics; OPTN: optineurin; OSF: open software foundation; PE: phosphatidylethanolamine, PLEKHM1: pleckstrin homology domain-containing family M 1; PSN: protein structure network; PTM: post-translational modification; SA: structural alphabet; SLiM: short linear motif; SQSTM1/p62: sequestosome 1; WT: wild-type.

Funding

This project was supported by LEO fondet grants (LF17006, LF17024), Carlsberg fondet Distinguished Fellowship (CF18-0314), Danmarks Frie Forskningsfond, Natural Science, Project 1 (102517), Danmarks Grundforskningsfond (DNRF125). Moreover, the project has been supported by a KBVU pre-graduate fellowship to MM and a Netaji Subhash ICAR international fellowship (Govt. of India) to MK to work in EP group. BAF is partially supported by COST-STSM-BM1405-34558. The calculations described in this paper were performed using the DeiC National Life Science Supercomputer Computerome at DTU (DK), a DeiC Pilot grant OULC3P62 on Abacus (DK) DECI-PRACE 14th and 15th HPC Grants for calculations on Archer (UK), and ISCRA-CINECA HP10C0T58M and HP10C0T58.

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