Molecular Dynamics Simulations of Microtubule-associated protein 1A/1B-light chain 3 (LC3) and its membrane associated form(LC3-II)

Autophagy is the process by which cells eliminate its unwanted or dysfunctional components. A major step in autophagy is the formation of autophagosome, the double membrane that engulfs the unwanted cellular components. Dysregulation of autophagy affects neurodegenerative disorders, infectious diseases, cancer, and aging. In yeast, Atg8 protein is considered to play a crucial role in autophagosome maturation. Studies have shown that yeast lacking Atg8 protein form extremely small autophagosomes. Similarly, mammalian cells lacking Atg8 homologues produced “open” autophagosomes. Microtubule-associated protein (MAP) light chain3 (LC3), a human homologue of Atg8 protein is considered to play a major role in autophagosome maturation. However the exact mechanism by which Atg8/LC3 affects the autophagosome maturation is not completely known. A possible mechanism evolving from various studies is the following: Upon binding to the autophagosome, Atg8 family undergoes a conformational transition, which allows it to associate with another membrane-bound Atg8 in a trans-fashion. The proposed goals of this research include testing this hypothesis, identifying the stable conformations of LC3 and LC3-II (membrane bound LC3) and getting insights into the molecular mechanism by which LC3 influence autophagosome maturation. To accomplish this, we are performing Hamiltonian replica exchange molecular dynamics (HREMD) simulations on LC3 and on LC3-II. The most stable conformations of LC3, and LC3-II are identified via clustering analysis. As autophagy modulation is considered as a potential therapeutic target for various diseases, understanding the molecular mechanisms of different stages of autophagy is very important.