Abstract
Here we explore the possibility of combining Molecular Dynamics (MD) simulation together with Monte-Carlo simulation in order to predict the gating pathway for a tension-gated pore protein, the Mechanosensitive Channel of Large Conductance from Mycobacterium Tuberculosis (Tb-MscL). To mimic its native environment, we embed the channel protein in a native-like lipid membrane, itself first equilibrated by MD, and the whole system is then equilibrated using MD, followed by rigid cluster decomposition by FIRST software and Monte-Carlo simulation of channel opening using FRODA software. Our goal was to explore in a more atomistic level protein-lipid interactions that were explored by continuum models, and uncover the role played by various components of the protein-membrane system during the channel gating. Our results suggest that protein-lipid interactions are necessary in order to produce an asymmetric motion of channel subunits, which was observed in previous experimental studies.
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