Abstract
KR2 rhodopsin is known to pump sodium ions instead of protons unlike other bacterial rhodopsins. Crystal structures of KR2 contain several deeply buried water molecules around the channel. Using atomistic molecular dynamics (MD) simulations we find several spatially disjoint water filled cavities with significant heterogeneity in the structure and dynamics of these hydration sites. Movement of water between these cavities is regulated by dynamic bottlenecks controlled by protein side-chain motions. We find there exists an intricate coupling between the protein and water dynamics that gets modulated in different stages of the photocycle. We track the molecular events and energetics followed by the photoisomerization of retinal and dissect how the local energetic perturbation leads to the cascade of conformational changes leading to the eventual channel opening for Na+ pumping. Computed free energy surfaces of the key conformational changes during the photocycle provides a consistent thermodynamic basis of channel opening and ion uptake.
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