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"Structure and Ion Permeation of the Gramicidin Channel Using Molecular Dynamics" icon

Structure and Ion Permeation of the Gramicidin Channel Using Molecular Dynamics

Molecular dynamics (MD) has become an essential tool for obtaining microscopic insight into biological function. The gramicidin channel as an excellent benchmark system for this purpose. Using extensive MD simulations with explicit solvent and membrane, we determine the backbone structure and side-chain rotameric states compliant with solid-state Nuclear Magnetic Resonance and fluorescence spectroscopic observations. Such agreement is not possible without dynamical simulation and underscores the utility of MD for the analysis and interpretation of experimental observations. Ion conduction through the gramicidin channel is then characterized with free energy simulation techniques. We determine the roles played by protein, water and membrane in creating a free energy pathway for ions. This... Show More
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