Computational approaches to investigate fluoride binding, selectivity and transport across the membrane

The use of molecular dynamics (MD) simulations to study biomolecular systems has proven reliable in elucidating atomic-level details of structure and function. In this chapter, MD simulations were used to uncover new insights into two phylogenetically unrelated bacterial fluoride (F^-) exporters: the CLC^F F^-/H⁺ antiporter and the Fluc F^- channel. The CLC^F antiporter, a member of the broader CLC family, has previously revealed unique stoichiometry, anion-coordinating residues, and the absence of an internal glutamate crucial for proton import in the CLCs. Through MD simulations enhanced with umbrella sampling, we provide insights into the energetics and mechanism of the CLC^F transport process, including its selectivity for F^- over HF. In contrast, the Fluc F^- channel presents a novel architecture as a dual topology dimer, featuring two pores for F^- export and a central non-transported sodium ion. Using computational electrophysiology, we simulate the electrochemical gradient necessary for F^- export in Fluc and reveal details about the coordination and hydration of both F^- and the central sodium ion. The procedures described here delineate the specifics of these advanced techniques and can also be adapted to investigate other membrane protein systems.